From 62ab716c518d76cf255247c96d1b87612c4e4077 Mon Sep 17 00:00:00 2001
From: Kristian Ullrich <ullrich@evolbio.mpg.de>
Date: Wed, 13 Nov 2024 21:37:29 +0100
Subject: [PATCH] # MSA2dist 1.11.1 (2024-11-14)
BUG FIXES
* fixed pal2nal
* fixed aastring2aabin to return alignment
NEW FEATURES
* added globalDeletionAA
---
.gitlab-ci.yml | 5 +-
DESCRIPTION | 5 +-
NAMESPACE | 11 +
NEWS.md | 12 +
R/aastring2aabin.R | 9 +-
R/cdsstring2codonaln.R | 2 +-
R/globalDeletionAA.R | 31 +++
R/pal2nal.R | 3 +-
_pkgdown.yml | 8 +-
man/aastring2aabin.Rd | 6 +-
man/globalDeletionAA.Rd | 30 +++
public/404.html | 16 +-
public/CODE_OF_CONDUCT.html | 16 +-
public/LICENSE-text.html | 16 +-
public/articles/MSA2dist.html | 108 ++++----
.../figure-html/unnamed-chunk-28-1.png | Bin 166669 -> 166532 bytes
public/articles/index.html | 16 +-
public/authors.html | 34 ++-
public/index.html | 39 ++-
public/news/index.html | 26 +-
public/pkgdown.yml | 7 +-
public/reference/AAMatrix-data.html | 24 +-
public/reference/GENETIC_CODE_TCAG.html | 28 +--
public/reference/aa2selfscore.html | 32 ++-
public/reference/aabin2aastring.html | 28 +--
public/reference/aastring2aabin.html | 37 ++-
public/reference/aastring2aln.html | 42 ++--
public/reference/aastring2dist.html | 38 ++-
public/reference/addmask2string.html | 32 ++-
public/reference/addpop2string.html | 30 ++-
public/reference/addpos2string.html | 34 ++-
public/reference/addregion2string.html | 32 ++-
public/reference/aln2aastring.html | 28 +--
public/reference/aln2dnastring.html | 28 +--
public/reference/cds2aa.html | 38 ++-
public/reference/cds2codonaln.html | 52 ++--
public/reference/cdsstring2codonaln.html | 50 ++--
public/reference/codon2numberAMBIG.html | 28 +--
public/reference/codon2numberTCAG.html | 28 +--
public/reference/codonmat2pnps.html | 81 ++----
public/reference/codonmat2xy.html | 63 ++---
public/reference/compareCodons.html | 28 +--
public/reference/dnabin2dnastring.html | 28 +--
public/reference/dnastring2aln.html | 42 ++--
public/reference/dnastring2codonmat.html | 48 ++--
public/reference/dnastring2dist.html | 42 ++--
public/reference/dnastring2dnabin.html | 28 +--
public/reference/dnastring2kaks.html | 42 ++--
public/reference/getmask.html | 28 +--
public/reference/getpos.html | 28 +--
public/reference/gff2cds.html | 36 ++-
public/reference/globalDeletion.html | 28 +--
public/reference/globalDeletionAA.html | 119 +++++++++
public/reference/granthamMatrix.html | 24 +-
public/reference/hiv-data.html | 18 +-
public/reference/index.html | 20 +-
public/reference/indices2kaks.html | 40 +--
public/reference/iupac-data.html | 18 +-
public/reference/iupacMatrix.html | 24 +-
public/reference/makePostalignedSeqs.html | 30 +--
public/reference/pal2nal.html | 36 ++-
public/reference/popinteger.html | 28 +--
public/reference/popnames.html | 28 +--
public/reference/rcpp_KaKs.html | 34 ++-
public/reference/rcpp_distSTRING.html | 32 +--
public/reference/rcpp_pairwiseDeletionAA.html | 30 +--
.../reference/rcpp_pairwiseDeletionDNA.html | 30 +--
public/reference/region.html | 28 +--
public/reference/regionused.html | 28 +--
public/reference/string2region.html | 40 ++-
public/reference/subString.html | 30 +--
public/reference/uptriidx.html | 28 +--
public/sitemap.xml | 237 +++++-------------
tests/testthat/test-globalDeletionAA.R | 8 +
74 files changed, 1167 insertions(+), 1274 deletions(-)
create mode 100644 R/globalDeletionAA.R
create mode 100644 man/globalDeletionAA.Rd
create mode 100644 public/reference/globalDeletionAA.html
create mode 100644 tests/testthat/test-globalDeletionAA.R
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 322eab9..5a17141 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 7e4fa15..7af7bba 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 ab2b7cf..13d402d 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 e833df5..aaf67af 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 e688761..b398b7d 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 de3f011..00e7175 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 0000000..4ca8889
--- /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 29b0359..0678854 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 c991613..bcf364c 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 e785752..26e7d78 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 0000000..f15e55b
--- /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 11078e8..1d14c47 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 6dfd21b..de7f276 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 cb966cf..30f7780 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 87dc535..e09c229 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">|></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> >>>
<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">|></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">|></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>
-
-
+
+
</body>
</html>
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diff --git a/public/articles/index.html b/public/articles/index.html
index 03163fb..0d1c6fd 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 f77e3b0..672e6c7 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]>
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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-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 4465deb..e7e7891 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">
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<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">
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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]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -35,7 +26,7 @@
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</head>
<body data-spy="scroll" data-target="#toc">
-
+
<div class="container template-home">
<header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -49,7 +40,7 @@
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<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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</li>
</ul>
@@ -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/geom_point.html" class="external-link">geom_point</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>colour<span class="op">=</span><span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></span><span class="op">(</span><span class="va">variable</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span>
<span> <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">ggtitle</a></span><span class="op">(</span><span class="st">"HIV-1 sample 136 patient 1 from Sweden envelope glycoprotein (env) gene"</span><span class="op">)</span></span></code></pre>
</div>
<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>
</footer>
</div>
-
-
+
+
</body>
</html>
diff --git a/public/news/index.html b/public/news/index.html
index be5e76d..108a67f 100644
--- a/public/news/index.html
+++ b/public/news/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>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/3.4.1/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="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]>
+<!-- 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]>
<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-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>
</span>
</div>
@@ -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 @@
</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/pkgdown.yml b/public/pkgdown.yml
index fb8a136..71ce43c 100644
--- a/public/pkgdown.yml
+++ b/public/pkgdown.yml
@@ -1,7 +1,6 @@
-pandoc: 3.1.1
-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 d798fa3..5ebca0f 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 f9f7fa6..b9c2c68 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 c5c413a..2e776da 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 3dd85e0..c7269ca 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 44330ae..9755cfb 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">|></span> <span class="fu"><a href="cds2aa.html">cds2aa</a></span><span class="op">(</span><span class="op">)</span> <span class="op">|></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">#></span> 2 amino acid sequences in a list</span>
-<span class="r-out co"><span class="r-pr">#></span> </span>
+<span class="r-out co"><span class="r-pr">#></span> 2 amino acid sequences in a matrix</span>
<span class="r-out co"><span class="r-pr">#></span> All sequences of the same length: 4 </span>
<span class="r-out co"><span class="r-pr">#></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 fad9d35..92f9db7 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 0f07fdc..3a69f25 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 7229f23..ed335e3 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 4d96b4c..fee7182 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 6f05ca8..d2f4880 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 f9718f7..7501654 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 45b8741..5f40e12 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 109ca28..ab950db 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 137e87b..ba4611e 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 abb6283..02865ae 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]>
<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>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 696e122..e353f33 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 e1db262..617afaa 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 24e77a4..ad70b25 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 3d0ea11..be85e0a 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 ef013d1..ee40442 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 8e077db..3827e8c 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 b6bd422..042efc2 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 e30e129..29ae3e4 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 609bf08..6afd0a5 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]>
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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">
@@ -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 83297fe..43593cc 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>
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</footer></div>
-
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diff --git a/public/reference/dnastring2dnabin.html b/public/reference/dnastring2dnabin.html
index 79f23bf..e785be6 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 14c8f85..84517b9 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">#></span> result.1.6 0.130057803468208 0.118421052631579 0.910526315789474</span>
<span class="r-out co"><span class="r-pr">#></span> result.2.6 0.136231884057971 0.0982211910286156 0.72098533840154</span>
<span class="r-out co"><span class="r-pr">#></span> result.3.6 0.119186046511628 0.0935085007727975 0.784559128435179</span>
-<span class="r-out co"><span class="r-pr">#></span> result.4.6 0.144508670520231 0.114551083591331 0.792693498452012</span>
+<span class="r-out co"><span class="r-pr">#></span> result.4.6 0.144508670520231 0.114551083591331 0.792693498452013</span>
<span class="r-out co"><span class="r-pr">#></span> result.5.6 0.126074498567335 0.100853374709077 0.799950631215178</span>
<span class="r-out co"><span class="r-pr">#></span> result.6.6 0.144508670520231 0.123839009287926 0.856965944272446</span>
<span class="r-out co"><span class="r-pr">#></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">#></span> result.1.6 0.130057803468208 0.118421052631579 0.910526315789474</span>
<span class="r-out co"><span class="r-pr">#></span> result.2.6 0.136231884057971 0.0982211910286156 0.72098533840154</span>
<span class="r-out co"><span class="r-pr">#></span> result.3.6 0.119186046511628 0.0935085007727975 0.784559128435179</span>
-<span class="r-out co"><span class="r-pr">#></span> result.4.6 0.144508670520231 0.114551083591331 0.792693498452012</span>
+<span class="r-out co"><span class="r-pr">#></span> result.4.6 0.144508670520231 0.114551083591331 0.792693498452013</span>
<span class="r-out co"><span class="r-pr">#></span> result.5.6 0.126074498567335 0.100853374709077 0.799950631215178</span>
<span class="r-out co"><span class="r-pr">#></span> result.6.6 0.144508670520231 0.123839009287926 0.856965944272446</span>
<span class="r-out co"><span class="r-pr">#></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 4b69cc7..b42e1ff 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 6ae0ad7..3ae1c5a 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 35ff2f9..d68e0b6 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 dd413a3..e9b8f5d 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 0000000..5a0b92c
--- /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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+ <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="">1.11.1</span>
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+
+ <div id="navbar" class="navbar-collapse collapse">
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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>
+ <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist" class="external-link">
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+
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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"><-</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"><-</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"><-</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">|></span> <span class="fu"><a href="cds2aa.html">cds2aa</a></span><span class="op">(</span><span class="op">)</span> <span class="op">|></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">#></span> AAStringSet object of length 2:</span>
+<span class="r-out co"><span class="r-pr">#></span> width seq</span>
+<span class="r-out co"><span class="r-pr">#></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">#></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 da17cb2..0b5d080 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 35e62a9..80ab627 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>
-
-
+
+
</body></html>
diff --git a/public/reference/index.html b/public/reference/index.html
index ddbe2f3..d82c5f6 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 00efd2f..f8b9856 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 9521948..b66e925 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 7ebd26d..b88024a 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 ebd928f..7d10faf 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"><-</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"><-</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">#></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 502248f..124ea8c 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"><-</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"><-</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"><-</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"><-</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"><-</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"><-</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 8aac05a..9eb410e 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 7c507d0..710a501 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 77b4e09..8e7620d 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 & 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 972d0dd..9c67465 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 27d527c..9d10df9 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 d2a27a6..75412a4 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 e886b38..c991731 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 02ebdeb..804ab56 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 226d59d..c1a493f 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 31a4e24..3b09082 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 86bf75e..bf802da 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 da68e28..f4e9c30 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>
- <url>
- <loc>/reference/aln2aastring.html</loc>
- </url>
- <url>
- <loc>/reference/aln2dnastring.html</loc>
- </url>
- <url>
- <loc>/reference/cds2aa.html</loc>
- </url>
- <url>
- <loc>/reference/cds2codonaln.html</loc>
- </url>
- <url>
- <loc>/reference/cdsstring2codonaln.html</loc>
- </url>
- <url>
- <loc>/reference/codon2numberAMBIG.html</loc>
- </url>
- <url>
- <loc>/reference/codon2numberTCAG.html</loc>
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diff --git a/tests/testthat/test-globalDeletionAA.R b/tests/testthat/test-globalDeletionAA.R
new file mode 100644
index 0000000..292ae08
--- /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")
+})
--
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