diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 322eab9436cc6f3ac454ba04d7a0818c49b8a753..5a1714130b0637ad37fd79f4422ad6b23c3af21c 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,8 +1,9 @@
-image: r-base
+image: rocker/r-ver:4.4.2
 
 before_script:
   - apt-get update
-  - apt-get -y install pandoc r-cran-rcpp r-cran-devtools r-cran-testthat r-cran-curl r-cran-seqinr r-cran-ape r-bioc-biostrings r-cran-uuid r-cran-callr r-cran-rmarkdown r-bioc-biocstyle
+  - apt-get -y install pandoc libcurl4-openssl-dev r-cran-rcpp r-cran-devtools r-cran-testthat r-cran-curl r-cran-seqinr r-cran-ape r-bioc-biostrings r-cran-uuid r-cran-callr r-cran-rmarkdown r-bioc-biocstyle
+  - R -e "install.packages('BiocManager'); BiocManager::install(version = '3.20')"
   - R -e "dir(); getwd(); sessionInfo(); install.packages('tidyverse', repos='http://cran.rstudio.com'); install.packages('pkgdown', repos='http://cran.rstudio.com'); install.packages('RcppThread', repos='http://cran.rstudio.com'); Rcpp::compileAttributes(); devtools::install(); update.packages(ask = FALSE, checkBuilt = TRUE)"
 
 pages:
diff --git a/DESCRIPTION b/DESCRIPTION
index 7e4fa15d91ce800c14bd770d04319e5464ba3610..7af7bbaac1a4ae8c54b9009c101ec231fc466adc 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -3,7 +3,7 @@ Type: Package
 Title: MSA2dist calculates pairwise distances between all sequences of a
     DNAStringSet or a AAStringSet using a custom score matrix and conducts
     codon based analysis
-Version: 1.7.6
+Version: 1.11.1
 Authors@R: 
     person(given = "Kristian K",
            family = "Ullrich",
@@ -34,6 +34,7 @@ Imports:
   methods,
   parallel,
   pwalign,
+  readr,
   rlang,
   seqinr,
   stats,
@@ -57,4 +58,4 @@ NeedsCompilation: yes
 SystemRequirements: C++11
 URL: https://gitlab.gwdg.de/mpievolbio-it/MSA2dist, https://mpievolbio-it.pages.gwdg.de/MSA2dist/
 BugReports: https://gitlab.gwdg.de/mpievolbio-it/MSA2dist/issues
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
diff --git a/NAMESPACE b/NAMESPACE
index ab2b7cf49cd6b869bb958c13f572c593eac8fe54..13d402d7af6a85cc218e9e3eaa786ab55733b851 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -28,7 +28,9 @@ export(dnastring2dnabin)
 export(dnastring2kaks)
 export(getmask)
 export(getpos)
+export(gff2cds)
 export(globalDeletion)
+export(globalDeletionAA)
 export(granthamMatrix)
 export(indices2kaks)
 export(iupacMatrix)
@@ -46,6 +48,7 @@ export(string2region)
 export(subString)
 export(uptriidx)
 import(Rcpp)
+importFrom(Biostrings,AAMultipleAlignment)
 importFrom(Biostrings,AAString)
 importFrom(Biostrings,AAStringSet)
 importFrom(Biostrings,BString)
@@ -77,13 +80,19 @@ importFrom(ape,as.AAbin)
 importFrom(ape,as.DNAbin.alignment)
 importFrom(ape,dist.dna)
 importFrom(doParallel,registerDoParallel)
+importFrom(dplyr,arrange)
 importFrom(dplyr,count)
+importFrom(dplyr,desc)
+importFrom(dplyr,distinct)
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
 importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
+importFrom(dplyr,reframe)
+importFrom(dplyr,select)
 importFrom(dplyr,slice)
 importFrom(dplyr,summarise)
+importFrom(dplyr,ungroup)
 importFrom(foreach,"%do%")
 importFrom(foreach,"%dopar%")
 importFrom(foreach,foreach)
@@ -92,11 +101,13 @@ importFrom(methods,slot)
 importFrom(parallel,makeForkCluster)
 importFrom(parallel,stopCluster)
 importFrom(pwalign,pairwiseAlignment)
+importFrom(readr,read_tsv)
 importFrom(rlang,.data)
 importFrom(seqinr,as.alignment)
 importFrom(seqinr,kaks)
 importFrom(stats,setNames)
 importFrom(stringr,str_split)
+importFrom(stringr,str_split_fixed)
 importFrom(stringr,str_sub)
 importFrom(stringr,word)
 importFrom(tibble,add_column)
diff --git a/NEWS.md b/NEWS.md
index e833df568e4a6a9768e4c2572a47cb85ef7ee56e..aaf67af0d6e93b79155d2e83e9eb3fbb7219a4b7 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,14 @@
+# MSA2dist 1.11.1 (2024-11-14)
+
+BUG FIXES
+
+* fixed pal2nal
+* fixed aastring2aabin to return alignment
+
+NEW FEATURES
+
+* added globalDeletionAA
+
 # MSA2dist 1.7.5 (2024-03-28)
 
 BUG FIXES
@@ -144,3 +155,4 @@ CHANGES
 
 * Changed version number into 0.99.1
 * Changed name from distSTRING into MSA2dist
+
diff --git a/R/aastring2aabin.R b/R/aastring2aabin.R
index e688761df9b5be411ee186bb23477139d6043521..b398b7db72ae4a768c926927a394cce38c08d5a7 100644
--- a/R/aastring2aabin.R
+++ b/R/aastring2aabin.R
@@ -1,12 +1,13 @@
 #' @title aastring2aabin
 #' @name aastring2aabin
-#' @description This function converts a \code{AAStringSet} into an \code{ape}
-#' \code{DNAbin}.
+#' @description This function converts an \code{AAStringSet}
+#' into an \code{ape} \code{AAbin}.
 #' @param aa \code{AAStringSet} [mandatory]
-#' @return An object of class \code{DNAbin}
+#' @return An object of class \code{AAbin}
 #' @importFrom methods is slot
 #' @importFrom Biostrings DNAString DNAStringSet AAString AAStringSet
 #' readDNAStringSet readAAStringSet writeXStringSet width subseq
+#' AAMultipleAlignment
 #' @importFrom ape as.AAbin
 #' @seealso \code{\link[seqinr]{as.alignment}}
 #' \code{\link[ape]{as.DNAbin.alignment}}
@@ -25,5 +26,5 @@
 aastring2aabin <- function(aa){
     stopifnot("Error: input needs to be an AAStringSet"=
                 methods::is(aa, "AAStringSet"))
-    return(ape::as.AAbin(aa))
+    return(ape::as.AAbin(Biostrings::AAMultipleAlignment(aa)))
 }
diff --git a/R/cdsstring2codonaln.R b/R/cdsstring2codonaln.R
index de3f0116bcf1cd101d8c256cf7169701559af4d2..00e7175869e028668579c3aaf333056afab02766 100644
--- a/R/cdsstring2codonaln.R
+++ b/R/cdsstring2codonaln.R
@@ -40,7 +40,7 @@ cdsstring2codonaln <- function(cds, aa, type="global",
     remove.gaps=FALSE){
     stopifnot("Error: cds needs to be DNAStringSet"=
         {methods::is(cds, "DNAStringSet")})
-    stopifnot("Error: aa needs to be either AAStringSet"=
+    stopifnot("Error: aa needs to be an AAStringSet"=
         {methods::is(aa, "AAStringSet")})
     if(methods::is(cds, "DNAStringSet")){
         stopifnot("Error: cds needs to only contain two sequences"=
diff --git a/R/globalDeletionAA.R b/R/globalDeletionAA.R
new file mode 100644
index 0000000000000000000000000000000000000000..4ca8889603a83af6022885930196cc5d2b6e3162
--- /dev/null
+++ b/R/globalDeletionAA.R
@@ -0,0 +1,31 @@
+#' @title globalDeletionAA
+#' @name globalDeletionAA
+#' @description This function returns an \code{AAStringSet} reduced by all
+#' sites containing any gaps ("-", "+", ".") or missing ("X") sites.
+#' @return \code{AAStringSet}
+#' @importFrom methods is slot
+#' @importFrom Biostrings consensusMatrix
+#' @param aa \code{AAStringSet} [mandatory]
+#' @examples
+#' ## define two cds sequences
+#' cds1 <- Biostrings::DNAString("ATGCAACATTGC")
+#' cds2 <- Biostrings::DNAString("ATG---CATTGC")
+#' cds1.cds2.aln <- c(Biostrings::DNAStringSet(cds1),
+#'     Biostrings::DNAStringSet(cds2))
+#' #globalDeletionAA(cds2aa(cds1.cds2.aln))
+#' cds1.cds2.aln |> cds2aa() |> globalDeletionAA()
+#' @export globalDeletionAA
+#' @author Kristian K Ullrich
+
+globalDeletionAA<-function(aa){
+    stopifnot("Error: input needs to be an AAStringSet"=
+        methods::is(aa, "AAStringSet"))
+    cM <- Biostrings::consensusMatrix(aa)
+    globalDeletionSites <- which(apply(cM, 2, function(x) {
+        sum(x[c(26, 28:30)])} >= 1))
+    if(length(globalDeletionSites) == 0){
+        return(aa)
+    }
+    return(MSA2dist::aabin2aastring(
+        MSA2dist::aastring2aabin(aa)[, -(globalDeletionSites)]))
+}
diff --git a/R/pal2nal.R b/R/pal2nal.R
index 29b03593116aab29834e9ccd4f531edb0581f7cb..067885499211c8e500f6a9a2482f0099da223959 100644
--- a/R/pal2nal.R
+++ b/R/pal2nal.R
@@ -59,7 +59,8 @@ pal2nal <- function(pal,
                 if(gap_pos==1){
                     n_i <- paste0(n_i, gap)
                 } else {
-                    n_i_codons_to_add <- gap_pos-n_i_codons_added-1
+                    n_i_codons_to_add <- gap_pos-n_i_codons_added-
+                        gap_len_cumsum+gap_len-1
                     n_i<- paste0(n_i, substr(nal_i,
                         (n_i_codons_added*3)+1,
                         (n_i_codons_added+n_i_codons_to_add)*3))
diff --git a/_pkgdown.yml b/_pkgdown.yml
index c9916138b3f4bcd21710835e64a0f853c1836027..bcf364c809542e738e8a43f2c123481f37d3a143 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -1,6 +1,8 @@
 destination: public
+template:
+  bootstrap: 5
 repo:
   url:
-    home: https://gitlab.gwdg.de/mpievolbio-it/msa2dist
-    source: https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master
-    issue: https://gitlab.gwdg.de/mpievolbio-it/msa2dist/issues
+    home: https://gitlab.gwdg.de/mpievolbio-it/MSA2dist
+    source: https://gitlab.gwdg.de/mpievolbio-it/MSA2dist/blob/main
+    issue: https://gitlab.gwdg.de/mpievolbio-it/MSA2dist/issues
diff --git a/man/aastring2aabin.Rd b/man/aastring2aabin.Rd
index e7857529ad5b260184569fc6d24f61cf4862ee7f..26e7d781f470451219a923aa640f10e287fa9908 100644
--- a/man/aastring2aabin.Rd
+++ b/man/aastring2aabin.Rd
@@ -10,11 +10,11 @@ aastring2aabin(aa)
 \item{aa}{\code{AAStringSet} [mandatory]}
 }
 \value{
-An object of class \code{DNAbin}
+An object of class \code{AAbin}
 }
 \description{
-This function converts a \code{AAStringSet} into an \code{ape}
-\code{DNAbin}.
+This function converts an \code{AAStringSet}
+into an \code{ape} \code{AAbin}.
 }
 \examples{
 ## define two cds sequences
diff --git a/man/globalDeletionAA.Rd b/man/globalDeletionAA.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..f15e55bfca3caa12837db88d2fc7160412bdb075
--- /dev/null
+++ b/man/globalDeletionAA.Rd
@@ -0,0 +1,30 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/globalDeletionAA.R
+\name{globalDeletionAA}
+\alias{globalDeletionAA}
+\title{globalDeletionAA}
+\usage{
+globalDeletionAA(aa)
+}
+\arguments{
+\item{aa}{\code{AAStringSet} [mandatory]}
+}
+\value{
+\code{AAStringSet}
+}
+\description{
+This function returns an \code{AAStringSet} reduced by all
+sites containing any gaps ("-", "+", ".") or missing ("X") sites.
+}
+\examples{
+## define two cds sequences
+cds1 <- Biostrings::DNAString("ATGCAACATTGC")
+cds2 <- Biostrings::DNAString("ATG---CATTGC")
+cds1.cds2.aln <- c(Biostrings::DNAStringSet(cds1),
+    Biostrings::DNAStringSet(cds2))
+#globalDeletionAA(cds2aa(cds1.cds2.aln))
+cds1.cds2.aln |> cds2aa() |> globalDeletionAA()
+}
+\author{
+Kristian K Ullrich
+}
diff --git a/public/404.html b/public/404.html
index 11078e88edc956338e3dba63a8fc0345b66d2683..1d14c477fdb739c7b93095714856f824aaa1eeb0 100644
--- a/public/404.html
+++ b/public/404.html
@@ -12,7 +12,7 @@
 <link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png">
 <link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png">
 <link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png">
-<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
+<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
 <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="bootstrap-toc.css">
 <script src="bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
 <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
@@ -25,7 +25,7 @@
 <![endif]-->
 </head>
 <body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-title-body">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -39,7 +39,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -59,7 +59,7 @@
 <li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul>
@@ -70,7 +70,7 @@
 </div>
 <!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="contents col-md-9">
@@ -98,16 +98,16 @@ Content not found. Please use links in the navbar.
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer>
 </div>
 
-  
 
 
-  
+
+
 
   </body>
 </html>
diff --git a/public/CODE_OF_CONDUCT.html b/public/CODE_OF_CONDUCT.html
index 6dfd21b0362e2bb0743ed5cac5158224bcc353c1..de7f276186a2b246bee43395f726c322e5cd433a 100644
--- a/public/CODE_OF_CONDUCT.html
+++ b/public/CODE_OF_CONDUCT.html
@@ -1,9 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Contributor Covenant Code of Conduct • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="bootstrap-toc.css"><script src="bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet"><script src="pkgdown.js"></script><meta property="og:title" content="Contributor Covenant Code of Conduct"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Contributor Covenant Code of Conduct • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="bootstrap-toc.css"><script src="bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet"><script src="pkgdown.js"></script><meta property="og:title" content="Contributor Covenant Code of Conduct"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-title-body">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -34,14 +34,14 @@
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="contents col-md-9">
@@ -132,15 +132,15 @@
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/LICENSE-text.html b/public/LICENSE-text.html
index cb966cfa3ee457cfc7c11e407fae73089f07ac3d..30f7780777750863fab06bf140a25f881a835097 100644
--- a/public/LICENSE-text.html
+++ b/public/LICENSE-text.html
@@ -1,9 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>License • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="bootstrap-toc.css"><script src="bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet"><script src="pkgdown.js"></script><meta property="og:title" content="License"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>License • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="bootstrap-toc.css"><script src="bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet"><script src="pkgdown.js"></script><meta property="og:title" content="License"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-title-body">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -34,14 +34,14 @@
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="contents col-md-9">
@@ -740,15 +740,15 @@ Public License instead of this License.  But first, please read
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/articles/MSA2dist.html b/public/articles/MSA2dist.html
index 87dc535f2dac7437bfb51d5a45bcaa8b5241c7f0..e09c229f0a7821273a15d64c844e208f284168bf 100644
--- a/public/articles/MSA2dist.html
+++ b/public/articles/MSA2dist.html
@@ -12,21 +12,19 @@
 <link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
 <link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
 <link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
-<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
+<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
 <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
 <script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
 <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
 <!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
 <script src="../pkgdown.js"></script><meta property="og:title" content="MSA2dist Vignette">
-<meta property="og:description" content="MSA2dist">
-<meta property="og:image" content="/logo.png">
 <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]-->
 </head>
 <body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-article">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -40,7 +38,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -60,7 +58,7 @@
 <li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul>
@@ -71,7 +69,7 @@
 </div>
 <!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
@@ -80,9 +78,9 @@
                         <h4 data-toc-skip class="author">Kristian K
 Ullrich</h4>
             
-            <h4 data-toc-skip class="date">2024-03-28</h4>
+            <h4 data-toc-skip class="date">2024-11-13</h4>
       
-      <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/mastervignettes/MSA2dist.Rmd" class="external-link"><code>vignettes/MSA2dist.Rmd</code></a></small>
+      <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/vignettes/MSA2dist.Rmd" class="external-link"><code>vignettes/MSA2dist.Rmd</code></a></small>
       <div class="hidden name"><code>MSA2dist.Rmd</code></div>
 
     </div>
@@ -294,8 +292,7 @@ Here, some examples are shown, how to convert from and to a
 <div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="co">## convert into AAbin</span></span>
 <span><span class="va">aa1.aa2.aln</span> <span class="op">|&gt;</span> <span class="fu"><a href="../reference/aastring2aabin.html">aastring2aabin</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
-<pre><code><span><span class="co">## 2 amino acid sequences in a list</span></span>
-<span><span class="co">## </span></span>
+<pre><code><span><span class="co">## 2 amino acid sequences in a matrix</span></span>
 <span><span class="co">## All sequences of the same length: 4</span></span></code></pre>
 <p><code>?ape::as.AAbin()</code> &gt;&gt;&gt;
 <code>?Biostrings::AAStringSet()</code></p>
@@ -574,12 +571,12 @@ trees:</p>
 <span><span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">hiv</span> <span class="op">|&gt;</span> <span class="fu"><a href="../reference/dnastring2dist.html">dnastring2dist</a></span><span class="op">(</span>model<span class="op">=</span><span class="st">"IUPAC"</span>, threads<span class="op">=</span><span class="fl">1</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
 <pre><code><span><span class="co">## Computing: [========================================] 100% (done)</span></span></code></pre>
 <pre><code><span><span class="co">##    user  system elapsed </span></span>
-<span><span class="co">##   0.002   0.000   0.003</span></span></code></pre>
+<span><span class="co">##   0.001   0.000   0.001</span></span></code></pre>
 <div class="sourceCode" id="cb62"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">hiv</span> <span class="op">|&gt;</span> <span class="fu"><a href="../reference/dnastring2dist.html">dnastring2dist</a></span><span class="op">(</span>model<span class="op">=</span><span class="st">"IUPAC"</span>, threads<span class="op">=</span><span class="fl">2</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
 <pre><code><span><span class="co">## Computing: [========================================] 100% (done)</span></span></code></pre>
 <pre><code><span><span class="co">##    user  system elapsed </span></span>
-<span><span class="co">##   0.003   0.000   0.003</span></span></code></pre>
+<span><span class="co">##   0.001   0.000   0.001</span></span></code></pre>
 <p>Woodmouse data example:</p>
 <div class="sourceCode" id="cb65"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="co">## use woodmouse data</span></span>
@@ -997,7 +994,7 @@ different frames.</p>
 <div class="section level2">
 <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a>
 </h2>
-<div id="refs" class="references csl-bib-body hanging-indent">
+<div id="refs" class="references csl-bib-body hanging-indent" entry-spacing="0">
 <div id="ref-chang2017whole" class="csl-entry">
 Chang, Peter L, Emily Kopania, Sara Keeble, Brice AJ Sarver, Erica
 Larson, Annie Orth, Khalid Belkhir, et al. 2017. <span>“Whole Exome
@@ -1061,9 +1058,10 @@ Nucleotide Substitutions.”</span> <em>Molecular Biology and
 Evolution</em> 21 (12): 2290–98.
 </div>
 <div id="ref-wang2009gamma" class="csl-entry">
-Wang, Da-Peng, Hao-Lei Wan, Song Zhang, and Jun Yu. 2009. <span>“<span class="math inline">\(\gamma\)</span>-MYN: A New Algorithm for
-Estimating Ka and Ks with Consideration of Variable Substitution
-Rates.”</span> <em>Biology Direct</em> 4 (1): 1–18.
+Wang, Da-Peng, Hao-Lei Wan, Song Zhang, and Jun Yu. 2009.
+<span>“<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>γ</mi><annotation encoding="application/x-tex">\gamma</annotation></semantics></math>-MYN:
+A New Algorithm for Estimating Ka and Ks with Consideration of Variable
+Substitution Rates.”</span> <em>Biology Direct</em> 4 (1): 1–18.
 </div>
 <div id="ref-wang2010kaks_calculator" class="csl-entry">
 Wang, Dapeng, Yubin Zhang, Zhang Zhang, Jiang Zhu, and Jun Yu. 2010.
@@ -1089,13 +1087,13 @@ Evolutionary Biology</em> 6 (1): 1–10.
 </h2>
 <div class="sourceCode" id="cb89"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/sessionInfo.html" class="external-link">sessionInfo</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
-<pre><code><span><span class="co">## R Under development (unstable) (2024-03-12 r86109)</span></span>
-<span><span class="co">## Platform: x86_64-apple-darwin20</span></span>
-<span><span class="co">## Running under: macOS Monterey 12.7.3</span></span>
+<pre><code><span><span class="co">## R version 4.4.2 (2024-10-31)</span></span>
+<span><span class="co">## Platform: aarch64-apple-darwin20</span></span>
+<span><span class="co">## Running under: macOS Sonoma 14.6</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Matrix products: default</span></span>
-<span><span class="co">## BLAS:   /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.0.dylib </span></span>
-<span><span class="co">## LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0</span></span>
+<span><span class="co">## BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib </span></span>
+<span><span class="co">## LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## locale:</span></span>
 <span><span class="co">## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8</span></span>
@@ -1108,44 +1106,42 @@ Evolutionary Biology</em> 6 (1): 1–10.
 <span><span class="co">## [8] base     </span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## other attached packages:</span></span>
-<span><span class="co">##  [1] ggplot2_3.5.0       tidyr_1.3.1         dplyr_1.1.4        </span></span>
-<span><span class="co">##  [4] ape_5.7-1           Biostrings_2.71.3   GenomeInfoDb_1.39.8</span></span>
-<span><span class="co">##  [7] XVector_0.43.1      IRanges_2.37.1      S4Vectors_0.41.4   </span></span>
-<span><span class="co">## [10] BiocGenerics_0.49.1 MSA2dist_1.7.5      BiocStyle_2.31.0   </span></span>
+<span><span class="co">##  [1] ggplot2_3.5.1       tidyr_1.3.1         dplyr_1.1.4        </span></span>
+<span><span class="co">##  [4] ape_5.8             Biostrings_2.74.0   GenomeInfoDb_1.42.0</span></span>
+<span><span class="co">##  [7] XVector_0.46.0      IRanges_2.40.0      S4Vectors_0.44.0   </span></span>
+<span><span class="co">## [10] BiocGenerics_0.52.0 MSA2dist_1.11.1     BiocStyle_2.34.0   </span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## loaded via a namespace (and not attached):</span></span>
-<span><span class="co">##  [1] gtable_0.3.4            xfun_0.42               bslib_0.6.1            </span></span>
-<span><span class="co">##  [4] lattice_0.22-5          tzdb_0.4.0              vctrs_0.6.5            </span></span>
-<span><span class="co">##  [7] tools_4.4.0             bitops_1.0-7            generics_0.1.3         </span></span>
-<span><span class="co">## [10] parallel_4.4.0          tibble_3.2.1            fansi_1.0.6            </span></span>
-<span><span class="co">## [13] highr_0.10              pkgconfig_2.0.3         desc_1.4.3             </span></span>
-<span><span class="co">## [16] lifecycle_1.0.4         GenomeInfoDbData_1.2.11 farver_2.1.1           </span></span>
-<span><span class="co">## [19] stringr_1.5.1           compiler_4.4.0          textshaping_0.3.7      </span></span>
-<span><span class="co">## [22] munsell_0.5.0           codetools_0.2-19        htmltools_0.5.7        </span></span>
-<span><span class="co">## [25] sass_0.4.8              RCurl_1.98-1.14         yaml_2.3.8             </span></span>
-<span><span class="co">## [28] pkgdown_2.0.7           pillar_1.9.0            crayon_1.5.2           </span></span>
-<span><span class="co">## [31] jquerylib_0.1.4         seqinr_4.2-36           MASS_7.3-60.2          </span></span>
-<span><span class="co">## [34] cachem_1.0.8            iterators_1.0.14        foreach_1.5.2          </span></span>
-<span><span class="co">## [37] nlme_3.1-164            tidyselect_1.2.1        digest_0.6.35          </span></span>
-<span><span class="co">## [40] stringi_1.8.3           purrr_1.0.2             bookdown_0.38          </span></span>
-<span><span class="co">## [43] labeling_0.4.3          ade4_1.7-22             fastmap_1.1.1          </span></span>
-<span><span class="co">## [46] grid_4.4.0              colorspace_2.1-0        cli_3.6.2              </span></span>
-<span><span class="co">## [49] magrittr_2.0.3          utf8_1.2.4              withr_3.0.0            </span></span>
-<span><span class="co">## [52] readr_2.1.5             scales_1.3.0            rmarkdown_2.26         </span></span>
-<span><span class="co">## [55] ragg_1.2.7              hms_1.1.3               memoise_2.0.1          </span></span>
-<span><span class="co">## [58] evaluate_0.23           knitr_1.45              GenomicRanges_1.55.3   </span></span>
-<span><span class="co">## [61] doParallel_1.0.17       rlang_1.1.3             Rcpp_1.0.12            </span></span>
-<span><span class="co">## [64] glue_1.7.0              BiocManager_1.30.22     rstudioapi_0.15.0      </span></span>
-<span><span class="co">## [67] jsonlite_1.8.8          R6_2.5.1                systemfonts_1.0.6      </span></span>
-<span><span class="co">## [70] fs_1.6.3                zlibbioc_1.49.0</span></span></code></pre>
+<span><span class="co">##  [1] gtable_0.3.6            xfun_0.49               bslib_0.8.0            </span></span>
+<span><span class="co">##  [4] htmlwidgets_1.6.4       lattice_0.22-6          tzdb_0.4.0             </span></span>
+<span><span class="co">##  [7] vctrs_0.6.5             tools_4.4.2             generics_0.1.3         </span></span>
+<span><span class="co">## [10] parallel_4.4.2          tibble_3.2.1            fansi_1.0.6            </span></span>
+<span><span class="co">## [13] pkgconfig_2.0.3         desc_1.4.3              lifecycle_1.0.4        </span></span>
+<span><span class="co">## [16] GenomeInfoDbData_1.2.13 farver_2.1.2            stringr_1.5.1          </span></span>
+<span><span class="co">## [19] compiler_4.4.2          textshaping_0.4.0       munsell_0.5.1          </span></span>
+<span><span class="co">## [22] codetools_0.2-20        htmltools_0.5.8.1       sass_0.4.9             </span></span>
+<span><span class="co">## [25] yaml_2.3.10             pkgdown_2.1.1           pillar_1.9.0           </span></span>
+<span><span class="co">## [28] crayon_1.5.3            jquerylib_0.1.4         seqinr_4.2-36          </span></span>
+<span><span class="co">## [31] MASS_7.3-61             cachem_1.1.0            iterators_1.0.14       </span></span>
+<span><span class="co">## [34] foreach_1.5.2           nlme_3.1-166            tidyselect_1.2.1       </span></span>
+<span><span class="co">## [37] digest_0.6.37           stringi_1.8.4           purrr_1.0.2            </span></span>
+<span><span class="co">## [40] bookdown_0.41           labeling_0.4.3          ade4_1.7-22            </span></span>
+<span><span class="co">## [43] fastmap_1.2.0           grid_4.4.2              colorspace_2.1-1       </span></span>
+<span><span class="co">## [46] cli_3.6.3               magrittr_2.0.3          utf8_1.2.4             </span></span>
+<span><span class="co">## [49] withr_3.0.2             readr_2.1.5             scales_1.3.0           </span></span>
+<span><span class="co">## [52] UCSC.utils_1.2.0        rmarkdown_2.29          pwalign_1.2.0          </span></span>
+<span><span class="co">## [55] httr_1.4.7              ragg_1.3.3              hms_1.1.3              </span></span>
+<span><span class="co">## [58] evaluate_1.0.1          knitr_1.49              GenomicRanges_1.58.0   </span></span>
+<span><span class="co">## [61] doParallel_1.0.17       rlang_1.1.4             Rcpp_1.0.13-1          </span></span>
+<span><span class="co">## [64] glue_1.8.0              BiocManager_1.30.25     rstudioapi_0.17.1      </span></span>
+<span><span class="co">## [67] jsonlite_1.8.9          R6_2.5.1                systemfonts_1.1.0      </span></span>
+<span><span class="co">## [70] fs_1.6.5                zlibbioc_1.52.0</span></span></code></pre>
 </div>
   </div>
 
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
 
-        <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2>
-    </nav>
-</div>
+      </div>
 
 </div>
 
@@ -1158,16 +1154,16 @@ Evolutionary Biology</em> 6 (1): 1–10.
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer>
 </div>
 
-  
 
 
-  
+
+
 
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 </html>
diff --git a/public/articles/MSA2dist_files/figure-html/unnamed-chunk-28-1.png b/public/articles/MSA2dist_files/figure-html/unnamed-chunk-28-1.png
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index 03163fbb1087b6b6789d28ca14c982303f820367..0d1c6fd01795d169901707c4a02d6f80a0b1301f 100644
--- a/public/articles/index.html
+++ b/public/articles/index.html
@@ -1,9 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Articles • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Articles"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Articles • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Articles"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-article-index">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -34,14 +34,14 @@
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
@@ -65,15 +65,15 @@
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/authors.html b/public/authors.html
index f77e3b081cdfc96f434ef98dd5f81ac10f5e3256..672e6c7df39854a7a5c26ad662f0a3dd33fe185d 100644
--- a/public/authors.html
+++ b/public/authors.html
@@ -1,9 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Authors and Citation • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="bootstrap-toc.css"><script src="bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet"><script src="pkgdown.js"></script><meta property="og:title" content="Authors and Citation"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Authors and Citation • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="bootstrap-toc.css"><script src="bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet"><script src="pkgdown.js"></script><meta property="og:title" content="Authors and Citation"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-citation-authors">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -34,23 +34,23 @@
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="contents col-md-9">
     <div class="section level2 authors-section">
       <div class="page-header">
-        <h1>Authors</h1>
+        <h1>Authors and Citation</h1>
       </div>
 
-      
+
       <ul class="list-unstyled"><li>
           <p><strong>Kristian K Ullrich</strong>. Author, maintainer. <a href="https://orcid.org/0000-0003-4308-9626" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
           </p>
@@ -59,24 +59,20 @@
     <div class="section level2 citation-section">
     <div>
       <h1 id="citation">Citation</h1>
-      <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterDESCRIPTION" class="external-link"><code>DESCRIPTION</code></a></small>
+      <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/DESCRIPTION" class="external-link"><code>DESCRIPTION</code></a></small>
     </div>
     </div>
 
 
     <p>Ullrich K (2024).
-<em>MSA2dist: MSA2dist calculates pairwise distances between all sequences of a
-DNAStringSet or a AAStringSet using a custom score matrix and conducts
-codon based analysis</em>.
-R package version 1.7.5, https://mpievolbio-it.pages.gwdg.de/MSA2dist/, <a href="https://gitlab.gwdg.de/mpievolbio-it/MSA2dist" class="external-link">https://gitlab.gwdg.de/mpievolbio-it/MSA2dist</a>. 
+<em>MSA2dist: MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis</em>.
+R package version 1.11.1, https://mpievolbio-it.pages.gwdg.de/MSA2dist/, <a href="https://gitlab.gwdg.de/mpievolbio-it/MSA2dist" class="external-link">https://gitlab.gwdg.de/mpievolbio-it/MSA2dist</a>.
 </p>
     <pre>@Manual{,
-  title = {MSA2dist: MSA2dist calculates pairwise distances between all sequences of a
-DNAStringSet or a AAStringSet using a custom score matrix and conducts
-codon based analysis},
+  title = {MSA2dist: MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis},
   author = {Kristian K Ullrich},
   year = {2024},
-  note = {R package version 1.7.5, https://mpievolbio-it.pages.gwdg.de/MSA2dist/},
+  note = {R package version 1.11.1, https://mpievolbio-it.pages.gwdg.de/MSA2dist/},
   url = {https://gitlab.gwdg.de/mpievolbio-it/MSA2dist},
 }</pre>
 
@@ -91,15 +87,15 @@ codon based analysis},
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/index.html b/public/index.html
index 4465debb2d8fa7518aef82f717dc264d0513c3e1..e7e789175d30ea83595e99d30d1ff5b2be7f2d30 100644
--- a/public/index.html
+++ b/public/index.html
@@ -5,29 +5,20 @@
 <meta charset="utf-8">
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>MSA2dist calculates pairwise distances between all sequences of a
-    DNAStringSet or a AAStringSet using a custom score matrix and conducts
-    codon based analysis • MSA2dist</title>
+<title>MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis • MSA2dist</title>
 <!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png">
 <link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png">
 <link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png">
 <link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png">
 <link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png">
 <link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png">
-<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
+<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
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-<script src="pkgdown.js"></script><meta property="og:title" content="MSA2dist calculates pairwise distances between all sequences of a
-    DNAStringSet or a AAStringSet using a custom score matrix and conducts
-    codon based analysis">
-<meta property="og:description" content="MSA2dist calculates pairwise distances between all sequences of
-    a DNAStringSet or a AAStringSet using a custom score matrix and conducts
-    codon based analysis. It uses scoring matrices to be used in these pairwise
-    distance calcualtions which can be adapted to any scoring for DNA or AA
-    characters. E.g. by using literal distances MSA2dist calculates pairwise
-    IUPAC distances.">
+<script src="pkgdown.js"></script><meta property="og:title" content="MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis">
+<meta property="og:description" content="MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis. It uses scoring matrices to be used in these pairwise distance calcualtions which can be adapted to any scoring for DNA or AA characters. E.g. by using literal distances MSA2dist calculates pairwise IUPAC distances.">
 <meta property="og:image" content="/logo.png">
 <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@@ -35,7 +26,7 @@
 <![endif]-->
 </head>
 <body data-spy="scroll" data-target="#toc">
-    
+
 
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       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -49,7 +40,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -69,7 +60,7 @@
 <li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
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@@ -80,7 +71,7 @@
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+
 
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@@ -239,10 +230,10 @@
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+<span>  <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>x<span class="op">=</span><span class="va">Codon</span>, y<span class="op">=</span><span class="va">values</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span>
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 <div class="section level2">
@@ -342,16 +333,16 @@
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
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 </div>
 
-  
 
 
-  
+
+
 
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diff --git a/public/news/index.html b/public/news/index.html
index be5e76d3ca6c2ad831fb0b13c4e0b2905571d516..108a67fefc968b49b6bc9b63bbe0a54a40be8aed 100644
--- a/public/news/index.html
+++ b/public/news/index.html
@@ -1,9 +1,9 @@
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Changelog • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Changelog"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-news">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
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@@ -34,22 +34,30 @@
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
       <h1 data-toc-skip>Changelog <small></small></h1>
-      <small>Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterNEWS.md" class="external-link"><code>NEWS.md</code></a></small>
+      <small>Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
     </div>
 
+    <div class="section level2">
+<h2 class="page-header" data-toc-text="1.11.1" id="msa2dist-1111-2024-11-14">MSA2dist 1.11.1 (2024-11-14)<a class="anchor" aria-label="anchor" href="#msa2dist-1111-2024-11-14"></a></h2>
+<p>BUG FIXES</p>
+<ul><li>fixed pal2nal</li>
+<li>fixed aastring2aabin to return alignment</li>
+</ul><p>NEW FEATURES</p>
+<ul><li>added globalDeletionAA</li>
+</ul></div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="1.7.5" id="msa2dist-175-2024-03-28">MSA2dist 1.7.5 (2024-03-28)<a class="anchor" aria-label="anchor" href="#msa2dist-175-2024-03-28"></a></h2>
 <p>BUG FIXES</p>
@@ -182,15 +190,15 @@
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 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/pkgdown.yml b/public/pkgdown.yml
index fb8a136218f58c48df95a4a7ce3af66b6730bb69..71ce43cf43fb7ecba73fe4a2b44a0d741e579f53 100644
--- a/public/pkgdown.yml
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-pkgdown: 2.0.7
+pandoc: '3.5'
+pkgdown: 2.1.1
 pkgdown_sha: ~
 articles:
   MSA2dist: MSA2dist.html
-last_built: 2024-03-28T13:42Z
-
+last_built: 2024-11-13T20:25Z
diff --git a/public/reference/AAMatrix-data.html b/public/reference/AAMatrix-data.html
index d798fa3fea8aed5a4bc267927c73439290c80c01..5ebca0f3c4618e799f756f54afb9611274322f2f 100644
--- a/public/reference/AAMatrix-data.html
+++ b/public/reference/AAMatrix-data.html
@@ -1,9 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>AAMatrix-data — AAMatrix-data • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="AAMatrix-data — AAMatrix-data"><meta property="og:description" content="getAAMatrix()  from the alakazam package."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>AAMatrix-data — AAMatrix-data • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="AAMatrix-data — AAMatrix-data"><meta property="og:description" content="getAAMatrix()  from the alakazam package."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -34,20 +34,20 @@
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>AAMatrix-data</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/AAMatrix-data.R" class="external-link"><code>R/AAMatrix-data.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/AAMatrix-data.R" class="external-link"><code>R/AAMatrix-data.R</code></a></small>
     <div class="hidden name"><code>AAMatrix-data.Rd</code></div>
     </div>
 
@@ -65,11 +65,7 @@
     </div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p><code>score matrix</code></p>
-
-
+    <p><code>score matrix</code></p>
     </div>
     <div id="references">
     <h2>References</h2>
@@ -96,15 +92,15 @@ immunoglobulin repertoire sequencing data. <em>Bioinformatics.</em>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/GENETIC_CODE_TCAG.html b/public/reference/GENETIC_CODE_TCAG.html
index f9f7fa622ced164e56e507e74650ec9e56996d8b..b9c2c689dfdef08aa6391c27138c54e3f70f2734 100644
--- a/public/reference/GENETIC_CODE_TCAG.html
+++ b/public/reference/GENETIC_CODE_TCAG.html
@@ -1,10 +1,10 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>GENETIC_CODE_TCAG — GENETIC_CODE_TCAG • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="GENETIC_CODE_TCAG — GENETIC_CODE_TCAG"><meta property="og:description" content="GENETIC_CODE from Biostrings extended by codon
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>GENETIC_CODE_TCAG — GENETIC_CODE_TCAG • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="GENETIC_CODE_TCAG — GENETIC_CODE_TCAG"><meta property="og:description" content="GENETIC_CODE from Biostrings extended by codon
 number and number of syn sites."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -18,7 +18,7 @@ number and number of syn sites."><meta property="og:image" content="/logo.png"><
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -35,20 +35,20 @@ number and number of syn sites."><meta property="og:image" content="/logo.png"><
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>GENETIC_CODE_TCAG</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/GENETIC_CODE_TCAG.R" class="external-link"><code>R/GENETIC_CODE_TCAG.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/GENETIC_CODE_TCAG.R" class="external-link"><code>R/GENETIC_CODE_TCAG.R</code></a></small>
     <div class="hidden name"><code>GENETIC_CODE_TCAG.Rd</code></div>
     </div>
 
@@ -63,17 +63,15 @@ number and number of syn sites.</p>
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>codon</dt>
+
+
+<dl><dt id="arg-codon">codon<a class="anchor" aria-label="anchor" href="#arg-codon"></a></dt>
 <dd><p><code>codon</code> [mandatory]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>An object of class <code>numeric</code></p>
-
-
+    <p>An object of class <code>numeric</code></p>
     </div>
     <div id="see-also">
     <h2>See also</h2>
@@ -166,15 +164,15 @@ number and number of syn sites.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/aa2selfscore.html b/public/reference/aa2selfscore.html
index c5c413a87a9f7c33a7f83bd5c3d661788363bbd7..2e776da6ac26c5faf10186ed16deaba38bb49e77 100644
--- a/public/reference/aa2selfscore.html
+++ b/public/reference/aa2selfscore.html
@@ -1,9 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>aa2selfscore — aa2selfscore • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="aa2selfscore — aa2selfscore"><meta property="og:description" content="This function return the selfscore from an AAStringSet."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>aa2selfscore — aa2selfscore • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="aa2selfscore — aa2selfscore"><meta property="og:description" content="This function return the selfscore from an AAStringSet."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -34,20 +34,20 @@
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>aa2selfscore</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/aa2selfscore.R" class="external-link"><code>R/aa2selfscore.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/aa2selfscore.R" class="external-link"><code>R/aa2selfscore.R</code></a></small>
     <div class="hidden name"><code>aa2selfscore.Rd</code></div>
     </div>
 
@@ -61,26 +61,24 @@
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>aa</dt>
+
+
+<dl><dt id="arg-aa">aa<a class="anchor" aria-label="anchor" href="#arg-aa"></a></dt>
 <dd><p><code>AAStringSet</code> [mandatory]</p></dd>
 
 
-<dt>scorematrix</dt>
+<dt id="arg-scorematrix">scorematrix<a class="anchor" aria-label="anchor" href="#arg-scorematrix"></a></dt>
 <dd><p>score matrix to use [default: BLOSUM62]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p><code>data.frame</code></p>
-
-
+    <p><code>data.frame</code></p>
     </div>
     <div id="see-also">
     <h2>See also</h2>
     <div class="dont-index"><p><code><a href="https://rdrr.io/pkg/Biostrings/man/XStringSet-class.html" class="external-link">XStringSet-class</a></code>,
-<code><a href="https://rdrr.io/pkg/Biostrings/man/substitution_matrices.html" class="external-link">substitution.matrices</a></code></p></div>
+<code><a href="https://rdrr.io/pkg/pwalign/man/substitution_matrices.html" class="external-link">substitution_matrices</a></code></p></div>
     </div>
     <div id="author">
     <h2>Author</h2>
@@ -124,15 +122,15 @@
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/aabin2aastring.html b/public/reference/aabin2aastring.html
index 3dd85e08734c50f5157b27a8682d54cc2193fccc..c7269cae0c2015d945e990ba24a5698a89d8900e 100644
--- a/public/reference/aabin2aastring.html
+++ b/public/reference/aabin2aastring.html
@@ -1,10 +1,10 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>aabin2aastring — aabin2aastring • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="aabin2aastring — aabin2aastring"><meta property="og:description" content="This function converts an ape AAbin into
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>aabin2aastring — aabin2aastring • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="aabin2aastring — aabin2aastring"><meta property="og:description" content="This function converts an ape AAbin into
 AAStringSet."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -18,7 +18,7 @@ AAStringSet."><meta property="og:image" content="/logo.png"><!-- mathjax --><scr
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -35,20 +35,20 @@ AAStringSet."><meta property="og:image" content="/logo.png"><!-- mathjax --><scr
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>aabin2aastring</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/aabin2aastring.R" class="external-link"><code>R/aabin2aastring.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/aabin2aastring.R" class="external-link"><code>R/aabin2aastring.R</code></a></small>
     <div class="hidden name"><code>aabin2aastring.Rd</code></div>
     </div>
 
@@ -63,17 +63,15 @@ AAStringSet."><meta property="og:image" content="/logo.png"><!-- mathjax --><scr
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>aabin</dt>
+
+
+<dl><dt id="arg-aabin">aabin<a class="anchor" aria-label="anchor" href="#arg-aabin"></a></dt>
 <dd><p><code>ape</code> <code>AAbin</code> [mandatory]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>An object of class <code>AAStringSet</code></p>
-
-
+    <p>An object of class <code>AAStringSet</code></p>
     </div>
     <div id="see-also">
     <h2>See also</h2>
@@ -120,15 +118,15 @@ AAStringSet."><meta property="og:image" content="/logo.png"><!-- mathjax --><scr
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/aastring2aabin.html b/public/reference/aastring2aabin.html
index 44330ae00b23af1338a10df443ffe3a0f130e360..9755cfb8c7724b66aafe91970919d4087411d2c5 100644
--- a/public/reference/aastring2aabin.html
+++ b/public/reference/aastring2aabin.html
@@ -1,10 +1,10 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>aastring2aabin — aastring2aabin • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="aastring2aabin — aastring2aabin"><meta property="og:description" content="This function converts a AAStringSet into an ape
-DNAbin."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>aastring2aabin — aastring2aabin • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="aastring2aabin — aastring2aabin"><meta property="og:description" content="This function converts an AAStringSet
+into an ape AAbin."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -18,7 +18,7 @@ DNAbin."><meta property="og:image" content="/logo.png"><!-- mathjax --><script s
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -35,26 +35,26 @@ DNAbin."><meta property="og:image" content="/logo.png"><!-- mathjax --><script s
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>aastring2aabin</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/aastring2aabin.R" class="external-link"><code>R/aastring2aabin.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/aastring2aabin.R" class="external-link"><code>R/aastring2aabin.R</code></a></small>
     <div class="hidden name"><code>aastring2aabin.Rd</code></div>
     </div>
 
     <div class="ref-description">
-    <p>This function converts a <code>AAStringSet</code> into an <code>ape</code>
-<code>DNAbin</code>.</p>
+    <p>This function converts an <code>AAStringSet</code>
+into an <code>ape</code> <code>AAbin</code>.</p>
     </div>
 
     <div id="ref-usage">
@@ -63,17 +63,15 @@ DNAbin."><meta property="og:image" content="/logo.png"><!-- mathjax --><script s
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>aa</dt>
+
+
+<dl><dt id="arg-aa">aa<a class="anchor" aria-label="anchor" href="#arg-aa"></a></dt>
 <dd><p><code>AAStringSet</code> [mandatory]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>An object of class <code>DNAbin</code></p>
-
-
+    <p>An object of class <code>AAbin</code></p>
     </div>
     <div id="see-also">
     <h2>See also</h2>
@@ -95,8 +93,7 @@ DNAbin."><meta property="og:image" content="/logo.png"><!-- mathjax --><script s
 <span class="r-in"><span><span class="co">## convert into AAbin</span></span></span>
 <span class="r-in"><span><span class="co">#aastring2aabin(cds2aa(cds1.cds2.aln))</span></span></span>
 <span class="r-in"><span><span class="va">cds1.cds2.aln</span> <span class="op">|&gt;</span> <span class="fu"><a href="cds2aa.html">cds2aa</a></span><span class="op">(</span><span class="op">)</span> <span class="op">|&gt;</span> <span class="fu">aastring2aabin</span><span class="op">(</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2 amino acid sequences in a list</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2 amino acid sequences in a matrix</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> All sequences of the same length: 4 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 </code></pre></div>
@@ -113,15 +110,15 @@ DNAbin."><meta property="og:image" content="/logo.png"><!-- mathjax --><script s
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/aastring2aln.html b/public/reference/aastring2aln.html
index fad9d35363d26fc3a2ab015cf86002270caf6507..92f9db70091197119289eea2ec9268443230875d 100644
--- a/public/reference/aastring2aln.html
+++ b/public/reference/aastring2aln.html
@@ -1,10 +1,10 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>aastring2aln — aastring2aln • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="aastring2aln — aastring2aln"><meta property="og:description" content="This function converts a AAStringSet into an
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>aastring2aln — aastring2aln • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="aastring2aln — aastring2aln"><meta property="og:description" content="This function converts a AAStringSet into an
 seqinr alignment."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -18,7 +18,7 @@ seqinr alignment."><meta property="og:image" content="/logo.png"><!-- mathjax --
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -35,20 +35,20 @@ seqinr alignment."><meta property="og:image" content="/logo.png"><!-- mathjax --
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>aastring2aln</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/aastring2aln.R" class="external-link"><code>R/aastring2aln.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/aastring2aln.R" class="external-link"><code>R/aastring2aln.R</code></a></small>
     <div class="hidden name"><code>aastring2aln.Rd</code></div>
     </div>
 
@@ -63,29 +63,17 @@ seqinr alignment."><meta property="og:image" content="/logo.png"><!-- mathjax --
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>aa</dt>
+
+
+<dl><dt id="arg-aa">aa<a class="anchor" aria-label="anchor" href="#arg-aa"></a></dt>
 <dd><p><code>AAStringSet</code> [mandatory]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>An object of class <code>alignment</code> which is a list with the
-following components:<br></p>
-
-
-<p><code>nb</code> the number of aligned sequences<br></p>
-
-
-<p><code>nam</code> a vector of strings containing the names of the aligned
-sequences<br></p>
-
-
-<p><code>seq</code> a vector of strings containing the aligned sequences<br></p>
-
-
-<p><code>com</code> a vector of strings containing the commentaries for each sequence
+    <p>An object of class <code>alignment</code> which is a list with the
+following components:<br><code>nb</code> the number of aligned sequences<br><code>nam</code> a vector of strings containing the names of the aligned
+sequences<br><code>seq</code> a vector of strings containing the aligned sequences<br><code>com</code> a vector of strings containing the commentaries for each sequence
 or <code>NA</code> if there are no comments</p>
     </div>
     <div id="see-also">
@@ -134,15 +122,15 @@ or <code>NA</code> if there are no comments</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/aastring2dist.html b/public/reference/aastring2dist.html
index 0f07fdcedfb241a5e7a60034cf78c9f800ba4351..3a69f25b1ff19ce4d1fca5bcdced96b18225124e 100644
--- a/public/reference/aastring2dist.html
+++ b/public/reference/aastring2dist.html
@@ -1,10 +1,10 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>aastring2dist — aastring2dist • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="aastring2dist — aastring2dist"><meta property="og:description" content="This function calculates pairwise distances for all combinations
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>aastring2dist — aastring2dist • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="aastring2dist — aastring2dist"><meta property="og:description" content="This function calculates pairwise distances for all combinations
 of a AAStringSet."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -18,7 +18,7 @@ of a AAStringSet."><meta property="og:image" content="/logo.png"><!-- mathjax --
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -35,20 +35,20 @@ of a AAStringSet."><meta property="og:image" content="/logo.png"><!-- mathjax --
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>aastring2dist</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/aastring2dist.R" class="external-link"><code>R/aastring2dist.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/aastring2dist.R" class="external-link"><code>R/aastring2dist.R</code></a></small>
     <div class="hidden name"><code>aastring2dist.Rd</code></div>
     </div>
 
@@ -70,42 +70,40 @@ of a <code>AAStringSet</code>.</p>
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>aa</dt>
+
+
+<dl><dt id="arg-aa">aa<a class="anchor" aria-label="anchor" href="#arg-aa"></a></dt>
 <dd><p><code>AAStringSet</code> [mandatory]</p></dd>
 
 
-<dt>threads</dt>
+<dt id="arg-threads">threads<a class="anchor" aria-label="anchor" href="#arg-threads"></a></dt>
 <dd><p>number of parallel threads [default: 1]</p></dd>
 
 
-<dt>symmetric</dt>
+<dt id="arg-symmetric">symmetric<a class="anchor" aria-label="anchor" href="#arg-symmetric"></a></dt>
 <dd><p>symmetric score matrix [default: TRUE]</p></dd>
 
 
-<dt>score</dt>
+<dt id="arg-score">score<a class="anchor" aria-label="anchor" href="#arg-score"></a></dt>
 <dd><p><code>score matrix</code> use a score matrix to calculate distances
 [mandatory]</p></dd>
 
 
-<dt>mask</dt>
+<dt id="arg-mask">mask<a class="anchor" aria-label="anchor" href="#arg-mask"></a></dt>
 <dd><p><code>IRanges</code> object indicating masked sites
 [default: NULL]</p></dd>
 
 
-<dt>region</dt>
+<dt id="arg-region">region<a class="anchor" aria-label="anchor" href="#arg-region"></a></dt>
 <dd><p><code>IRanges</code> object indicating region to use for dist
 calculation (by default all sites are used) [default: NULL]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>A <code>data.frame</code> of pairwise distance values
+    <p>A <code>data.frame</code> of pairwise distance values
 <code>distSTRING</code>, sites used <code>sitesUsed</code> and region used
 <code>regionUsed</code></p>
-
-
     </div>
     <div id="see-also">
     <h2>See also</h2>
@@ -429,15 +427,15 @@ calculation (by default all sites are used) [default: NULL]</p></dd>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/addmask2string.html b/public/reference/addmask2string.html
index 7229f2316e9037c0eb10ac52c5de4b2491a88802..ed335e3445c01e4c5bfadea85220e80571e137f1 100644
--- a/public/reference/addmask2string.html
+++ b/public/reference/addmask2string.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>addmask2string — addmask2string • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="addmask2string — addmask2string"><meta property="og:description" content="This function adds mask information as an IRanges object,
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>addmask2string — addmask2string • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="addmask2string — addmask2string"><meta property="og:description" content="This function adds mask information as an IRanges object,
 START and END information, to a
 DNAStringSet or an AAStringSet and puts them into the
 metadata information.
@@ -8,7 +8,7 @@ specific regions of the DNAStringSet or the AAStringSet."><meta property="og:ima
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -22,7 +22,7 @@ specific regions of the DNAStringSet or the AAStringSet."><meta property="og:ima
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -39,20 +39,20 @@ specific regions of the DNAStringSet or the AAStringSet."><meta property="og:ima
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>addmask2string</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/addmask2string.R" class="external-link"><code>R/addmask2string.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/addmask2string.R" class="external-link"><code>R/addmask2string.R</code></a></small>
     <div class="hidden name"><code>addmask2string.Rd</code></div>
     </div>
 
@@ -71,26 +71,24 @@ specific regions of the <code>DNAStringSet</code> or the <code>AAStringSet</code
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>seq</dt>
+
+
+<dl><dt id="arg-seq">seq<a class="anchor" aria-label="anchor" href="#arg-seq"></a></dt>
 <dd><p><code>DNAStringSet</code> or <code>AAStringSet</code> [mandatory]</p></dd>
 
 
-<dt>mask</dt>
+<dt id="arg-mask">mask<a class="anchor" aria-label="anchor" href="#arg-mask"></a></dt>
 <dd><p><code>IRanges</code> object [mandatory]</p></dd>
 
 
-<dt>append</dt>
+<dt id="arg-append">append<a class="anchor" aria-label="anchor" href="#arg-append"></a></dt>
 <dd><p>indicate if mask should be appended or overwritten
 [default: TRUE]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>An object of class <code>DNAStringSet</code> or <code>AAStringSet</code></p>
-
-
+    <p>An object of class <code>DNAStringSet</code> or <code>AAStringSet</code></p>
     </div>
     <div id="see-also">
     <h2>See also</h2>
@@ -162,15 +160,15 @@ specific regions of the <code>DNAStringSet</code> or the <code>AAStringSet</code
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/addpop2string.html b/public/reference/addpop2string.html
index 4d96b4c31246360e1e3f22056a65f85144a7d8a5..fee7182c727988aee7c011feb1ff3d09d6ab933f 100644
--- a/public/reference/addpop2string.html
+++ b/public/reference/addpop2string.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>addpop2string — addpop2string • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="addpop2string — addpop2string"><meta property="og:description" content='This function adds population information to a
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>addpop2string — addpop2string • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="addpop2string — addpop2string"><meta property="og:description" content='This function adds population information to a
 DNAStringSet or an AAStringSet and puts them into the
 metadata information.
 __Note__: All unassigned sequences will be put into pop "unassigned"!
@@ -9,7 +9,7 @@ __Note__: Duplicated assignments are allowed!'><meta property="og:image" content
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -23,7 +23,7 @@ __Note__: Duplicated assignments are allowed!'><meta property="og:image" content
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -40,20 +40,20 @@ __Note__: Duplicated assignments are allowed!'><meta property="og:image" content
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>addpop2string</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/addpop2string.R" class="external-link"><code>R/addpop2string.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/addpop2string.R" class="external-link"><code>R/addpop2string.R</code></a></small>
     <div class="hidden name"><code>addpop2string.Rd</code></div>
     </div>
 
@@ -73,22 +73,20 @@ __Note__: Duplicated assignments are allowed!<br></p>
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>seq</dt>
+
+
+<dl><dt id="arg-seq">seq<a class="anchor" aria-label="anchor" href="#arg-seq"></a></dt>
 <dd><p><code>DNAStringSet</code> or <code>AAStringSet</code> [mandatory]</p></dd>
 
 
-<dt>poplist</dt>
+<dt id="arg-poplist">poplist<a class="anchor" aria-label="anchor" href="#arg-poplist"></a></dt>
 <dd><p>named <code>list</code> of populations either as index or names per
 population (do not mix index and names in one population) [mandatory]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>An object of class <code>DNAStringSet</code> or <code>AAStringSet</code></p>
-
-
+    <p>An object of class <code>DNAStringSet</code> or <code>AAStringSet</code></p>
     </div>
     <div id="see-also">
     <h2>See also</h2>
@@ -232,15 +230,15 @@ population (do not mix index and names in one population) [mandatory]</p></dd>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/addpos2string.html b/public/reference/addpos2string.html
index 6f05ca88ce33700c1559e04eb5e7a7d89e87b558..d2f4880787da6ce734b0c8de4f48b6269c18b332 100644
--- a/public/reference/addpos2string.html
+++ b/public/reference/addpos2string.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>addpos2string — addpos2string • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="addpos2string — addpos2string"><meta property="og:description" content="This function adds GenomicRanges information,
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>addpos2string — addpos2string • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="addpos2string — addpos2string"><meta property="og:description" content="This function adds GenomicRanges information,
 CHROM, START and END to a
 DNAStringSet or an AAStringSet and puts them into the
 metadata information.
@@ -7,7 +7,7 @@ This information can be used to find overlaps with a chromosome wide mask."><met
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -21,7 +21,7 @@ This information can be used to find overlaps with a chromosome wide mask."><met
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -38,20 +38,20 @@ This information can be used to find overlaps with a chromosome wide mask."><met
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>addpos2string</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/addpos2string.R" class="external-link"><code>R/addpos2string.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/addpos2string.R" class="external-link"><code>R/addpos2string.R</code></a></small>
     <div class="hidden name"><code>addpos2string.Rd</code></div>
     </div>
 
@@ -69,29 +69,27 @@ This information can be used to find overlaps with a chromosome wide mask.</p>
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>seq</dt>
+
+
+<dl><dt id="arg-seq">seq<a class="anchor" aria-label="anchor" href="#arg-seq"></a></dt>
 <dd><p><code>DNAStringSet</code> or <code>AAStringSet</code> [mandatory]</p></dd>
 
 
-<dt>chrom</dt>
+<dt id="arg-chrom">chrom<a class="anchor" aria-label="anchor" href="#arg-chrom"></a></dt>
 <dd><p>chromosome name [mandatory]</p></dd>
 
 
-<dt>start</dt>
+<dt id="arg-start">start<a class="anchor" aria-label="anchor" href="#arg-start"></a></dt>
 <dd><p>start position [mandatory]</p></dd>
 
 
-<dt>end</dt>
+<dt id="arg-end">end<a class="anchor" aria-label="anchor" href="#arg-end"></a></dt>
 <dd><p>end position [mandatory]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>An object of class <code>DNAStringSet</code> or <code>AAStringSet</code></p>
-
-
+    <p>An object of class <code>DNAStringSet</code> or <code>AAStringSet</code></p>
     </div>
     <div id="see-also">
     <h2>See also</h2>
@@ -132,15 +130,15 @@ This information can be used to find overlaps with a chromosome wide mask.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/addregion2string.html b/public/reference/addregion2string.html
index f9718f750e83c6d700ef06ddc25356c78b1e59b4..7501654868a284c4444c358f6e0060c1d159fa63 100644
--- a/public/reference/addregion2string.html
+++ b/public/reference/addregion2string.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>addregion2string — addregion2string • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="addregion2string — addregion2string"><meta property="og:description" content="This function adds region information as an IRanges
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>addregion2string — addregion2string • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="addregion2string — addregion2string"><meta property="og:description" content="This function adds region information as an IRanges
 object, START and END information, to a
 DNAStringSet or an AAStringSet and puts them into the
 metadata information.
@@ -8,7 +8,7 @@ specific regions of the DNAStringSet or the AAStringSet."><meta property="og:ima
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -22,7 +22,7 @@ specific regions of the DNAStringSet or the AAStringSet."><meta property="og:ima
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -39,20 +39,20 @@ specific regions of the DNAStringSet or the AAStringSet."><meta property="og:ima
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>addregion2string</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/addregion2string.R" class="external-link"><code>R/addregion2string.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/addregion2string.R" class="external-link"><code>R/addregion2string.R</code></a></small>
     <div class="hidden name"><code>addregion2string.Rd</code></div>
     </div>
 
@@ -71,26 +71,24 @@ specific regions of the <code>DNAStringSet</code> or the <code>AAStringSet</code
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>seq</dt>
+
+
+<dl><dt id="arg-seq">seq<a class="anchor" aria-label="anchor" href="#arg-seq"></a></dt>
 <dd><p><code>DNAStringSet</code> or <code>AAStringSet</code> [mandatory]</p></dd>
 
 
-<dt>region</dt>
+<dt id="arg-region">region<a class="anchor" aria-label="anchor" href="#arg-region"></a></dt>
 <dd><p><code>IRanges</code> object [mandatory]</p></dd>
 
 
-<dt>append</dt>
+<dt id="arg-append">append<a class="anchor" aria-label="anchor" href="#arg-append"></a></dt>
 <dd><p>indicate if region should be appended or overwritten
 [default: TRUE]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>An object of class <code>DNAStringSet</code> or <code>AAStringSet</code></p>
-
-
+    <p>An object of class <code>DNAStringSet</code> or <code>AAStringSet</code></p>
     </div>
     <div id="see-also">
     <h2>See also</h2>
@@ -162,15 +160,15 @@ specific regions of the <code>DNAStringSet</code> or the <code>AAStringSet</code
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/aln2aastring.html b/public/reference/aln2aastring.html
index 45b8741bea982d31b3d0b4a67173e08d9a1743ad..5f40e12179bd7e7e9a83c54f1cac3dea07fe0330 100644
--- a/public/reference/aln2aastring.html
+++ b/public/reference/aln2aastring.html
@@ -1,10 +1,10 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>aln2aastring — aln2aastring • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="aln2aastring — aln2aastring"><meta property="og:description" content="This function converts a seqinr alignment into
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>aln2aastring — aln2aastring • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="aln2aastring — aln2aastring"><meta property="og:description" content="This function converts a seqinr alignment into
 an AAStringSet."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -18,7 +18,7 @@ an AAStringSet."><meta property="og:image" content="/logo.png"><!-- mathjax --><
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -35,20 +35,20 @@ an AAStringSet."><meta property="og:image" content="/logo.png"><!-- mathjax --><
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>aln2aastring</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/aln2aastring.R" class="external-link"><code>R/aln2aastring.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/aln2aastring.R" class="external-link"><code>R/aln2aastring.R</code></a></small>
     <div class="hidden name"><code>aln2aastring.Rd</code></div>
     </div>
 
@@ -63,17 +63,15 @@ an <code>AAStringSet</code>.</p>
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>aln</dt>
+
+
+<dl><dt id="arg-aln">aln<a class="anchor" aria-label="anchor" href="#arg-aln"></a></dt>
 <dd><p><code>seqinr</code> <code>alignment</code> [mandatory]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>An object of class <code>AAStringSet</code></p>
-
-
+    <p>An object of class <code>AAStringSet</code></p>
     </div>
     <div id="see-also">
     <h2>See also</h2>
@@ -112,15 +110,15 @@ an <code>AAStringSet</code>.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/aln2dnastring.html b/public/reference/aln2dnastring.html
index 109ca28f0cef1ea1361d73fa95ed3d83fd9234f0..ab950db277909af4230f4f2ceb27ee3d6b3b3ffe 100644
--- a/public/reference/aln2dnastring.html
+++ b/public/reference/aln2dnastring.html
@@ -1,10 +1,10 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>aln2dnastring — aln2dnastring • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="aln2dnastring — aln2dnastring"><meta property="og:description" content="This function converts a seqinr alignment into
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>aln2dnastring — aln2dnastring • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="aln2dnastring — aln2dnastring"><meta property="og:description" content="This function converts a seqinr alignment into
 an DNAStringSet."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -18,7 +18,7 @@ an DNAStringSet."><meta property="og:image" content="/logo.png"><!-- mathjax -->
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -35,20 +35,20 @@ an DNAStringSet."><meta property="og:image" content="/logo.png"><!-- mathjax -->
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>aln2dnastring</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/aln2dnastring.R" class="external-link"><code>R/aln2dnastring.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/aln2dnastring.R" class="external-link"><code>R/aln2dnastring.R</code></a></small>
     <div class="hidden name"><code>aln2dnastring.Rd</code></div>
     </div>
 
@@ -63,17 +63,15 @@ an <code>DNAStringSet</code>.</p>
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>aln</dt>
+
+
+<dl><dt id="arg-aln">aln<a class="anchor" aria-label="anchor" href="#arg-aln"></a></dt>
 <dd><p><code>seqinr</code> <code>alignment</code> [mandatory]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>An object of class <code>DNAStringSet</code></p>
-
-
+    <p>An object of class <code>DNAStringSet</code></p>
     </div>
     <div id="see-also">
     <h2>See also</h2>
@@ -130,15 +128,15 @@ an <code>DNAStringSet</code>.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/cds2aa.html b/public/reference/cds2aa.html
index 137e87b123420de15efc23d9e621358ca92729b5..ba4611e160f04d05d144c46dee80fc3c9d753922 100644
--- a/public/reference/cds2aa.html
+++ b/public/reference/cds2aa.html
@@ -1,10 +1,10 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>cds2aa — cds2aa • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="cds2aa — cds2aa"><meta property="og:description" content="This function translates a DNAStringSet into an
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>cds2aa — cds2aa • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="cds2aa — cds2aa"><meta property="og:description" content="This function translates a DNAStringSet into an
 AAStringSet."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -18,7 +18,7 @@ AAStringSet."><meta property="og:image" content="/logo.png"><!-- mathjax --><scr
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -35,20 +35,20 @@ AAStringSet."><meta property="og:image" content="/logo.png"><!-- mathjax --><scr
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>cds2aa</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/cds2aa.R" class="external-link"><code>R/cds2aa.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/cds2aa.R" class="external-link"><code>R/cds2aa.R</code></a></small>
     <div class="hidden name"><code>cds2aa.Rd</code></div>
     </div>
 
@@ -70,38 +70,36 @@ AAStringSet."><meta property="og:image" content="/logo.png"><!-- mathjax --><scr
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>cds</dt>
+
+
+<dl><dt id="arg-cds">cds<a class="anchor" aria-label="anchor" href="#arg-cds"></a></dt>
 <dd><p><code>DNAStringSet</code> [mandatory]</p></dd>
 
 
-<dt>shorten</dt>
+<dt id="arg-shorten">shorten<a class="anchor" aria-label="anchor" href="#arg-shorten"></a></dt>
 <dd><p>shorten all sequences to multiple of three [default: FALSE]</p></dd>
 
 
-<dt>frame</dt>
+<dt id="arg-frame">frame<a class="anchor" aria-label="anchor" href="#arg-frame"></a></dt>
 <dd><p>indicates the first base of a the first codon [default: 1]</p></dd>
 
 
-<dt>framelist</dt>
+<dt id="arg-framelist">framelist<a class="anchor" aria-label="anchor" href="#arg-framelist"></a></dt>
 <dd><p>supply vector of frames for each entry [default: NULL]</p></dd>
 
 
-<dt>genetic.code</dt>
+<dt id="arg-genetic-code">genetic.code<a class="anchor" aria-label="anchor" href="#arg-genetic-code"></a></dt>
 <dd><p>The genetic code to use for the translation of codons
 into Amino Acid letters [default: NULL]</p></dd>
 
 
-<dt>return.cds</dt>
+<dt id="arg-return-cds">return.cds<a class="anchor" aria-label="anchor" href="#arg-return-cds"></a></dt>
 <dd><p>return shorten cds instead of aa [default: FALSE]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p><code>AAStringSet</code></p>
-
-
+    <p><code>AAStringSet</code></p>
     </div>
     <div id="see-also">
     <h2>See also</h2>
@@ -189,15 +187,15 @@ into Amino Acid letters [default: NULL]</p></dd>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/cds2codonaln.html b/public/reference/cds2codonaln.html
index abb6283e9c288fbd90f6d34bee7051e742719a49..02865ae4d9a7db0012e84395dda3b85bcb550061 100644
--- a/public/reference/cds2codonaln.html
+++ b/public/reference/cds2codonaln.html
@@ -1,11 +1,11 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>cds2codonaln — cds2codonaln • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="cds2codonaln — cds2codonaln"><meta property="og:description" content="This function takes two single sequence DNAString's or
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>cds2codonaln — cds2codonaln • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="cds2codonaln — cds2codonaln"><meta property="og:description" content="This function takes two single sequence DNAString's or
 two single sequence DNAStringSet's, converts them into aa, calculates
 a global alignment and converts this alignment back into a codon alignment."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -19,7 +19,7 @@ a global alignment and converts this alignment back into a codon alignment."><me
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -36,20 +36,20 @@ a global alignment and converts this alignment back into a codon alignment."><me
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>cds2codonaln</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/cds2codonaln.R" class="external-link"><code>R/cds2codonaln.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/cds2codonaln.R" class="external-link"><code>R/cds2codonaln.R</code></a></small>
     <div class="hidden name"><code>cds2codonaln.Rd</code></div>
     </div>
 
@@ -74,54 +74,52 @@ a global alignment and converts this alignment back into a codon alignment.</p>
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>cds1</dt>
+
+
+<dl><dt id="arg-cds-">cds1<a class="anchor" aria-label="anchor" href="#arg-cds-"></a></dt>
 <dd><p>single sequence <code>DNAStringSet</code> or <code>DNAString</code>
 [mandatory]</p></dd>
 
 
-<dt>cds2</dt>
+<dt id="arg-cds-">cds2<a class="anchor" aria-label="anchor" href="#arg-cds-"></a></dt>
 <dd><p>single sequence <code>DNAStringSet</code> or <code>DNAString</code>
 [mandatory]</p></dd>
 
 
-<dt>type</dt>
+<dt id="arg-type">type<a class="anchor" aria-label="anchor" href="#arg-type"></a></dt>
 <dd><p>type of alignment (see
-<code><a href="https://rdrr.io/pkg/Biostrings/man/pairwiseAlignment.html" class="external-link">pairwiseAlignment</a></code>) [default: global]</p></dd>
+<code>pairwiseAlignment</code>) [default: global]</p></dd>
 
 
-<dt>substitutionMatrix</dt>
+<dt id="arg-substitutionmatrix">substitutionMatrix<a class="anchor" aria-label="anchor" href="#arg-substitutionmatrix"></a></dt>
 <dd><p>substitution matrix representing the fixed
 substitution scores for an alignment (see
-<code><a href="https://rdrr.io/pkg/Biostrings/man/pairwiseAlignment.html" class="external-link">pairwiseAlignment</a></code>) [default: BLOSUM62]</p></dd>
+<code>pairwiseAlignment</code>) [default: BLOSUM62]</p></dd>
 
 
-<dt>gapOpening</dt>
+<dt id="arg-gapopening">gapOpening<a class="anchor" aria-label="anchor" href="#arg-gapopening"></a></dt>
 <dd><p>the cost for opening a gap in the alignment (see
-<code><a href="https://rdrr.io/pkg/Biostrings/man/pairwiseAlignment.html" class="external-link">pairwiseAlignment</a></code>) [default: 10]</p></dd>
+<code>pairwiseAlignment</code>) [default: 10]</p></dd>
 
 
-<dt>gapExtension</dt>
+<dt id="arg-gapextension">gapExtension<a class="anchor" aria-label="anchor" href="#arg-gapextension"></a></dt>
 <dd><p>the incremental cost incurred along the length of the
-gap in the alignment (see <code><a href="https://rdrr.io/pkg/Biostrings/man/pairwiseAlignment.html" class="external-link">pairwiseAlignment</a></code>)
+gap in the alignment (see <code>pairwiseAlignment</code>)
 [default: 0.5]</p></dd>
 
 
-<dt>remove.gaps</dt>
+<dt id="arg-remove-gaps">remove.gaps<a class="anchor" aria-label="anchor" href="#arg-remove-gaps"></a></dt>
 <dd><p>specify if gaps in the codon alignment should be removed
 [default: FALSE]</p></dd>
 
 
-<dt>...</dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
 <dd><p>other cds2aa parameters</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>codon alignment as <code>DNAStringSet</code></p>
-
-
+    <p>codon alignment as <code>DNAStringSet</code></p>
     </div>
     <div id="references">
     <h2>References</h2>
@@ -130,7 +128,7 @@ biological strings. <em>R package version</em>, <b>2(0)</b>.</p>
     </div>
     <div id="see-also">
     <h2>See also</h2>
-    <div class="dont-index"><p><code><a href="https://rdrr.io/pkg/Biostrings/man/pairwiseAlignment.html" class="external-link">pairwiseAlignment</a></code></p></div>
+    <div class="dont-index"><p><code>pairwiseAlignment</code></p></div>
     </div>
     <div id="author">
     <h2>Author</h2>
@@ -161,15 +159,15 @@ biological strings. <em>R package version</em>, <b>2(0)</b>.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/cdsstring2codonaln.html b/public/reference/cdsstring2codonaln.html
index 696e122a6cf240567c2d196d4247aae815670bfa..e353f33c8ac5848d221e758534427309ded9ff2b 100644
--- a/public/reference/cdsstring2codonaln.html
+++ b/public/reference/cdsstring2codonaln.html
@@ -1,11 +1,11 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>cdsstring2codonaln — cdsstring2codonaln • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="cdsstring2codonaln — cdsstring2codonaln"><meta property="og:description" content="This function takes two sequences as DNAStringSet,
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>cdsstring2codonaln — cdsstring2codonaln • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="cdsstring2codonaln — cdsstring2codonaln"><meta property="og:description" content="This function takes two sequences as DNAStringSet,
 and their corresponding AAStringSet, calculates
 a global alignment and converts this alignment back into a codon alignment."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -19,7 +19,7 @@ a global alignment and converts this alignment back into a codon alignment."><me
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -36,20 +36,20 @@ a global alignment and converts this alignment back into a codon alignment."><me
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>cdsstring2codonaln</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/cdsstring2codonaln.R" class="external-link"><code>R/cdsstring2codonaln.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/cdsstring2codonaln.R" class="external-link"><code>R/cdsstring2codonaln.R</code></a></small>
     <div class="hidden name"><code>cdsstring2codonaln.Rd</code></div>
     </div>
 
@@ -73,48 +73,46 @@ a global alignment and converts this alignment back into a codon alignment.</p>
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>cds</dt>
+
+
+<dl><dt id="arg-cds">cds<a class="anchor" aria-label="anchor" href="#arg-cds"></a></dt>
 <dd><p>two sequences <code>DNAStringSet</code> [mandatory]</p></dd>
 
 
-<dt>aa</dt>
+<dt id="arg-aa">aa<a class="anchor" aria-label="anchor" href="#arg-aa"></a></dt>
 <dd><p>two sequences <code>AAStringSet</code> [mandatory]</p></dd>
 
 
-<dt>type</dt>
+<dt id="arg-type">type<a class="anchor" aria-label="anchor" href="#arg-type"></a></dt>
 <dd><p>type of alignment (see
-<code><a href="https://rdrr.io/pkg/Biostrings/man/pairwiseAlignment.html" class="external-link">pairwiseAlignment</a></code>) [default: global]</p></dd>
+<code>pairwiseAlignment</code>) [default: global]</p></dd>
 
 
-<dt>substitutionMatrix</dt>
+<dt id="arg-substitutionmatrix">substitutionMatrix<a class="anchor" aria-label="anchor" href="#arg-substitutionmatrix"></a></dt>
 <dd><p>substitution matrix representing the fixed
 substitution scores for an alignment (see
-<code><a href="https://rdrr.io/pkg/Biostrings/man/pairwiseAlignment.html" class="external-link">pairwiseAlignment</a></code>) [default: BLOSUM62]</p></dd>
+<code>pairwiseAlignment</code>) [default: BLOSUM62]</p></dd>
 
 
-<dt>gapOpening</dt>
+<dt id="arg-gapopening">gapOpening<a class="anchor" aria-label="anchor" href="#arg-gapopening"></a></dt>
 <dd><p>the cost for opening a gap in the alignment (see
-<code><a href="https://rdrr.io/pkg/Biostrings/man/pairwiseAlignment.html" class="external-link">pairwiseAlignment</a></code>) [default: 10]</p></dd>
+<code>pairwiseAlignment</code>) [default: 10]</p></dd>
 
 
-<dt>gapExtension</dt>
+<dt id="arg-gapextension">gapExtension<a class="anchor" aria-label="anchor" href="#arg-gapextension"></a></dt>
 <dd><p>the incremental cost incurred along the length of the
-gap in the alignment (see <code><a href="https://rdrr.io/pkg/Biostrings/man/pairwiseAlignment.html" class="external-link">pairwiseAlignment</a></code>)
+gap in the alignment (see <code>pairwiseAlignment</code>)
 [default: 0.5]</p></dd>
 
 
-<dt>remove.gaps</dt>
+<dt id="arg-remove-gaps">remove.gaps<a class="anchor" aria-label="anchor" href="#arg-remove-gaps"></a></dt>
 <dd><p>specify if gaps in the codon alignment should be removed
 [default: FALSE]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>codon alignment as <code>DNAStringSet</code></p>
-
-
+    <p>codon alignment as <code>DNAStringSet</code></p>
     </div>
     <div id="references">
     <h2>References</h2>
@@ -123,7 +121,7 @@ biological strings. <em>R package version</em>, <b>2(0)</b>.</p>
     </div>
     <div id="see-also">
     <h2>See also</h2>
-    <div class="dont-index"><p><code><a href="https://rdrr.io/pkg/Biostrings/man/pairwiseAlignment.html" class="external-link">pairwiseAlignment</a></code></p></div>
+    <div class="dont-index"><p><code>pairwiseAlignment</code></p></div>
     </div>
     <div id="author">
     <h2>Author</h2>
@@ -156,15 +154,15 @@ biological strings. <em>R package version</em>, <b>2(0)</b>.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/codon2numberAMBIG.html b/public/reference/codon2numberAMBIG.html
index e1db262b44204c589b7be954210d852664ec5d54..617afaa1c98195902fadcad5404ce866655da944 100644
--- a/public/reference/codon2numberAMBIG.html
+++ b/public/reference/codon2numberAMBIG.html
@@ -1,10 +1,10 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>codon2numberAMBIG — codon2numberAMBIG • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="codon2numberAMBIG — codon2numberAMBIG"><meta property="og:description" content="This function converts a codon into a number,
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>codon2numberAMBIG — codon2numberAMBIG • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="codon2numberAMBIG — codon2numberAMBIG"><meta property="og:description" content="This function converts a codon into a number,
 but accept N and -."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -18,7 +18,7 @@ but accept N and -."><meta property="og:image" content="/logo.png"><!-- mathjax
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -35,20 +35,20 @@ but accept N and -."><meta property="og:image" content="/logo.png"><!-- mathjax
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>codon2numberAMBIG</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/codon2numberAMBIG.R" class="external-link"><code>R/codon2numberAMBIG.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/codon2numberAMBIG.R" class="external-link"><code>R/codon2numberAMBIG.R</code></a></small>
     <div class="hidden name"><code>codon2numberAMBIG.Rd</code></div>
     </div>
 
@@ -63,17 +63,15 @@ but accept N and -.</p>
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>codon</dt>
+
+
+<dl><dt id="arg-codon">codon<a class="anchor" aria-label="anchor" href="#arg-codon"></a></dt>
 <dd><p>[mandatory]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>An object of class <code>numeric</code></p>
-
-
+    <p>An object of class <code>numeric</code></p>
     </div>
     <div id="see-also">
     <h2>See also</h2>
@@ -110,15 +108,15 @@ but accept N and -.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/codon2numberTCAG.html b/public/reference/codon2numberTCAG.html
index 24e77a40ec5774cfbd25a5564933d3e9b3bbcb85..ad70b25adaefcd4d029d0d77b61029b27687a3bc 100644
--- a/public/reference/codon2numberTCAG.html
+++ b/public/reference/codon2numberTCAG.html
@@ -1,9 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>codon2numberTCAG — codon2numberTCAG • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="codon2numberTCAG — codon2numberTCAG"><meta property="og:description" content="This function converts a codon into a number."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>codon2numberTCAG — codon2numberTCAG • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="codon2numberTCAG — codon2numberTCAG"><meta property="og:description" content="This function converts a codon into a number."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -34,20 +34,20 @@
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>codon2numberTCAG</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/codon2numberTCAG.R" class="external-link"><code>R/codon2numberTCAG.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/codon2numberTCAG.R" class="external-link"><code>R/codon2numberTCAG.R</code></a></small>
     <div class="hidden name"><code>codon2numberTCAG.Rd</code></div>
     </div>
 
@@ -61,17 +61,15 @@
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>codon</dt>
+
+
+<dl><dt id="arg-codon">codon<a class="anchor" aria-label="anchor" href="#arg-codon"></a></dt>
 <dd><p>[mandatory]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>An object of class <code>numeric</code></p>
-
-
+    <p>An object of class <code>numeric</code></p>
     </div>
     <div id="see-also">
     <h2>See also</h2>
@@ -108,15 +106,15 @@
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/codonmat2pnps.html b/public/reference/codonmat2pnps.html
index 3d0ea11d0a4013fbb98c8dddd8fd477821dab1d5..be85e0a587d20374b0c8a1f2fa36d2a321872dd2 100644
--- a/public/reference/codonmat2pnps.html
+++ b/public/reference/codonmat2pnps.html
@@ -1,10 +1,10 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>codonmat2pnps — codonmat2pnps • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="codonmat2pnps — codonmat2pnps"><meta property="og:description" content="This function calculates pn/ps according to Nei and
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>codonmat2pnps — codonmat2pnps • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="codonmat2pnps — codonmat2pnps"><meta property="og:description" content="This function calculates pn/ps according to Nei and
 Gojobori (1986)."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -18,7 +18,7 @@ Gojobori (1986)."><meta property="og:image" content="/logo.png"><!-- mathjax -->
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -35,20 +35,20 @@ Gojobori (1986)."><meta property="og:image" content="/logo.png"><!-- mathjax -->
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>codonmat2pnps</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/codonmat2pnps.R" class="external-link"><code>R/codonmat2pnps.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/codonmat2pnps.R" class="external-link"><code>R/codonmat2pnps.R</code></a></small>
     <div class="hidden name"><code>codonmat2pnps.Rd</code></div>
     </div>
 
@@ -63,70 +63,17 @@ Gojobori (1986)</em>.</p>
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>codonmat</dt>
+
+
+<dl><dt id="arg-codonmat">codonmat<a class="anchor" aria-label="anchor" href="#arg-codonmat"></a></dt>
 <dd><p><code>codon matrix</code> of two columns to be
 compared [mandatory]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>An object of class <code>pnps</code> which is a list with the following
-components:<br></p>
-
-
-<p><code>seq1</code> sequence1 name<br></p>
-
-
-<p><code>seq2</code> sequence2 name<br></p>
-
-
-<p><code>Codons</code> sequence2 name<br></p>
-
-
-<p><code>Compared</code> sequence2 name<br></p>
-
-
-<p><code>Ambigiuous</code> sequence2 name<br></p>
-
-
-<p><code>Indels</code> sequence2 name<br></p>
-
-
-<p><code>Ns</code> sequence2 name<br></p>
-
-
-<p><code>Sd</code> sequence2 name<br></p>
-
-
-<p><code>Sn</code> sequence2 name<br></p>
-
-
-<p><code>S</code> sequence2 name<br></p>
-
-
-<p><code>N</code> sequence2 name<br></p>
-
-
-<p><code>ps</code> sequence2 name<br></p>
-
-
-<p><code>pn</code> sequence2 name<br></p>
-
-
-<p><code>pnps</code> sequence2 name<br></p>
-
-
-<p><code>ds</code> sequence2 name<br></p>
-
-
-<p><code>dn</code> sequence2 name<br></p>
-
-
-<p><code>dnds</code> sequence2 name<br></p>
-
-
+    <p>An object of class <code>pnps</code> which is a list with the following
+components:<br><code>seq1</code> sequence1 name<br><code>seq2</code> sequence2 name<br><code>Codons</code> sequence2 name<br><code>Compared</code> sequence2 name<br><code>Ambigiuous</code> sequence2 name<br><code>Indels</code> sequence2 name<br><code>Ns</code> sequence2 name<br><code>Sd</code> sequence2 name<br><code>Sn</code> sequence2 name<br><code>S</code> sequence2 name<br><code>N</code> sequence2 name<br><code>ps</code> sequence2 name<br><code>pn</code> sequence2 name<br><code>pnps</code> sequence2 name<br><code>ds</code> sequence2 name<br><code>dn</code> sequence2 name<br><code>dnds</code> sequence2 name<br></p>
     </div>
     <div id="references">
     <h2>References</h2>
@@ -183,15 +130,15 @@ selection pressure at amino acid sites. <em>Genetics.</em>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/codonmat2xy.html b/public/reference/codonmat2xy.html
index ef013d1efa60ff1479d5bdf075669db0835fbc28..ee404422ccd2e7a9a18f7bc1691170cbb6f7b024 100644
--- a/public/reference/codonmat2xy.html
+++ b/public/reference/codonmat2xy.html
@@ -1,11 +1,11 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>codonmat2xy — codonmat2xy • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="codonmat2xy — codonmat2xy"><meta property="og:description" content="This function calculates average behavior of each codon for all
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>codonmat2xy — codonmat2xy • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="codonmat2xy — codonmat2xy"><meta property="og:description" content="This function calculates average behavior of each codon for all
 pairwise comparisons for indels, syn, and nonsyn mutations according to
 Nei and Gojobori (1986)."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -19,7 +19,7 @@ Nei and Gojobori (1986)."><meta property="og:image" content="/logo.png"><!-- mat
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -36,20 +36,20 @@ Nei and Gojobori (1986)."><meta property="og:image" content="/logo.png"><!-- mat
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>codonmat2xy</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/codonmat2xy.R" class="external-link"><code>R/codonmat2xy.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/codonmat2xy.R" class="external-link"><code>R/codonmat2xy.R</code></a></small>
     <div class="hidden name"><code>codonmat2xy.Rd</code></div>
     </div>
 
@@ -65,55 +65,20 @@ pairwise comparisons for indels, syn, and nonsyn mutations according to
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>codonmat</dt>
+
+
+<dl><dt id="arg-codonmat">codonmat<a class="anchor" aria-label="anchor" href="#arg-codonmat"></a></dt>
 <dd><p><code>codon matrix</code> obtained via
 <code><a href="dnastring2codonmat.html">dnastring2codonmat</a></code> [mandatory]</p></dd>
 
 
-<dt>threads</dt>
+<dt id="arg-threads">threads<a class="anchor" aria-label="anchor" href="#arg-threads"></a></dt>
 <dd><p>number of parallel threads [default: 1]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>A <code>data.frame</code> object with the following components:<br></p>
-
-
-<p><code>Codon</code> Codon index<br></p>
-
-
-<p><code>n</code> number of comparison<br></p>
-
-
-<p><code>SynSum</code> Sum of syn<br></p>
-
-
-<p><code>NonSynSum</code> Sum of nonsyn<br></p>
-
-
-<p><code>IndelSum</code> Sum of indels<br></p>
-
-
-<p><code>SynMean</code> average syn per codon<br></p>
-
-
-<p><code>NonSynMean</code> average nonsyn per codon<br></p>
-
-
-<p><code>IndelMean</code> average indels per codon<br></p>
-
-
-<p><code>CumSumSynMean</code> cumulative average syn per codon<br></p>
-
-
-<p><code>CumSumNonSynMean</code> cumulative average nonsyn per codon<br></p>
-
-
-<p><code>CumSumIndelMean</code> cumulative indels per codon<br></p>
-
-
+    <p>A <code>data.frame</code> object with the following components:<br><code>Codon</code> Codon index<br><code>n</code> number of comparison<br><code>SynSum</code> Sum of syn<br><code>NonSynSum</code> Sum of nonsyn<br><code>IndelSum</code> Sum of indels<br><code>SynMean</code> average syn per codon<br><code>NonSynMean</code> average nonsyn per codon<br><code>IndelMean</code> average indels per codon<br><code>CumSumSynMean</code> cumulative average syn per codon<br><code>CumSumNonSynMean</code> cumulative average nonsyn per codon<br><code>CumSumIndelMean</code> cumulative indels per codon<br></p>
     </div>
     <div id="references">
     <h2>References</h2>
@@ -201,15 +166,15 @@ selection pressure at amino acid sites. <em>Genetics.</em>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/compareCodons.html b/public/reference/compareCodons.html
index 8e077db720b256f3773c20fa19b3ae5aa57edfeb..3827e8cc429b94c9b1981dc84d8c86f806f3f1fd 100644
--- a/public/reference/compareCodons.html
+++ b/public/reference/compareCodons.html
@@ -1,10 +1,10 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>compareCodons — compareCodons • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="compareCodons — compareCodons"><meta property="og:description" content="This function compares two codons and returns the number of syn
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>compareCodons — compareCodons • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="compareCodons — compareCodons"><meta property="og:description" content="This function compares two codons and returns the number of syn
 and non-syn sites according to Nei and Gojobori (1986)."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -18,7 +18,7 @@ and non-syn sites according to Nei and Gojobori (1986)."><meta property="og:imag
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -35,20 +35,20 @@ and non-syn sites according to Nei and Gojobori (1986)."><meta property="og:imag
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>compareCodons</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/compareCodons.R" class="external-link"><code>R/compareCodons.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/compareCodons.R" class="external-link"><code>R/compareCodons.R</code></a></small>
     <div class="hidden name"><code>compareCodons.Rd</code></div>
     </div>
 
@@ -63,19 +63,19 @@ and non-syn sites according to <em>Nei and Gojobori (1986)</em>.</p>
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>codA</dt>
+
+
+<dl><dt id="arg-coda">codA<a class="anchor" aria-label="anchor" href="#arg-coda"></a></dt>
 <dd><p><code>codon</code> A [mandatory]</p></dd>
 
 
-<dt>codB</dt>
+<dt id="arg-codb">codB<a class="anchor" aria-label="anchor" href="#arg-codb"></a></dt>
 <dd><p><code>codon</code> B [mandatory]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>vector of syn and non-syn sites</p>
+    <p>vector of syn and non-syn sites</p>
     </div>
     <div id="references">
     <h2>References</h2>
@@ -126,15 +126,15 @@ selection pressure at amino acid sites. <em>Genetics.</em>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/dnabin2dnastring.html b/public/reference/dnabin2dnastring.html
index b6bd422636a3cacf23f7f1d261ae5f64cb19599b..042efc25d4949b0afaf2271721eccd1b569aca17 100644
--- a/public/reference/dnabin2dnastring.html
+++ b/public/reference/dnabin2dnastring.html
@@ -1,10 +1,10 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>dnabin2dnastring — dnabin2dnastring • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="dnabin2dnastring — dnabin2dnastring"><meta property="og:description" content="This function converts an ape DNAbin into a
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>dnabin2dnastring — dnabin2dnastring • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="dnabin2dnastring — dnabin2dnastring"><meta property="og:description" content="This function converts an ape DNAbin into a
 DNAStringSet."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -18,7 +18,7 @@ DNAStringSet."><meta property="og:image" content="/logo.png"><!-- mathjax --><sc
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -35,20 +35,20 @@ DNAStringSet."><meta property="og:image" content="/logo.png"><!-- mathjax --><sc
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>dnabin2dnastring</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/dnabin2dnastring.R" class="external-link"><code>R/dnabin2dnastring.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/dnabin2dnastring.R" class="external-link"><code>R/dnabin2dnastring.R</code></a></small>
     <div class="hidden name"><code>dnabin2dnastring.Rd</code></div>
     </div>
 
@@ -63,17 +63,15 @@ DNAStringSet."><meta property="og:image" content="/logo.png"><!-- mathjax --><sc
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>dnabin</dt>
+
+
+<dl><dt id="arg-dnabin">dnabin<a class="anchor" aria-label="anchor" href="#arg-dnabin"></a></dt>
 <dd><p><code>ape</code> <code>DNAbin</code> [mandatory]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>An object of class <code>DNAStringSet</code></p>
-
-
+    <p>An object of class <code>DNAStringSet</code></p>
     </div>
     <div id="see-also">
     <h2>See also</h2>
@@ -119,15 +117,15 @@ DNAStringSet."><meta property="og:image" content="/logo.png"><!-- mathjax --><sc
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/dnastring2aln.html b/public/reference/dnastring2aln.html
index e30e129870c161625753e92b0c120618d5b12232..29ae3e409ed2bfa4b9f4f344ccf8c5b3a8434bb0 100644
--- a/public/reference/dnastring2aln.html
+++ b/public/reference/dnastring2aln.html
@@ -1,10 +1,10 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>dnastring2aln — dnastring2aln • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="dnastring2aln — dnastring2aln"><meta property="og:description" content="This function converts a DNAStringSet into an
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>dnastring2aln — dnastring2aln • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="dnastring2aln — dnastring2aln"><meta property="og:description" content="This function converts a DNAStringSet into an
 seqinr alignment."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -18,7 +18,7 @@ seqinr alignment."><meta property="og:image" content="/logo.png"><!-- mathjax --
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -35,20 +35,20 @@ seqinr alignment."><meta property="og:image" content="/logo.png"><!-- mathjax --
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>dnastring2aln</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/dnastring2aln.R" class="external-link"><code>R/dnastring2aln.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/dnastring2aln.R" class="external-link"><code>R/dnastring2aln.R</code></a></small>
     <div class="hidden name"><code>dnastring2aln.Rd</code></div>
     </div>
 
@@ -63,29 +63,17 @@ seqinr alignment."><meta property="og:image" content="/logo.png"><!-- mathjax --
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>dna</dt>
+
+
+<dl><dt id="arg-dna">dna<a class="anchor" aria-label="anchor" href="#arg-dna"></a></dt>
 <dd><p><code>DNAStringSet</code> [mandatory]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>An object of class <code>alignment</code> which is a list with the
-following components:<br></p>
-
-
-<p><code>nb</code> the number of aligned sequences<br></p>
-
-
-<p><code>nam</code> a vector of strings containing the names of the aligned
-sequences<br></p>
-
-
-<p><code>seq</code> a vector of strings containing the aligned sequences<br></p>
-
-
-<p><code>com</code> a vector of strings containing the commentaries for each sequence
+    <p>An object of class <code>alignment</code> which is a list with the
+following components:<br><code>nb</code> the number of aligned sequences<br><code>nam</code> a vector of strings containing the names of the aligned
+sequences<br><code>seq</code> a vector of strings containing the aligned sequences<br><code>com</code> a vector of strings containing the commentaries for each sequence
 or <code>NA</code> if there are no comments</p>
     </div>
     <div id="see-also">
@@ -135,15 +123,15 @@ or <code>NA</code> if there are no comments</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/dnastring2codonmat.html b/public/reference/dnastring2codonmat.html
index 609bf0851bd511136e4974c37e65ffa251bd7128..6afd0a5b6f338ca26189157d05ef2fe4749c2f59 100644
--- a/public/reference/dnastring2codonmat.html
+++ b/public/reference/dnastring2codonmat.html
@@ -1,10 +1,10 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>dnastring2codonmat — dnastring2codonmat • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="dnastring2codonmat — dnastring2codonmat"><meta property="og:description" content="This function converts a DNAStringSet into a
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>dnastring2codonmat — dnastring2codonmat • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="dnastring2codonmat — dnastring2codonmat"><meta property="og:description" content="This function converts a DNAStringSet into a
 codon matrix."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -18,7 +18,7 @@ codon matrix."><meta property="og:image" content="/logo.png"><!-- mathjax --><sc
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -35,20 +35,20 @@ codon matrix."><meta property="og:image" content="/logo.png"><!-- mathjax --><sc
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>dnastring2codonmat</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/dnastring2codonmat.R" class="external-link"><code>R/dnastring2codonmat.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/dnastring2codonmat.R" class="external-link"><code>R/dnastring2codonmat.R</code></a></small>
     <div class="hidden name"><code>dnastring2codonmat.Rd</code></div>
     </div>
 
@@ -63,41 +63,29 @@ codon matrix."><meta property="og:image" content="/logo.png"><!-- mathjax --><sc
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>cds</dt>
+
+
+<dl><dt id="arg-cds">cds<a class="anchor" aria-label="anchor" href="#arg-cds"></a></dt>
 <dd><p><code>DNAStringSet</code> [mandatory]</p></dd>
 
 
-<dt>shorten</dt>
+<dt id="arg-shorten">shorten<a class="anchor" aria-label="anchor" href="#arg-shorten"></a></dt>
 <dd><p>shorten all sequences to multiple of three [default: FALSE]</p></dd>
 
 
-<dt>frame</dt>
+<dt id="arg-frame">frame<a class="anchor" aria-label="anchor" href="#arg-frame"></a></dt>
 <dd><p>indicates the first base of a the first codon [default: 1]</p></dd>
 
 
-<dt>framelist</dt>
+<dt id="arg-framelist">framelist<a class="anchor" aria-label="anchor" href="#arg-framelist"></a></dt>
 <dd><p>supply vector of frames for each entry [default: NULL]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>An object of class <code>alignment</code> which is a list with the
-following components:<br></p>
-
-
-<p><code>nb</code> the number of aligned sequences<br></p>
-
-
-<p><code>nam</code> a vector of strings containing the names of the aligned
-sequences<br></p>
-
-
-<p><code>seq</code> a vector of strings containing the aligned sequences<br></p>
-
-
-<p><code>com</code> a vector of strings containing the commentaries for each sequence
+    <p>An object of class <code>alignment</code> which is a list with the
+following components:<br><code>nb</code> the number of aligned sequences<br><code>nam</code> a vector of strings containing the names of the aligned
+sequences<br><code>seq</code> a vector of strings containing the aligned sequences<br><code>com</code> a vector of strings containing the commentaries for each sequence
 or <code>NA</code> if there are no comments</p>
     </div>
     <div id="see-also">
@@ -149,15 +137,15 @@ or <code>NA</code> if there are no comments</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/dnastring2dist.html b/public/reference/dnastring2dist.html
index 83297febe76a42041e8b6945c893e0e9180f44d5..43593cca907bf6662c7839b25405aa7540392352 100644
--- a/public/reference/dnastring2dist.html
+++ b/public/reference/dnastring2dist.html
@@ -1,10 +1,10 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>dnastring2dist — dnastring2dist • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="dnastring2dist — dnastring2dist"><meta property="og:description" content="This function calculates pairwise distances for all
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>dnastring2dist — dnastring2dist • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="dnastring2dist — dnastring2dist"><meta property="og:description" content="This function calculates pairwise distances for all
 combinations of a DNAStringSet."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -18,7 +18,7 @@ combinations of a DNAStringSet."><meta property="og:image" content="/logo.png"><
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -35,20 +35,20 @@ combinations of a DNAStringSet."><meta property="og:image" content="/logo.png"><
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>dnastring2dist</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/dnastring2dist.R" class="external-link"><code>R/dnastring2dist.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/dnastring2dist.R" class="external-link"><code>R/dnastring2dist.R</code></a></small>
     <div class="hidden name"><code>dnastring2dist.Rd</code></div>
     </div>
 
@@ -72,51 +72,49 @@ combinations of a <code>DNAStringSet</code>.</p>
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>dna</dt>
+
+
+<dl><dt id="arg-dna">dna<a class="anchor" aria-label="anchor" href="#arg-dna"></a></dt>
 <dd><p><code>DNAStringSet</code> [mandatory]</p></dd>
 
 
-<dt>model</dt>
+<dt id="arg-model">model<a class="anchor" aria-label="anchor" href="#arg-model"></a></dt>
 <dd><p>specify model either "IUPAC" or any model from
 <code><a href="https://rdrr.io/pkg/ape/man/dist.dna.html" class="external-link">ape::dist.dna</a></code> [default: IUPAC]</p></dd>
 
 
-<dt>threads</dt>
+<dt id="arg-threads">threads<a class="anchor" aria-label="anchor" href="#arg-threads"></a></dt>
 <dd><p>number of parallel threads [default: 1]</p></dd>
 
 
-<dt>symmetric</dt>
+<dt id="arg-symmetric">symmetric<a class="anchor" aria-label="anchor" href="#arg-symmetric"></a></dt>
 <dd><p>symmetric score matrix [default: TRUE]</p></dd>
 
 
-<dt>score</dt>
+<dt id="arg-score">score<a class="anchor" aria-label="anchor" href="#arg-score"></a></dt>
 <dd><p><code>score matrix</code> use score matrix to calculate
 distances [default: NULL]</p></dd>
 
 
-<dt>mask</dt>
+<dt id="arg-mask">mask<a class="anchor" aria-label="anchor" href="#arg-mask"></a></dt>
 <dd><p><code>IRanges</code> object indicating masked sites
 [default: NULL]</p></dd>
 
 
-<dt>region</dt>
+<dt id="arg-region">region<a class="anchor" aria-label="anchor" href="#arg-region"></a></dt>
 <dd><p><code>IRanges</code> object indicating region to use for dist
 calculation. Default is null, meaning all sites are used [default: NULL]</p></dd>
 
 
-<dt>...</dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
 <dd><p>other <code><a href="https://rdrr.io/pkg/ape/man/dist.dna.html" class="external-link">ape::dist.dna</a></code> parameters
 (see <code><a href="https://rdrr.io/pkg/ape/man/dist.dna.html" class="external-link">dist.dna</a></code>)</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>A data.frame of pairwise distance values <code>distSTRING</code> and
+    <p>A data.frame of pairwise distance values <code>distSTRING</code> and
 sites used <code>sitesUsed</code></p>
-
-
     </div>
     <div id="see-also">
     <h2>See also</h2>
@@ -752,15 +750,15 @@ sites used <code>sitesUsed</code></p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/dnastring2dnabin.html b/public/reference/dnastring2dnabin.html
index 79f23bf97df935fc35a4eab3e626d1e1e0630046..e785be6b153b51cdef16ddb4098e54c6d779cd4d 100644
--- a/public/reference/dnastring2dnabin.html
+++ b/public/reference/dnastring2dnabin.html
@@ -1,10 +1,10 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>dnastring2dnabin — dnastring2dnabin • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="dnastring2dnabin — dnastring2dnabin"><meta property="og:description" content="This function converts a DNAStringSet into an
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>dnastring2dnabin — dnastring2dnabin • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="dnastring2dnabin — dnastring2dnabin"><meta property="og:description" content="This function converts a DNAStringSet into an
 ape DNAbin."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -18,7 +18,7 @@ ape DNAbin."><meta property="og:image" content="/logo.png"><!-- mathjax --><scri
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -35,20 +35,20 @@ ape DNAbin."><meta property="og:image" content="/logo.png"><!-- mathjax --><scri
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>dnastring2dnabin</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/dnastring2dnabin.R" class="external-link"><code>R/dnastring2dnabin.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/dnastring2dnabin.R" class="external-link"><code>R/dnastring2dnabin.R</code></a></small>
     <div class="hidden name"><code>dnastring2dnabin.Rd</code></div>
     </div>
 
@@ -63,17 +63,15 @@ ape DNAbin."><meta property="og:image" content="/logo.png"><!-- mathjax --><scri
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>dna</dt>
+
+
+<dl><dt id="arg-dna">dna<a class="anchor" aria-label="anchor" href="#arg-dna"></a></dt>
 <dd><p><code>DNAStringSet</code> [mandatory]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>An object of class <code>DNAbin</code></p>
-
-
+    <p>An object of class <code>DNAbin</code></p>
     </div>
     <div id="see-also">
     <h2>See also</h2>
@@ -119,15 +117,15 @@ ape DNAbin."><meta property="og:image" content="/logo.png"><!-- mathjax --><scri
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/dnastring2kaks.html b/public/reference/dnastring2kaks.html
index 14c8f8590ba0115bfe0efb647beeea190188b173..84517b96c2a467f5c53569d36595a691ee0aac71 100644
--- a/public/reference/dnastring2kaks.html
+++ b/public/reference/dnastring2kaks.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>dnastring2kaks — dnastring2kaks • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="dnastring2kaks — dnastring2kaks"><meta property="og:description" content="This function calculates Ka/Ks (pN/pS)
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>dnastring2kaks — dnastring2kaks • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="dnastring2kaks — dnastring2kaks"><meta property="og:description" content="This function calculates Ka/Ks (pN/pS)
 for all combinations of a DNAStringSet.
 If the sequences in the DNAStringSet are not a multiple-sequence
 alignment, pairwise codon alignments can be calculated on the fly.
@@ -10,7 +10,7 @@ KaKs_Calculator2 ported to MSA2dist with Rcpp."><meta property="og:image" conten
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -24,7 +24,7 @@ KaKs_Calculator2 ported to MSA2dist with Rcpp."><meta property="og:image" conten
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -41,20 +41,20 @@ KaKs_Calculator2 ported to MSA2dist with Rcpp."><meta property="og:image" conten
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>dnastring2kaks</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/dnastring2kaks.R" class="external-link"><code>R/dnastring2kaks.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/dnastring2kaks.R" class="external-link"><code>R/dnastring2kaks.R</code></a></small>
     <div class="hidden name"><code>dnastring2kaks.Rd</code></div>
     </div>
 
@@ -83,43 +83,43 @@ Models used and implemented according to
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>cds</dt>
+
+
+<dl><dt id="arg-cds">cds<a class="anchor" aria-label="anchor" href="#arg-cds"></a></dt>
 <dd><p><code>DNAStringSet</code> coding sequence alignment [mandatory]</p></dd>
 
 
-<dt>model</dt>
+<dt id="arg-model">model<a class="anchor" aria-label="anchor" href="#arg-model"></a></dt>
 <dd><p>specify codon model either "Li" or "NG86" or
 one of <code>KaKs_Calculator2</code> model "NG", "LWL", "LPB", "MLWL", "MLPB",
 "GY", "YN", "MYN", "MS", "MA", "GNG", "GLWL", "GLPB", "GMLWL", "GMLPB",
 "GYN", "GMYN" [default: Li]</p></dd>
 
 
-<dt>threads</dt>
+<dt id="arg-threads">threads<a class="anchor" aria-label="anchor" href="#arg-threads"></a></dt>
 <dd><p>number of parallel threads [default: 1]</p></dd>
 
 
-<dt>isMSA</dt>
+<dt id="arg-ismsa">isMSA<a class="anchor" aria-label="anchor" href="#arg-ismsa"></a></dt>
 <dd><p>cds <code>DNAStringSet</code> represents MSA [default: TRUE]</p></dd>
 
 
-<dt>sgc</dt>
+<dt id="arg-sgc">sgc<a class="anchor" aria-label="anchor" href="#arg-sgc"></a></dt>
 <dd><p>standard genetic code (for KaKs Calculator models)
 [default: 1]</p></dd>
 
 
-<dt>verbose</dt>
+<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
 <dd><p>verbosity (for KaKs Calculator models) [default: FALSE]</p></dd>
 
 
-<dt>...</dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
 <dd><p>other codon alignment parameters</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>A <code>data.frame</code> of <code>KaKs</code> values</p>
+    <p>A <code>data.frame</code> of <code>KaKs</code> values</p>
     </div>
     <div id="references">
     <h2>References</h2>
@@ -556,7 +556,7 @@ and Ks with consideration of variable substitution rates.
 <span class="r-out co"><span class="r-pr">#&gt;</span> result.1.6   0.130057803468208  0.118421052631579 0.910526315789474</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> result.2.6   0.136231884057971 0.0982211910286156  0.72098533840154</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> result.3.6   0.119186046511628 0.0935085007727975 0.784559128435179</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> result.4.6   0.144508670520231  0.114551083591331 0.792693498452012</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> result.4.6   0.144508670520231  0.114551083591331 0.792693498452013</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> result.5.6   0.126074498567335  0.100853374709077 0.799950631215178</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> result.6.6   0.144508670520231  0.123839009287926 0.856965944272446</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> result.1.7   0.122448979591837  0.106563706563707  0.87027027027027</span>
@@ -953,7 +953,7 @@ and Ks with consideration of variable substitution rates.
 <span class="r-out co"><span class="r-pr">#&gt;</span> result.1.6   0.130057803468208  0.118421052631579 0.910526315789474</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> result.2.6   0.136231884057971 0.0982211910286156  0.72098533840154</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> result.3.6   0.119186046511628 0.0935085007727975 0.784559128435179</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> result.4.6   0.144508670520231  0.114551083591331 0.792693498452012</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> result.4.6   0.144508670520231  0.114551083591331 0.792693498452013</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> result.5.6   0.126074498567335  0.100853374709077 0.799950631215178</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> result.6.6   0.144508670520231  0.123839009287926 0.856965944272446</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> result.1.7   0.122448979591837  0.106563706563707  0.87027027027027</span>
@@ -1161,15 +1161,15 @@ and Ks with consideration of variable substitution rates.
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/getmask.html b/public/reference/getmask.html
index 4b69cc7715711a21401a2fab4710a2151034819b..b42e1ff5831c4a49c772d4d3962e52d5271ce498 100644
--- a/public/reference/getmask.html
+++ b/public/reference/getmask.html
@@ -1,11 +1,11 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>getmask — getmask • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="getmask — getmask"><meta property="og:description" content="This function shows the mask slot from a
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>getmask — getmask • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="getmask — getmask"><meta property="og:description" content="This function shows the mask slot from a
 DNAStringSet or an AAStringSet
 metadata information."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -19,7 +19,7 @@ metadata information."><meta property="og:image" content="/logo.png"><!-- mathja
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -36,20 +36,20 @@ metadata information."><meta property="og:image" content="/logo.png"><!-- mathja
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>getmask</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/getmask.R" class="external-link"><code>R/getmask.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/getmask.R" class="external-link"><code>R/getmask.R</code></a></small>
     <div class="hidden name"><code>getmask.Rd</code></div>
     </div>
 
@@ -65,17 +65,15 @@ metadata information."><meta property="og:image" content="/logo.png"><!-- mathja
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>seq</dt>
+
+
+<dl><dt id="arg-seq">seq<a class="anchor" aria-label="anchor" href="#arg-seq"></a></dt>
 <dd><p><code>DNAStringSet</code> or <code>AAStringSet</code> [mandatory]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p><code>IRanges</code> information from <code>metadata</code></p>
-
-
+    <p><code>IRanges</code> information from <code>metadata</code></p>
     </div>
     <div id="see-also">
     <h2>See also</h2>
@@ -116,15 +114,15 @@ metadata information."><meta property="og:image" content="/logo.png"><!-- mathja
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/getpos.html b/public/reference/getpos.html
index 6ae0ad73fa2deb6e6812a5cac403907fd724f322..3ae1c5a573d85347c73b6e2c3378edee8c21ddb4 100644
--- a/public/reference/getpos.html
+++ b/public/reference/getpos.html
@@ -1,11 +1,11 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>getpos — getpos • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="getpos — getpos"><meta property="og:description" content="This function shows the position slot from a
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>getpos — getpos • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="getpos — getpos"><meta property="og:description" content="This function shows the position slot from a
 DNAStringSet or an AAStringSet
 metadata information."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -19,7 +19,7 @@ metadata information."><meta property="og:image" content="/logo.png"><!-- mathja
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -36,20 +36,20 @@ metadata information."><meta property="og:image" content="/logo.png"><!-- mathja
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>getpos</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/getpos.R" class="external-link"><code>R/getpos.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/getpos.R" class="external-link"><code>R/getpos.R</code></a></small>
     <div class="hidden name"><code>getpos.Rd</code></div>
     </div>
 
@@ -65,17 +65,15 @@ metadata information."><meta property="og:image" content="/logo.png"><!-- mathja
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>seq</dt>
+
+
+<dl><dt id="arg-seq">seq<a class="anchor" aria-label="anchor" href="#arg-seq"></a></dt>
 <dd><p><code>DNAStringSet</code> or <code>AAStringSet</code> [mandatory]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p><code>GenomicRanges</code> information from <code>metadata</code></p>
-
-
+    <p><code>GenomicRanges</code> information from <code>metadata</code></p>
     </div>
     <div id="see-also">
     <h2>See also</h2>
@@ -114,15 +112,15 @@ metadata information."><meta property="og:image" content="/logo.png"><!-- mathja
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/gff2cds.html b/public/reference/gff2cds.html
index 35ff2f90fd912e4ee243a69fafb39c73a020ff3d..d68e0b6d5fa2fd5bf03fb74f08f8e7bc90e66f72 100644
--- a/public/reference/gff2cds.html
+++ b/public/reference/gff2cds.html
@@ -1,10 +1,10 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>gff2cds — gff2cds • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="gff2cds — gff2cds"><meta property="og:description" content="This function extracts CDS as DNAStringSet from
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>gff2cds — gff2cds • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="gff2cds — gff2cds"><meta property="og:description" content="This function extracts CDS as DNAStringSet from
 GFF3 or GTF."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -18,7 +18,7 @@ GFF3 or GTF."><meta property="og:image" content="/logo.png"><!-- mathjax --><scr
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -35,20 +35,20 @@ GFF3 or GTF."><meta property="og:image" content="/logo.png"><!-- mathjax --><scr
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>gff2cds</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/gff2cds.R" class="external-link"><code>R/gff2cds.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/gff2cds.R" class="external-link"><code>R/gff2cds.R</code></a></small>
     <div class="hidden name"><code>gff2cds.Rd</code></div>
     </div>
 
@@ -63,34 +63,32 @@ GFF3 or GTF."><meta property="og:image" content="/logo.png"><!-- mathjax --><scr
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>file</dt>
+
+
+<dl><dt id="arg-file">file<a class="anchor" aria-label="anchor" href="#arg-file"></a></dt>
 <dd><p><code>GFF</code> or <code>GTF</code> file [mandatory]</p></dd>
 
 
-<dt>genome</dt>
+<dt id="arg-genome">genome<a class="anchor" aria-label="anchor" href="#arg-genome"></a></dt>
 <dd><p><code>DNAStringSet</code> [mandatory]</p></dd>
 
 
-<dt>format</dt>
+<dt id="arg-format">format<a class="anchor" aria-label="anchor" href="#arg-format"></a></dt>
 <dd><p>specify gff format either "gff3" or "gtf" [default: gff3]</p></dd>
 
 
-<dt>longest</dt>
+<dt id="arg-longest">longest<a class="anchor" aria-label="anchor" href="#arg-longest"></a></dt>
 <dd><p>specify if longest isoform should be retained [default: TRUE]</p></dd>
 
 
-<dt>source</dt>
+<dt id="arg-source">source<a class="anchor" aria-label="anchor" href="#arg-source"></a></dt>
 <dd><p>source indicating either BAKTA, ENSEMBL, GEMOMA or NCBI
 [default: NCBI]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p><code>DNAStringSet</code></p>
-
-
+    <p><code>DNAStringSet</code></p>
     </div>
     <div id="see-also">
     <h2>See also</h2>
@@ -114,15 +112,15 @@ GFF3 or GTF."><meta property="og:image" content="/logo.png"><!-- mathjax --><scr
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/globalDeletion.html b/public/reference/globalDeletion.html
index dd413a388f076c94710ca4aba4ebee77421774fc..e9b8f5d68d2aea9aa6d1008f1bce3d8f8abf8e91 100644
--- a/public/reference/globalDeletion.html
+++ b/public/reference/globalDeletion.html
@@ -1,10 +1,10 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>globalDeletion — globalDeletion • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="globalDeletion — globalDeletion"><meta property="og:description" content='This function returns a DNAStringSet reduced by all
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>globalDeletion — globalDeletion • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="globalDeletion — globalDeletion"><meta property="og:description" content='This function returns a DNAStringSet reduced by all
 sites containing any gaps ("-", "+", ".") or missing ("N") sites.'><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -18,7 +18,7 @@ sites containing any gaps ("-", "+", ".") or missing ("N") sites.'><meta propert
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -35,20 +35,20 @@ sites containing any gaps ("-", "+", ".") or missing ("N") sites.'><meta propert
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>globalDeletion</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/globalDeletion.R" class="external-link"><code>R/globalDeletion.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/globalDeletion.R" class="external-link"><code>R/globalDeletion.R</code></a></small>
     <div class="hidden name"><code>globalDeletion.Rd</code></div>
     </div>
 
@@ -63,17 +63,15 @@ sites containing any gaps ("-", "+", ".") or missing ("N") sites.</p>
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>dna</dt>
+
+
+<dl><dt id="arg-dna">dna<a class="anchor" aria-label="anchor" href="#arg-dna"></a></dt>
 <dd><p><code>DNAStringSet</code> [mandatory]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p><code>DNAStringSet</code></p>
-
-
+    <p><code>DNAStringSet</code></p>
     </div>
     <div id="author">
     <h2>Author</h2>
@@ -106,15 +104,15 @@ sites containing any gaps ("-", "+", ".") or missing ("N") sites.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/globalDeletionAA.html b/public/reference/globalDeletionAA.html
new file mode 100644
index 0000000000000000000000000000000000000000..5a0b92cba0fba6aa330f6027e4ee7025e48e2629
--- /dev/null
+++ b/public/reference/globalDeletionAA.html
@@ -0,0 +1,119 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>globalDeletionAA — globalDeletionAA • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="globalDeletionAA — globalDeletionAA"><meta property="og:description" content='This function returns an AAStringSet reduced by all
+sites containing any gaps ("-", "+", ".") or missing ("X") sites.'><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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+        <a class="navbar-link" href="../index.html">MSA2dist</a>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
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+  <a href="../articles/MSA2dist.html">Get started</a>
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+</li>
+      </ul><ul class="nav navbar-nav navbar-right"><li>
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+  </div><!--/.container -->
+</div><!--/.navbar -->
+
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+
+      </header><div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>globalDeletionAA</h1>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/globalDeletionAA.R" class="external-link"><code>R/globalDeletionAA.R</code></a></small>
+    <div class="hidden name"><code>globalDeletionAA.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>This function returns an <code>AAStringSet</code> reduced by all
+sites containing any gaps ("-", "+", ".") or missing ("X") sites.</p>
+    </div>
+
+    <div id="ref-usage">
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">globalDeletionAA</span><span class="op">(</span><span class="va">aa</span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div id="arguments">
+    <h2>Arguments</h2>
+
+
+<dl><dt id="arg-aa">aa<a class="anchor" aria-label="anchor" href="#arg-aa"></a></dt>
+<dd><p><code>AAStringSet</code> [mandatory]</p></dd>
+
+</dl></div>
+    <div id="value">
+    <h2>Value</h2>
+    <p><code>AAStringSet</code></p>
+    </div>
+    <div id="author">
+    <h2>Author</h2>
+    <p>Kristian K Ullrich</p>
+    </div>
+
+    <div id="ref-examples">
+    <h2>Examples</h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co">## define two cds sequences</span></span></span>
+<span class="r-in"><span><span class="va">cds1</span> <span class="op">&lt;-</span> <span class="fu">Biostrings</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/Biostrings/man/DNAString-class.html" class="external-link">DNAString</a></span><span class="op">(</span><span class="st">"ATGCAACATTGC"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">cds2</span> <span class="op">&lt;-</span> <span class="fu">Biostrings</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/Biostrings/man/DNAString-class.html" class="external-link">DNAString</a></span><span class="op">(</span><span class="st">"ATG---CATTGC"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">cds1.cds2.aln</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu">Biostrings</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/Biostrings/man/XStringSet-class.html" class="external-link">DNAStringSet</a></span><span class="op">(</span><span class="va">cds1</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>    <span class="fu">Biostrings</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/Biostrings/man/XStringSet-class.html" class="external-link">DNAStringSet</a></span><span class="op">(</span><span class="va">cds2</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="co">#globalDeletionAA(cds2aa(cds1.cds2.aln))</span></span></span>
+<span class="r-in"><span><span class="va">cds1.cds2.aln</span> <span class="op">|&gt;</span> <span class="fu"><a href="cds2aa.html">cds2aa</a></span><span class="op">(</span><span class="op">)</span> <span class="op">|&gt;</span> <span class="fu">globalDeletionAA</span><span class="op">(</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> AAStringSet object of length 2:</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>     width seq</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1]     3 <span style="color: #000000; background-color: #FFD7D7;">M</span><span style="color: #000000; background-color: #AFD7FF;">H</span><span style="color: #000000; background-color: #FFFFD7;">C</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [2]     3 <span style="color: #000000; background-color: #FFD7D7;">M</span><span style="color: #000000; background-color: #AFD7FF;">H</span><span style="color: #000000; background-color: #FFFFD7;">C</span></span>
+</code></pre></div>
+    </div>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
+</div>
+
+
+      <footer><div class="copyright">
+  <p></p><p>Developed by Kristian K Ullrich.</p>
+</div>
+
+<div class="pkgdown">
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
+</div>
+
+      </footer></div>
+
+
+
+
+
+
+  </body></html>
+
diff --git a/public/reference/granthamMatrix.html b/public/reference/granthamMatrix.html
index da17cb2db4ca33f0b55308aa0f20564b9764df73..0b5d080b3ef37a88f3bd840fc2d79e5f3e7897a0 100644
--- a/public/reference/granthamMatrix.html
+++ b/public/reference/granthamMatrix.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>granthamMatrix — granthamMatrix • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="granthamMatrix — granthamMatrix"><meta property="og:description" content="This function creates a granthamMatrix object to be used
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>granthamMatrix — granthamMatrix • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="granthamMatrix — granthamMatrix"><meta property="og:description" content="This function creates a granthamMatrix object to be used
 with the rcpp_distSTRING function. By default,the grantham matrix is
 defined as from Grantham 1974.
 (see https://link.springer.com/article/10.1007/s00335-017-9704-9)"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -20,7 +20,7 @@ defined as from Grantham 1974.
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -37,20 +37,20 @@ defined as from Grantham 1974.
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>granthamMatrix</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/granthamMatrix.R" class="external-link"><code>R/granthamMatrix.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/granthamMatrix.R" class="external-link"><code>R/granthamMatrix.R</code></a></small>
     <div class="hidden name"><code>granthamMatrix.Rd</code></div>
     </div>
 
@@ -67,11 +67,7 @@ defined as from <code>Grantham 1974</code>.
 
     <div id="value">
     <h2>Value</h2>
-    
-
-<p><code>matrix</code></p>
-
-
+    <p><code>matrix</code></p>
     </div>
     <div id="references">
     <h2>References</h2>
@@ -152,15 +148,15 @@ to Help Explain Protein Evolution. <em>Science</em>,<b>185(4154)</b>,862-864.</p
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/hiv-data.html b/public/reference/hiv-data.html
index 35e62a9b03d076a63c983b8a23a0da0fa7f50939..80ab627f7a3fa40dcd6116045081806b398fdd82 100644
--- a/public/reference/hiv-data.html
+++ b/public/reference/hiv-data.html
@@ -1,10 +1,10 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>hiv-data — hiv-data • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="hiv-data — hiv-data"><meta property="og:description" content="Example cds sequences from HIV-1 sample 136 patient 1 from
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>hiv-data — hiv-data • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="hiv-data — hiv-data"><meta property="og:description" content="Example cds sequences from HIV-1 sample 136 patient 1 from
 Sweden envelope glycoprotein (env) gene, V3 region as DNAStringSet."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -18,7 +18,7 @@ Sweden envelope glycoprotein (env) gene, V3 region as DNAStringSet."><meta prope
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -35,20 +35,20 @@ Sweden envelope glycoprotein (env) gene, V3 region as DNAStringSet."><meta prope
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>hiv-data</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/hiv-data.R" class="external-link"><code>R/hiv-data.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/hiv-data.R" class="external-link"><code>R/hiv-data.R</code></a></small>
     <div class="hidden name"><code>hiv-data.Rd</code></div>
     </div>
 
@@ -90,15 +90,15 @@ selection pressure at amino acid sites. <em>Genetics.</em>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
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diff --git a/public/reference/index.html b/public/reference/index.html
index ddbe2f3533ff756d188d1554b7a908104bb64e64..d82c5f67c297a27cd35f259826d2c588999c7d3b 100644
--- a/public/reference/index.html
+++ b/public/reference/index.html
@@ -1,9 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Function reference • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Function reference"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Package index • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Package index"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-index">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -34,14 +34,14 @@
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="contents col-md-9">
@@ -177,6 +177,10 @@
           <p><code><a href="globalDeletion.html">globalDeletion()</a></code> </p>
         </td>
         <td><p>globalDeletion</p></td>
+      </tr><tr><td>
+          <p><code><a href="globalDeletionAA.html">globalDeletionAA()</a></code> </p>
+        </td>
+        <td><p>globalDeletionAA</p></td>
       </tr><tr><td>
           <p><code><a href="granthamMatrix.html">granthamMatrix()</a></code> </p>
         </td>
@@ -262,15 +266,15 @@
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/indices2kaks.html b/public/reference/indices2kaks.html
index 00efd2f0221bdfadf4cfa2c46c84190c1a71f07b..f8b9856cab4fbeec5817a72103cd411ecb9954ea 100644
--- a/public/reference/indices2kaks.html
+++ b/public/reference/indices2kaks.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>indices2kaks — indices2kaks • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="indices2kaks — indices2kaks"><meta property="og:description" content="This function calculates Ka/Ks (pN/pS)
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>indices2kaks — indices2kaks • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="indices2kaks — indices2kaks"><meta property="og:description" content="This function calculates Ka/Ks (pN/pS)
 for all combinations given in an indices list of a
 DNAStringSet.
 If the sequences in the DNAStringSet are not a multiple-sequence
@@ -11,7 +11,7 @@ KaKs_Calculator2 ported to MSA2dist with Rcpp."><meta property="og:image" conten
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -25,7 +25,7 @@ KaKs_Calculator2 ported to MSA2dist with Rcpp."><meta property="og:image" conten
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -42,20 +42,20 @@ KaKs_Calculator2 ported to MSA2dist with Rcpp."><meta property="og:image" conten
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>indices2kaks</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/indices2kaks.R" class="external-link"><code>R/indices2kaks.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/indices2kaks.R" class="external-link"><code>R/indices2kaks.R</code></a></small>
     <div class="hidden name"><code>indices2kaks.Rd</code></div>
     </div>
 
@@ -86,47 +86,47 @@ Models used and implemented according to
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>cds</dt>
+
+
+<dl><dt id="arg-cds">cds<a class="anchor" aria-label="anchor" href="#arg-cds"></a></dt>
 <dd><p><code>DNAStringSet</code> coding sequence alignment [mandatory]</p></dd>
 
 
-<dt>indices</dt>
+<dt id="arg-indices">indices<a class="anchor" aria-label="anchor" href="#arg-indices"></a></dt>
 <dd><p><code>list</code> list of indices to calculate Ks/Ks [mandatory]</p></dd>
 
 
-<dt>model</dt>
+<dt id="arg-model">model<a class="anchor" aria-label="anchor" href="#arg-model"></a></dt>
 <dd><p>specify codon model either "Li" or "NG86" or
 one of <code>KaKs_Calculator2</code> model "NG", "LWL", "LPB", "MLWL", "MLPB",
 "GY", "YN", "MYN", "MS", "MA", "GNG", "GLWL", "GLPB", "GMLWL", "GMLPB",
 "GYN", "GMYN" [default: Li]</p></dd>
 
 
-<dt>threads</dt>
+<dt id="arg-threads">threads<a class="anchor" aria-label="anchor" href="#arg-threads"></a></dt>
 <dd><p>number of parallel threads [default: 1]</p></dd>
 
 
-<dt>isMSA</dt>
+<dt id="arg-ismsa">isMSA<a class="anchor" aria-label="anchor" href="#arg-ismsa"></a></dt>
 <dd><p>cds <code>DNAStringSet</code> represents MSA [default: TRUE]</p></dd>
 
 
-<dt>sgc</dt>
+<dt id="arg-sgc">sgc<a class="anchor" aria-label="anchor" href="#arg-sgc"></a></dt>
 <dd><p>standard genetic code (for KaKs Calculator models)
 [default: 1]</p></dd>
 
 
-<dt>verbose</dt>
+<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
 <dd><p>verbosity (for KaKs Calculator models) [default: FALSE]</p></dd>
 
 
-<dt>...</dt>
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
 <dd><p>other codon alignment parameters</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>A <code>data.frame</code> of <code>KaKs</code> values</p>
+    <p>A <code>data.frame</code> of <code>KaKs</code> values</p>
     </div>
     <div id="references">
     <h2>References</h2>
@@ -276,15 +276,15 @@ and Ks with consideration of variable substitution rates.
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/iupac-data.html b/public/reference/iupac-data.html
index 95219483abca75711192a3ef70663ef5adb6ad2d..b66e92526b20894e7b544cf6fa42b6112cb8f39d 100644
--- a/public/reference/iupac-data.html
+++ b/public/reference/iupac-data.html
@@ -1,11 +1,11 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>iupac-data — iupac-data • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="iupac-data — iupac-data"><meta property="og:description" content="Example IUPAC sequences created with angsd
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>iupac-data — iupac-data • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="iupac-data — iupac-data"><meta property="og:description" content="Example IUPAC sequences created with angsd
 from different house mouse (Mus musculus) sub-populations
 from Harr et al. (2016) DNAStringSet."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -19,7 +19,7 @@ from Harr et al. (2016) DNAStringSet."><meta property="og:image" content="/logo.
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -36,20 +36,20 @@ from Harr et al. (2016) DNAStringSet."><meta property="og:image" content="/logo.
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>iupac-data</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/iupac-data.R" class="external-link"><code>R/iupac-data.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/iupac-data.R" class="external-link"><code>R/iupac-data.R</code></a></small>
     <div class="hidden name"><code>iupac-data.Rd</code></div>
     </div>
 
@@ -92,15 +92,15 @@ Mus spretus. <em>Scientific data.</em> <b>3(1)</b>, 1-14.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/iupacMatrix.html b/public/reference/iupacMatrix.html
index 7ebd26df26c6036262e8fdf8862650849d24e3d8..b88024ad157258cb6b7d40718ba1540b18a20ef1 100644
--- a/public/reference/iupacMatrix.html
+++ b/public/reference/iupacMatrix.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>iupacMatrix — iupacMatrix • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="iupacMatrix — iupacMatrix"><meta property="og:description" content="This function creates a iupacMatrix object to be used
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>iupacMatrix — iupacMatrix • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="iupacMatrix — iupacMatrix"><meta property="og:description" content="This function creates a iupacMatrix object to be used
 with the rcpp_distSTRING function. By default, the iupac matrix
 is defined as literal distance obtained from Chang et al. 2017.
 (see https://link.springer.com/article/10.1007/s00335-017-9704-9)"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -20,7 +20,7 @@ is defined as literal distance obtained from Chang et al. 2017.
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -37,20 +37,20 @@ is defined as literal distance obtained from Chang et al. 2017.
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>iupacMatrix</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/iupacMatrix.R" class="external-link"><code>R/iupacMatrix.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/iupacMatrix.R" class="external-link"><code>R/iupacMatrix.R</code></a></small>
     <div class="hidden name"><code>iupacMatrix.Rd</code></div>
     </div>
 
@@ -67,11 +67,7 @@ is defined as literal distance obtained from <code>Chang et al. 2017</code>.
 
     <div id="value">
     <h2>Value</h2>
-    
-
-<p><code>score matrix</code></p>
-
-
+    <p><code>score matrix</code></p>
     </div>
     <div id="references">
     <h2>References</h2>
@@ -125,15 +121,15 @@ genotype. <em>Mammalian genome</em>,<b>28(9-10)</b>,416-425.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/makePostalignedSeqs.html b/public/reference/makePostalignedSeqs.html
index ebd928f9d4c4a4752215e961c46fe20bbb21df50..7d10faf1cde5cab4c6153e2fe6adf1c8b0a918b3 100644
--- a/public/reference/makePostalignedSeqs.html
+++ b/public/reference/makePostalignedSeqs.html
@@ -1,10 +1,10 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>makePostalignedSeqs — makePostalignedSeqs • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="makePostalignedSeqs — makePostalignedSeqs"><meta property="og:description" content="This function is a fork from an internal function from
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>makePostalignedSeqs — makePostalignedSeqs • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="makePostalignedSeqs — makePostalignedSeqs"><meta property="og:description" content="This function is a fork from an internal function from
 Biostrings"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -18,7 +18,7 @@ Biostrings"><meta property="og:image" content="/logo.png"><!-- mathjax --><scrip
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -35,20 +35,20 @@ Biostrings"><meta property="og:image" content="/logo.png"><!-- mathjax --><scrip
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>makePostalignedSeqs</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/makePostalignedSeqs.R" class="external-link"><code>R/makePostalignedSeqs.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/makePostalignedSeqs.R" class="external-link"><code>R/makePostalignedSeqs.R</code></a></small>
     <div class="hidden name"><code>makePostalignedSeqs.Rd</code></div>
     </div>
 
@@ -63,19 +63,19 @@ Biostrings"><meta property="og:image" content="/logo.png"><!-- mathjax --><scrip
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>x</dt>
+
+
+<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
 <dd><p>x</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>get internal function makePostalignedSeqs</p>
+    <p>get internal function makePostalignedSeqs</p>
     </div>
     <div id="see-also">
     <h2>See also</h2>
-    <div class="dont-index"><p><code><a href="https://rdrr.io/pkg/Biostrings/man/pairwiseAlignment.html" class="external-link">pairwiseAlignment</a></code>,
+    <div class="dont-index"><p><code>pairwiseAlignment</code>,
 <a href="cds2codonaln.html">cds2codonaln</a></p></div>
     </div>
     <div id="author">
@@ -88,7 +88,7 @@ Biostrings"><meta property="og:image" content="/logo.png"><!-- mathjax --><scrip
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co">## define two cds sequences</span></span></span>
 <span class="r-in"><span><span class="va">cds1</span> <span class="op">&lt;-</span> <span class="fu">Biostrings</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/Biostrings/man/DNAString-class.html" class="external-link">DNAString</a></span><span class="op">(</span><span class="st">"ATGCAACATTGC"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">cds2</span> <span class="op">&lt;-</span> <span class="fu">Biostrings</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/Biostrings/man/DNAString-class.html" class="external-link">DNAString</a></span><span class="op">(</span><span class="st">"ATGCATTGC"</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="fu">makePostalignedSeqs</span><span class="op">(</span><span class="fu">Biostrings</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/Biostrings/man/pairwiseAlignment.html" class="external-link">pairwiseAlignment</a></span><span class="op">(</span></span></span>
+<span class="r-in"><span><span class="fu">makePostalignedSeqs</span><span class="op">(</span><span class="fu">pwalign</span><span class="fu">::</span><span class="fu">pairwiseAlignment</span><span class="op">(</span></span></span>
 <span class="r-in"><span>    <span class="fu"><a href="cds2aa.html">cds2aa</a></span><span class="op">(</span><span class="fu">Biostrings</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/Biostrings/man/XStringSet-class.html" class="external-link">DNAStringSet</a></span><span class="op">(</span><span class="va">cds1</span><span class="op">)</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>    <span class="fu"><a href="cds2aa.html">cds2aa</a></span><span class="op">(</span><span class="fu">Biostrings</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/Biostrings/man/XStringSet-class.html" class="external-link">DNAStringSet</a></span><span class="op">(</span><span class="va">cds2</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [[1]]</span>
@@ -122,15 +122,15 @@ Biostrings"><meta property="og:image" content="/logo.png"><!-- mathjax --><scrip
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/pal2nal.html b/public/reference/pal2nal.html
index 502248fd4591633238da6073d13412c4e93373c9..124ea8cfda1016101bc4d52ba262ce93382a712d 100644
--- a/public/reference/pal2nal.html
+++ b/public/reference/pal2nal.html
@@ -1,11 +1,11 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>pal2nal — pal2nal • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="pal2nal — pal2nal"><meta property="og:description" content="This function takes an AAStringSet alignment and
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>pal2nal — pal2nal • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="pal2nal — pal2nal"><meta property="og:description" content="This function takes an AAStringSet alignment and
 its corresponding coding sequences DNAStringSet and converts
 the protein alignment into a codon alignment."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -19,7 +19,7 @@ the protein alignment into a codon alignment."><meta property="og:image" content
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -36,20 +36,20 @@ the protein alignment into a codon alignment."><meta property="og:image" content
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>pal2nal</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/pal2nal.R" class="external-link"><code>R/pal2nal.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/pal2nal.R" class="external-link"><code>R/pal2nal.R</code></a></small>
     <div class="hidden name"><code>pal2nal.Rd</code></div>
     </div>
 
@@ -65,26 +65,24 @@ the protein alignment into a codon alignment.</p>
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>pal</dt>
+
+
+<dl><dt id="arg-pal">pal<a class="anchor" aria-label="anchor" href="#arg-pal"></a></dt>
 <dd><p><code>AAStringSet</code> [mandatory]</p></dd>
 
 
-<dt>nal</dt>
+<dt id="arg-nal">nal<a class="anchor" aria-label="anchor" href="#arg-nal"></a></dt>
 <dd><p><code>DNAStringSet</code> [mandatory]</p></dd>
 
 
-<dt>remove.gaps</dt>
+<dt id="arg-remove-gaps">remove.gaps<a class="anchor" aria-label="anchor" href="#arg-remove-gaps"></a></dt>
 <dd><p>specify if gaps in the codon alignment should be removed
 [default: FALSE]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>codon alignment as <code>DNAStringSet</code></p>
-
-
+    <p>codon alignment as <code>DNAStringSet</code></p>
     </div>
     <div id="references">
     <h2>References</h2>
@@ -93,7 +91,7 @@ biological strings. <em>R package version</em>, <b>2(0)</b>.</p>
     </div>
     <div id="see-also">
     <h2>See also</h2>
-    <div class="dont-index"><p><code><a href="https://rdrr.io/pkg/Biostrings/man/pairwiseAlignment.html" class="external-link">pairwiseAlignment</a></code></p></div>
+    <div class="dont-index"><p><code>pairwiseAlignment</code></p></div>
     </div>
     <div id="author">
     <h2>Author</h2>
@@ -107,7 +105,7 @@ biological strings. <em>R package version</em>, <b>2(0)</b>.</p>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">cds</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"cds1"</span>, <span class="st">"cds2"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="co">## get protein alignment</span></span></span>
 <span class="r-in"><span><span class="va">aa</span> <span class="op">&lt;-</span> <span class="fu">MSA2dist</span><span class="fu">::</span><span class="fu"><a href="cds2aa.html">cds2aa</a></span><span class="op">(</span><span class="va">cds</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="va">msa</span> <span class="op">&lt;-</span> <span class="fu"><a href="makePostalignedSeqs.html">makePostalignedSeqs</a></span><span class="op">(</span><span class="fu">Biostrings</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/Biostrings/man/pairwiseAlignment.html" class="external-link">pairwiseAlignment</a></span><span class="op">(</span><span class="va">aa</span><span class="op">[</span><span class="fl">1</span><span class="op">]</span>, <span class="va">aa</span><span class="op">[</span><span class="fl">2</span><span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="fl">1L</span><span class="op">]</span><span class="op">]</span></span></span>
+<span class="r-in"><span><span class="va">msa</span> <span class="op">&lt;-</span> <span class="fu"><a href="makePostalignedSeqs.html">makePostalignedSeqs</a></span><span class="op">(</span><span class="fu">pwalign</span><span class="fu">::</span><span class="fu">pairwiseAlignment</span><span class="op">(</span><span class="va">aa</span><span class="op">[</span><span class="fl">1</span><span class="op">]</span>, <span class="va">aa</span><span class="op">[</span><span class="fl">2</span><span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="fl">1L</span><span class="op">]</span><span class="op">]</span></span></span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">msa</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">aa</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="co">## get codon alignment</span></span></span>
 <span class="r-in"><span><span class="va">nal</span> <span class="op">&lt;-</span> <span class="fu">MSA2dist</span><span class="fu">::</span><span class="fu">pal2nal</span><span class="op">(</span>pal<span class="op">=</span><span class="va">msa</span>, nal<span class="op">=</span><span class="va">cds</span><span class="op">)</span></span></span>
@@ -130,15 +128,15 @@ biological strings. <em>R package version</em>, <b>2(0)</b>.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/popinteger.html b/public/reference/popinteger.html
index 8aac05a87303623081f9096b84c2afd2997b102c..9eb410eb52742d757082a56ff9fd246f09f80b1a 100644
--- a/public/reference/popinteger.html
+++ b/public/reference/popinteger.html
@@ -1,11 +1,11 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>popinteger — popinteger • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="popinteger — popinteger"><meta property="og:description" content="This function shows the population integer slot from a
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>popinteger — popinteger • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="popinteger — popinteger"><meta property="og:description" content="This function shows the population integer slot from a
 DNAStringSet or an AAStringSet
 metadata information."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -19,7 +19,7 @@ metadata information."><meta property="og:image" content="/logo.png"><!-- mathja
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -36,20 +36,20 @@ metadata information."><meta property="og:image" content="/logo.png"><!-- mathja
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>popinteger</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/popinteger.R" class="external-link"><code>R/popinteger.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/popinteger.R" class="external-link"><code>R/popinteger.R</code></a></small>
     <div class="hidden name"><code>popinteger.Rd</code></div>
     </div>
 
@@ -65,17 +65,15 @@ metadata information."><meta property="og:image" content="/logo.png"><!-- mathja
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>seq</dt>
+
+
+<dl><dt id="arg-seq">seq<a class="anchor" aria-label="anchor" href="#arg-seq"></a></dt>
 <dd><p><code>DNAStringSet</code> or <code>AAStringSet</code> [mandatory]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>population integer from <code>metadata</code></p>
-
-
+    <p>population integer from <code>metadata</code></p>
     </div>
     <div id="see-also">
     <h2>See also</h2>
@@ -124,15 +122,15 @@ metadata information."><meta property="og:image" content="/logo.png"><!-- mathja
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/popnames.html b/public/reference/popnames.html
index 7c507d0ba44c07973c521fa6f3f3cf3d44c7b997..710a5018baca1a8a25935e2b216c216f885d5747 100644
--- a/public/reference/popnames.html
+++ b/public/reference/popnames.html
@@ -1,11 +1,11 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>popnames — popnames • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="popnames — popnames"><meta property="og:description" content="This function shows the population names slot from a
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>popnames — popnames • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="popnames — popnames"><meta property="og:description" content="This function shows the population names slot from a
 DNAStringSet or an AAStringSet
 metadata information."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -19,7 +19,7 @@ metadata information."><meta property="og:image" content="/logo.png"><!-- mathja
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -36,20 +36,20 @@ metadata information."><meta property="og:image" content="/logo.png"><!-- mathja
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>popnames</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/popnames.R" class="external-link"><code>R/popnames.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/popnames.R" class="external-link"><code>R/popnames.R</code></a></small>
     <div class="hidden name"><code>popnames.Rd</code></div>
     </div>
 
@@ -65,17 +65,15 @@ metadata information."><meta property="og:image" content="/logo.png"><!-- mathja
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>seq</dt>
+
+
+<dl><dt id="arg-seq">seq<a class="anchor" aria-label="anchor" href="#arg-seq"></a></dt>
 <dd><p><code>DNAStringSet</code> or <code>AAStringSet</code> [mandatory]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>population names from <code>metadata</code></p>
-
-
+    <p>population names from <code>metadata</code></p>
     </div>
     <div id="see-also">
     <h2>See also</h2>
@@ -129,15 +127,15 @@ metadata information."><meta property="og:image" content="/logo.png"><!-- mathja
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/rcpp_KaKs.html b/public/reference/rcpp_KaKs.html
index 77b4e097fa0571218610135ecc808733917329b3..8e7620dffc1c78a27916d7991b1b71aaee75b4f8 100644
--- a/public/reference/rcpp_KaKs.html
+++ b/public/reference/rcpp_KaKs.html
@@ -1,10 +1,10 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>rcpp_KaKs — rcpp_KaKs • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="rcpp_KaKs — rcpp_KaKs"><meta property="og:description" content="calculates KaKs as implememted in
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>rcpp_KaKs — rcpp_KaKs • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="rcpp_KaKs — rcpp_KaKs"><meta property="og:description" content="calculates KaKs as implememted in
 KaKs Calculator 2.0 MSA2dist with Rcpp."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -18,7 +18,7 @@ KaKs Calculator 2.0 MSA2dist with Rcpp."><meta property="og:image" content="/log
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -35,20 +35,20 @@ KaKs Calculator 2.0 MSA2dist with Rcpp."><meta property="og:image" content="/log
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>rcpp_KaKs</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/RcppExports.R" class="external-link"><code>R/RcppExports.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/RcppExports.R" class="external-link"><code>R/RcppExports.R</code></a></small>
     <div class="hidden name"><code>rcpp_KaKs.Rd</code></div>
     </div>
 
@@ -63,29 +63,27 @@ KaKs Calculator 2.0 <code>MSA2dist</code> with <code>Rcpp</code>.</p>
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>cdsstr</dt>
+
+
+<dl><dt id="arg-cdsstr">cdsstr<a class="anchor" aria-label="anchor" href="#arg-cdsstr"></a></dt>
 <dd><p>StringVector [mandatory]</p></dd>
 
 
-<dt>sgc</dt>
+<dt id="arg-sgc">sgc<a class="anchor" aria-label="anchor" href="#arg-sgc"></a></dt>
 <dd><p>standard genetic code to use [default: 1]</p></dd>
 
 
-<dt>method</dt>
+<dt id="arg-method">method<a class="anchor" aria-label="anchor" href="#arg-method"></a></dt>
 <dd><p>KaKs Calculator 2.0 codon model [default: YN]</p></dd>
 
 
-<dt>verbose</dt>
+<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
 <dd><p>specify if verbose output [default: FALSE]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p><code>list</code></p>
-
-
+    <p><code>list</code></p>
     </div>
     <div id="references">
     <h2>References</h2>
@@ -152,15 +150,15 @@ proteomics &amp; bioinformatics.</em> <b>8(1)</b>, 77-80.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/rcpp_distSTRING.html b/public/reference/rcpp_distSTRING.html
index 972d0ddae9915717903f67aa8676d1c45cd32b6a..9c674651980f6741efb7643a652ea22c471f99bc 100644
--- a/public/reference/rcpp_distSTRING.html
+++ b/public/reference/rcpp_distSTRING.html
@@ -1,9 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>rcpp_distSTRING — rcpp_distSTRING • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="rcpp_distSTRING — rcpp_distSTRING"><meta property="og:description" content="calculates pairwise distances using a score matrix"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>rcpp_distSTRING — rcpp_distSTRING • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="rcpp_distSTRING — rcpp_distSTRING"><meta property="og:description" content="calculates pairwise distances using a score matrix"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -34,20 +34,20 @@
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>rcpp_distSTRING</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/RcppExports.R" class="external-link"><code>R/RcppExports.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/RcppExports.R" class="external-link"><code>R/RcppExports.R</code></a></small>
     <div class="hidden name"><code>rcpp_distSTRING.Rd</code></div>
     </div>
 
@@ -61,27 +61,27 @@
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>dnavector</dt>
+
+
+<dl><dt id="arg-dnavector">dnavector<a class="anchor" aria-label="anchor" href="#arg-dnavector"></a></dt>
 <dd><p>StringVector [mandatory]</p></dd>
 
 
-<dt>scoreMatrix</dt>
+<dt id="arg-scorematrix">scoreMatrix<a class="anchor" aria-label="anchor" href="#arg-scorematrix"></a></dt>
 <dd><p>NumericMatrix [mandatory]</p></dd>
 
 
-<dt>ncores</dt>
+<dt id="arg-ncores">ncores<a class="anchor" aria-label="anchor" href="#arg-ncores"></a></dt>
 <dd><p>number of cores [default: 1]</p></dd>
 
 
-<dt>symmetric</dt>
+<dt id="arg-symmetric">symmetric<a class="anchor" aria-label="anchor" href="#arg-symmetric"></a></dt>
 <dd><p>symmetric score matrix [default: 1]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>list</p>
+    <p>list</p>
     </div>
     <div id="author">
     <h2>Author</h2>
@@ -182,15 +182,15 @@
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/rcpp_pairwiseDeletionAA.html b/public/reference/rcpp_pairwiseDeletionAA.html
index 27d527c9706abb9f919981f9ad90c9f19639a4e6..9d10df9b10852f3f79d3fcfaa68cbf535cbbfc48 100644
--- a/public/reference/rcpp_pairwiseDeletionAA.html
+++ b/public/reference/rcpp_pairwiseDeletionAA.html
@@ -1,9 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>rcpp_pairwiseDeletionAA — rcpp_pairwiseDeletionAA • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="rcpp_pairwiseDeletionAA — rcpp_pairwiseDeletionAA"><meta property="og:description" content="returns number of AA sites used"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>rcpp_pairwiseDeletionAA — rcpp_pairwiseDeletionAA • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="rcpp_pairwiseDeletionAA — rcpp_pairwiseDeletionAA"><meta property="og:description" content="returns number of AA sites used"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -34,20 +34,20 @@
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>rcpp_pairwiseDeletionAA</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/RcppExports.R" class="external-link"><code>R/RcppExports.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/RcppExports.R" class="external-link"><code>R/RcppExports.R</code></a></small>
     <div class="hidden name"><code>rcpp_pairwiseDeletionAA.Rd</code></div>
     </div>
 
@@ -61,23 +61,23 @@
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>aavector</dt>
+
+
+<dl><dt id="arg-aavector">aavector<a class="anchor" aria-label="anchor" href="#arg-aavector"></a></dt>
 <dd><p>StringVector [mandatory]</p></dd>
 
 
-<dt>ncores</dt>
+<dt id="arg-ncores">ncores<a class="anchor" aria-label="anchor" href="#arg-ncores"></a></dt>
 <dd><p>number of cores [default: 1]</p></dd>
 
 
-<dt>symmetric</dt>
+<dt id="arg-symmetric">symmetric<a class="anchor" aria-label="anchor" href="#arg-symmetric"></a></dt>
 <dd><p>symmetric score matrix [default: 1]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>list</p>
+    <p>list</p>
     </div>
     <div id="author">
     <h2>Author</h2>
@@ -135,15 +135,15 @@
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/rcpp_pairwiseDeletionDNA.html b/public/reference/rcpp_pairwiseDeletionDNA.html
index d2a27a68c4613fe8c2220d7db31e74f32c841029..75412a47964c0f69cc5ec0548ccfd0d6d4f6f7ea 100644
--- a/public/reference/rcpp_pairwiseDeletionDNA.html
+++ b/public/reference/rcpp_pairwiseDeletionDNA.html
@@ -1,9 +1,9 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>rcpp_pairwiseDeletionDNA — rcpp_pairwiseDeletionDNA • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="rcpp_pairwiseDeletionDNA — rcpp_pairwiseDeletionDNA"><meta property="og:description" content="returns number of DNA sites used"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>rcpp_pairwiseDeletionDNA — rcpp_pairwiseDeletionDNA • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="rcpp_pairwiseDeletionDNA — rcpp_pairwiseDeletionDNA"><meta property="og:description" content="returns number of DNA sites used"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -34,20 +34,20 @@
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>rcpp_pairwiseDeletionDNA</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/RcppExports.R" class="external-link"><code>R/RcppExports.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/RcppExports.R" class="external-link"><code>R/RcppExports.R</code></a></small>
     <div class="hidden name"><code>rcpp_pairwiseDeletionDNA.Rd</code></div>
     </div>
 
@@ -61,23 +61,23 @@
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>dnavector</dt>
+
+
+<dl><dt id="arg-dnavector">dnavector<a class="anchor" aria-label="anchor" href="#arg-dnavector"></a></dt>
 <dd><p>StringVector [mandatory]</p></dd>
 
 
-<dt>ncores</dt>
+<dt id="arg-ncores">ncores<a class="anchor" aria-label="anchor" href="#arg-ncores"></a></dt>
 <dd><p>number of cores [default: 1]</p></dd>
 
 
-<dt>symmetric</dt>
+<dt id="arg-symmetric">symmetric<a class="anchor" aria-label="anchor" href="#arg-symmetric"></a></dt>
 <dd><p>symmetric score matrix [default: 1]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>list</p>
+    <p>list</p>
     </div>
     <div id="author">
     <h2>Author</h2>
@@ -139,15 +139,15 @@
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/region.html b/public/reference/region.html
index e886b38e28cf1eb55b06cec850f98c193166101d..c9917317135d63bfc167c982a0ca4086efaa0fef 100644
--- a/public/reference/region.html
+++ b/public/reference/region.html
@@ -1,11 +1,11 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>region — region • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="region — region"><meta property="og:description" content="This function shows the region slot from a
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>region — region • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="region — region"><meta property="og:description" content="This function shows the region slot from a
 DNAStringSet or an AAStringSet
 metadata information."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -19,7 +19,7 @@ metadata information."><meta property="og:image" content="/logo.png"><!-- mathja
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -36,20 +36,20 @@ metadata information."><meta property="og:image" content="/logo.png"><!-- mathja
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>region</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/region.R" class="external-link"><code>R/region.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/region.R" class="external-link"><code>R/region.R</code></a></small>
     <div class="hidden name"><code>region.Rd</code></div>
     </div>
 
@@ -65,17 +65,15 @@ metadata information."><meta property="og:image" content="/logo.png"><!-- mathja
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>seq</dt>
+
+
+<dl><dt id="arg-seq">seq<a class="anchor" aria-label="anchor" href="#arg-seq"></a></dt>
 <dd><p><code>DNAStringSet</code> or <code>AAStringSet</code> [mandatory]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>region <code>IRanges</code> object from <code>metadata</code></p>
-
-
+    <p>region <code>IRanges</code> object from <code>metadata</code></p>
     </div>
     <div id="see-also">
     <h2>See also</h2>
@@ -115,15 +113,15 @@ metadata information."><meta property="og:image" content="/logo.png"><!-- mathja
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/regionused.html b/public/reference/regionused.html
index 02ebdeb164b695ff8b9feb6de21f4c1b4a4b4ef1..804ab56196d96a7265a6447ec82ade62cc6537c4 100644
--- a/public/reference/regionused.html
+++ b/public/reference/regionused.html
@@ -1,11 +1,11 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>regionused — regionused • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="regionused — regionused"><meta property="og:description" content="This function shows the region used slot from a
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>regionused — regionused • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="regionused — regionused"><meta property="og:description" content="This function shows the region used slot from a
 DNAStringSet or an AAStringSet
 metadata information."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -19,7 +19,7 @@ metadata information."><meta property="og:image" content="/logo.png"><!-- mathja
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -36,20 +36,20 @@ metadata information."><meta property="og:image" content="/logo.png"><!-- mathja
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>regionused</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/regionused.R" class="external-link"><code>R/regionused.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/regionused.R" class="external-link"><code>R/regionused.R</code></a></small>
     <div class="hidden name"><code>regionused.Rd</code></div>
     </div>
 
@@ -65,17 +65,15 @@ metadata information."><meta property="og:image" content="/logo.png"><!-- mathja
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>seq</dt>
+
+
+<dl><dt id="arg-seq">seq<a class="anchor" aria-label="anchor" href="#arg-seq"></a></dt>
 <dd><p><code>DNAStringSet</code> or <code>AAStringSet</code> [mandatory]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>population names from <code>metadata</code></p>
-
-
+    <p>population names from <code>metadata</code></p>
     </div>
     <div id="see-also">
     <h2>See also</h2>
@@ -117,15 +115,15 @@ metadata information."><meta property="og:image" content="/logo.png"><!-- mathja
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/string2region.html b/public/reference/string2region.html
index 226d59dedc798b4fd6e3d0a700525046421caed7..c1a493f3ce2fea82e45a985f4398b981140bff6e 100644
--- a/public/reference/string2region.html
+++ b/public/reference/string2region.html
@@ -1,11 +1,11 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>string2region — string2region • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="string2region — string2region"><meta property="og:description" content="This function subsets a DNAStringSet or an
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>string2region — string2region • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="string2region — string2region"><meta property="og:description" content="This function subsets a DNAStringSet or an
 AAStringSet by a mask and region given one or both
 options as IRanges."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -19,7 +19,7 @@ options as IRanges."><meta property="og:image" content="/logo.png"><!-- mathjax
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -36,20 +36,20 @@ options as IRanges."><meta property="og:image" content="/logo.png"><!-- mathjax
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>string2region</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/string2region.R" class="external-link"><code>R/string2region.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/string2region.R" class="external-link"><code>R/string2region.R</code></a></small>
     <div class="hidden name"><code>string2region.Rd</code></div>
     </div>
 
@@ -65,37 +65,29 @@ options as <code>IRanges</code>.</p>
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>seq</dt>
+
+
+<dl><dt id="arg-seq">seq<a class="anchor" aria-label="anchor" href="#arg-seq"></a></dt>
 <dd><p><code>DNAStringSet</code> or <code>AAStringSet</code> [mandatory]</p></dd>
 
 
-<dt>mask</dt>
+<dt id="arg-mask">mask<a class="anchor" aria-label="anchor" href="#arg-mask"></a></dt>
 <dd><p><code>IRanges</code> object indicating masked sites [default: NULL]</p></dd>
 
 
-<dt>region</dt>
+<dt id="arg-region">region<a class="anchor" aria-label="anchor" href="#arg-region"></a></dt>
 <dd><p><code>IRanges</code> object indicating region to use for dist
 calculation (by default all sites are used) [default: NULL]</p></dd>
 
 
-<dt>add</dt>
+<dt id="arg-add">add<a class="anchor" aria-label="anchor" href="#arg-add"></a></dt>
 <dd><p>indicate if mask and region should be added to <code>metadata</code>
 [default: TRUE]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>A <code>list</code> object with the following components:<br></p>
-
-
-<p><code>DNAStringSet</code> or <code>AAStringSet</code><br></p>
-
-
-<p><code>regionUsed</code><br></p>
-
-
+    <p>A <code>list</code> object with the following components:<br><code>DNAStringSet</code> or <code>AAStringSet</code><br><code>regionUsed</code><br></p>
     </div>
     <div id="see-also">
     <h2>See also</h2>
@@ -157,15 +149,15 @@ calculation (by default all sites are used) [default: NULL]</p></dd>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/subString.html b/public/reference/subString.html
index 31a4e242e52171f48ff5b5340045deebbd899bea..3b0908226bc62bbac670567ddceb81aff2809df2 100644
--- a/public/reference/subString.html
+++ b/public/reference/subString.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>subString — subString • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="subString — subString"><meta property="og:description" content="This function gets a subsequence from a DNAString,
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>subString — subString • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="subString — subString"><meta property="og:description" content="This function gets a subsequence from a DNAString,
 RNAString, AAString, BString, DNAStringSet,
 RNAStringSet, AAStringSet, BStringSet
 object from the Biostrings package."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -20,7 +20,7 @@ object from the Biostrings package."><meta property="og:image" content="/logo.pn
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -37,20 +37,20 @@ object from the Biostrings package."><meta property="og:image" content="/logo.pn
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>subString</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/subString.R" class="external-link"><code>R/subString.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/subString.R" class="external-link"><code>R/subString.R</code></a></small>
     <div class="hidden name"><code>subString.Rd</code></div>
     </div>
 
@@ -67,25 +67,25 @@ object from the <code>Biostrings</code> package.</p>
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>x</dt>
+
+
+<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
 <dd><p><code>DNAStringSet</code>, <code>RNAString</code>, <code>AAString</code>,
 <code>BString</code>, <code>DNAStringSet</code>, <code>RNAStringSet</code>,
 <code>AAStringSet</code>, <code>BStringSet</code> [mandatory]</p></dd>
 
 
-<dt>s</dt>
+<dt id="arg-s">s<a class="anchor" aria-label="anchor" href="#arg-s"></a></dt>
 <dd><p>start vector [mandatory]</p></dd>
 
 
-<dt>e</dt>
+<dt id="arg-e">e<a class="anchor" aria-label="anchor" href="#arg-e"></a></dt>
 <dd><p>end vector [mandatory]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>subsequence of an <code>Biostrings</code> object</p>
+    <p>subsequence of an <code>Biostrings</code> object</p>
     </div>
     <div id="see-also">
     <h2>See also</h2>
@@ -122,15 +122,15 @@ object from the <code>Biostrings</code> package.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/reference/uptriidx.html b/public/reference/uptriidx.html
index 86bf75e30a3e0c6bd0ecee43f2842a3ac133e213..bf802dafb72fc1e25ee7c070aec819acbbbe97c8 100644
--- a/public/reference/uptriidx.html
+++ b/public/reference/uptriidx.html
@@ -1,10 +1,10 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>uptriidx — uptriidx • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="uptriidx — uptriidx"><meta property="og:description" content="This function returns upper tri index for usage with
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>uptriidx — uptriidx • MSA2dist</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="uptriidx — uptriidx"><meta property="og:description" content="This function returns upper tri index for usage with
 pivot_long reduction."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body data-spy="scroll" data-target="#toc">
-    
+
 
     <div class="container template-reference-topic">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -18,7 +18,7 @@ pivot_long reduction."><meta property="og:image" content="/logo.png"><!-- mathja
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">MSA2dist</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.5</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.11.1</span>
       </span>
     </div>
 
@@ -35,20 +35,20 @@ pivot_long reduction."><meta property="og:image" content="/logo.png"><!-- mathja
       </ul><ul class="nav navbar-nav navbar-right"><li>
   <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
     <span class="fab fa-gitlab fa-lg"></span>
-     
+
   </a>
 </li>
       </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
-      
+
 
       </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>uptriidx</h1>
-    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterR/uptriidx.R" class="external-link"><code>R/uptriidx.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/master/R/uptriidx.R" class="external-link"><code>R/uptriidx.R</code></a></small>
     <div class="hidden name"><code>uptriidx.Rd</code></div>
     </div>
 
@@ -63,19 +63,19 @@ pivot_long reduction."><meta property="og:image" content="/logo.png"><!-- mathja
 
     <div id="arguments">
     <h2>Arguments</h2>
-    <dl><dt>n</dt>
+
+
+<dl><dt id="arg-n">n<a class="anchor" aria-label="anchor" href="#arg-n"></a></dt>
 <dd><p>dimension of initial matrix [mandatory]</p></dd>
 
 
-<dt>diag</dt>
+<dt id="arg-diag">diag<a class="anchor" aria-label="anchor" href="#arg-diag"></a></dt>
 <dd><p>indicate if diag should be retained [default: FALSE]</p></dd>
 
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    
-
-<p>list of positions</p>
+    <p>list of positions</p>
     </div>
     <div id="author">
     <h2>Author</h2>
@@ -101,15 +101,15 @@ pivot_long reduction."><meta property="og:image" content="/logo.png"><!-- mathja
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
       </footer></div>
 
-  
 
 
-  
+
+
 
   </body></html>
 
diff --git a/public/sitemap.xml b/public/sitemap.xml
index da68e28daec97fb61629646915c0d620338c5591..f4e9c30b050968f6d9db954d285bb296f1dd9913 100644
--- a/public/sitemap.xml
+++ b/public/sitemap.xml
@@ -1,177 +1,62 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
-  <url>
-    <loc>/404.html</loc>
-  </url>
-  <url>
-    <loc>/CODE_OF_CONDUCT.html</loc>
-  </url>
-  <url>
-    <loc>/LICENSE-text.html</loc>
-  </url>
-  <url>
-    <loc>/articles/MSA2dist.html</loc>
-  </url>
-  <url>
-    <loc>/articles/index.html</loc>
-  </url>
-  <url>
-    <loc>/authors.html</loc>
-  </url>
-  <url>
-    <loc>/index.html</loc>
-  </url>
-  <url>
-    <loc>/news/index.html</loc>
-  </url>
-  <url>
-    <loc>/reference/AAMatrix-data.html</loc>
-  </url>
-  <url>
-    <loc>/reference/GENETIC_CODE_TCAG.html</loc>
-  </url>
-  <url>
-    <loc>/reference/aa2selfscore.html</loc>
-  </url>
-  <url>
-    <loc>/reference/aabin2aastring.html</loc>
-  </url>
-  <url>
-    <loc>/reference/aastring2aabin.html</loc>
-  </url>
-  <url>
-    <loc>/reference/aastring2aln.html</loc>
-  </url>
-  <url>
-    <loc>/reference/aastring2dist.html</loc>
-  </url>
-  <url>
-    <loc>/reference/addmask2string.html</loc>
-  </url>
-  <url>
-    <loc>/reference/addpop2string.html</loc>
-  </url>
-  <url>
-    <loc>/reference/addpos2string.html</loc>
-  </url>
-  <url>
-    <loc>/reference/addregion2string.html</loc>
-  </url>
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+
diff --git a/tests/testthat/test-globalDeletionAA.R b/tests/testthat/test-globalDeletionAA.R
new file mode 100644
index 0000000000000000000000000000000000000000..292ae0883170f92e1813b37813443b9fe4eb538b
--- /dev/null
+++ b/tests/testthat/test-globalDeletionAA.R
@@ -0,0 +1,8 @@
+test_that("globalDeletionAA()", {
+    cds1 <- Biostrings::DNAString("ATGCAACATTGC")
+    cds2 <- Biostrings::DNAString("ATG---CATTGC")
+    cds1.cds2.aln <- c(Biostrings::DNAStringSet(cds1),
+        Biostrings::DNAStringSet(cds2))
+    aa.aln <- cds1.cds2.aln |> cds2aa()
+    expect_true(as.character(globalDeletionAA(aa.aln)[1]) == "MHC")
+})