From e6541f2b514d3fecd388e86ce389ebd6a5b09aee Mon Sep 17 00:00:00 2001
From: Kristian Ullrich <ullrich@evolbio.mpg.de>
Date: Mon, 18 Mar 2024 13:05:46 +0100
Subject: [PATCH] # fix pal2nal man
---
DESCRIPTION | 2 +-
NEWS.md | 6 ++++++
R/pal2nal.R | 2 ++
man/pal2nal.Rd | 3 +++
public/404.html | 2 +-
public/CODE_OF_CONDUCT.html | 2 +-
public/LICENSE-text.html | 2 +-
public/articles/MSA2dist.html | 8 ++++----
public/articles/index.html | 2 +-
public/authors.html | 6 +++---
public/index.html | 2 +-
public/news/index.html | 7 ++++++-
public/pkgdown.yml | 2 +-
public/reference/AAMatrix-data.html | 2 +-
public/reference/GENETIC_CODE_TCAG.html | 2 +-
public/reference/aa2selfscore.html | 2 +-
public/reference/aabin2aastring.html | 2 +-
public/reference/aastring2aabin.html | 2 +-
public/reference/aastring2aln.html | 2 +-
public/reference/aastring2dist.html | 2 +-
public/reference/addmask2string.html | 2 +-
public/reference/addpop2string.html | 2 +-
public/reference/addpos2string.html | 2 +-
public/reference/addregion2string.html | 2 +-
public/reference/aln2aastring.html | 2 +-
public/reference/aln2dnastring.html | 2 +-
public/reference/cds2aa.html | 2 +-
public/reference/cds2codonaln.html | 2 +-
public/reference/cdsstring2codonaln.html | 2 +-
public/reference/codon2numberAMBIG.html | 2 +-
public/reference/codon2numberTCAG.html | 2 +-
public/reference/codonmat2pnps.html | 2 +-
public/reference/codonmat2xy.html | 2 +-
public/reference/compareCodons.html | 2 +-
public/reference/dnabin2dnastring.html | 2 +-
public/reference/dnastring2aln.html | 2 +-
public/reference/dnastring2codonmat.html | 2 +-
public/reference/dnastring2dist.html | 2 +-
public/reference/dnastring2dnabin.html | 2 +-
public/reference/dnastring2kaks.html | 2 +-
public/reference/getmask.html | 2 +-
public/reference/getpos.html | 2 +-
public/reference/gff2cds.html | 2 +-
public/reference/globalDeletion.html | 2 +-
public/reference/granthamMatrix.html | 2 +-
public/reference/hiv-data.html | 2 +-
public/reference/index.html | 2 +-
public/reference/indices2kaks.html | 2 +-
public/reference/iupac-data.html | 2 +-
public/reference/iupacMatrix.html | 2 +-
public/reference/makePostalignedSeqs.html | 2 +-
public/reference/pal2nal.html | 7 ++++++-
public/reference/popinteger.html | 2 +-
public/reference/popnames.html | 2 +-
public/reference/rcpp_KaKs.html | 2 +-
public/reference/rcpp_distSTRING.html | 2 +-
public/reference/rcpp_pairwiseDeletionAA.html | 2 +-
public/reference/rcpp_pairwiseDeletionDNA.html | 2 +-
public/reference/region.html | 2 +-
public/reference/regionused.html | 2 +-
public/reference/string2region.html | 2 +-
public/reference/subString.html | 2 +-
public/reference/uptriidx.html | 2 +-
63 files changed, 86 insertions(+), 65 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 4b291b7..fee01df 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: 1.7.3
+Version: 1.7.4
Authors@R:
person(given = "Kristian K",
family = "Ullrich",
diff --git a/NEWS.md b/NEWS.md
index 77d1956..b4b0a5a 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,9 @@
+# MSA2dist 1.7.4 (2024-03-18)
+
+BUG FIXES
+
+* fixed pal2nal
+
# MSA2dist 1.7.3 (2024-03-14)
BUG FIXES
diff --git a/R/pal2nal.R b/R/pal2nal.R
index 48f7379..22d916d 100644
--- a/R/pal2nal.R
+++ b/R/pal2nal.R
@@ -5,6 +5,8 @@
#' the protein alignment into a codon alignment.
#' @param pal \code{AAStringSet} [mandatory]
#' @param nal \code{DNAStringSet} [mandatory]
+#' @param remove.gaps specify if gaps in the codon alignment should be removed
+#' [default: FALSE]
#' @return codon alignment as \code{DNAStringSet}
#' @importFrom Biostrings DNAString DNAStringSet AAString AAStringSet
#' readDNAStringSet readAAStringSet writeXStringSet width subseq
diff --git a/man/pal2nal.Rd b/man/pal2nal.Rd
index c515dcf..3f03c1a 100644
--- a/man/pal2nal.Rd
+++ b/man/pal2nal.Rd
@@ -10,6 +10,9 @@ pal2nal(pal, nal, remove.gaps = FALSE)
\item{pal}{\code{AAStringSet} [mandatory]}
\item{nal}{\code{DNAStringSet} [mandatory]}
+
+\item{remove.gaps}{specify if gaps in the codon alignment should be removed
+[default: FALSE]}
}
\value{
codon alignment as \code{DNAStringSet}
diff --git a/public/404.html b/public/404.html
index 56f6213..14b77bb 100644
--- a/public/404.html
+++ b/public/404.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/CODE_OF_CONDUCT.html b/public/CODE_OF_CONDUCT.html
index 5aefc37..6f39d76 100644
--- a/public/CODE_OF_CONDUCT.html
+++ b/public/CODE_OF_CONDUCT.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/LICENSE-text.html b/public/LICENSE-text.html
index 3c571f4..f11f3f4 100644
--- a/public/LICENSE-text.html
+++ b/public/LICENSE-text.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/articles/MSA2dist.html b/public/articles/MSA2dist.html
index bcc3fa4..7adcd73 100644
--- a/public/articles/MSA2dist.html
+++ b/public/articles/MSA2dist.html
@@ -40,7 +40,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">MSA2dist</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
@@ -80,7 +80,7 @@
<h4 data-toc-skip class="author">Kristian K
Ullrich</h4>
- <h4 data-toc-skip class="date">2024-03-14</h4>
+ <h4 data-toc-skip class="date">2024-03-18</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>
<div class="hidden name"><code>MSA2dist.Rmd</code></div>
@@ -574,7 +574,7 @@ 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">## 0.003 0.000 0.002</span></span></code></pre>
+<span><span class="co">## 0.002 0.000 0.003</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>
@@ -1111,7 +1111,7 @@ Evolutionary Biology</em> 6 (1): 1–10.
<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_1.7.3 BiocStyle_2.31.0 </span></span>
+<span><span class="co">## [10] BiocGenerics_0.49.1 MSA2dist_1.7.4 BiocStyle_2.31.0 </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>
diff --git a/public/articles/index.html b/public/articles/index.html
index 92e22df..daaf033 100644
--- a/public/articles/index.html
+++ b/public/articles/index.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/authors.html b/public/authors.html
index 3f9e6aa..df06082 100644
--- a/public/authors.html
+++ b/public/authors.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
@@ -68,7 +68,7 @@
<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 1.7.3, 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>.
+R package version 1.7.4, 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
@@ -76,7 +76,7 @@ DNAStringSet or a AAStringSet using a custom score matrix and conducts
codon based analysis},
author = {Kristian K Ullrich},
year = {2024},
- note = {R package version 1.7.3, https://mpievolbio-it.pages.gwdg.de/MSA2dist/},
+ note = {R package version 1.7.4, https://mpievolbio-it.pages.gwdg.de/MSA2dist/},
url = {https://gitlab.gwdg.de/mpievolbio-it/MSA2dist},
}</pre>
diff --git a/public/index.html b/public/index.html
index cece4c3..1b77b72 100644
--- a/public/index.html
+++ b/public/index.html
@@ -49,7 +49,7 @@
</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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/news/index.html b/public/news/index.html
index 965c32a..73f43c5 100644
--- a/public/news/index.html
+++ b/public/news/index.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
@@ -50,6 +50,11 @@
<small>Source: <a href="https://gitlab.gwdg.de/mpievolbio-it/msa2dist/blob/masterNEWS.md" class="external-link"><code>NEWS.md</code></a></small>
</div>
+ <div class="section level2">
+<h2 class="page-header" data-toc-text="1.7.4" id="msa2dist-174-2024-03-18">MSA2dist 1.7.4 (2024-03-18)<a class="anchor" aria-label="anchor" href="#msa2dist-174-2024-03-18"></a></h2>
+<p>BUG FIXES</p>
+<ul><li>fixed pal2nal</li>
+</ul></div>
<div class="section level2">
<h2 class="page-header" data-toc-text="1.7.3" id="msa2dist-173-2024-03-14">MSA2dist 1.7.3 (2024-03-14)<a class="anchor" aria-label="anchor" href="#msa2dist-173-2024-03-14"></a></h2>
<p>BUG FIXES</p>
diff --git a/public/pkgdown.yml b/public/pkgdown.yml
index 2082c37..f1f98f9 100644
--- a/public/pkgdown.yml
+++ b/public/pkgdown.yml
@@ -3,5 +3,5 @@ pkgdown: 2.0.7
pkgdown_sha: ~
articles:
MSA2dist: MSA2dist.html
-last_built: 2024-03-14T12:48Z
+last_built: 2024-03-18T11:57Z
diff --git a/public/reference/AAMatrix-data.html b/public/reference/AAMatrix-data.html
index 014c009..78c5bb5 100644
--- a/public/reference/AAMatrix-data.html
+++ b/public/reference/AAMatrix-data.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/GENETIC_CODE_TCAG.html b/public/reference/GENETIC_CODE_TCAG.html
index 9f4cfa5..b2185a9 100644
--- a/public/reference/GENETIC_CODE_TCAG.html
+++ b/public/reference/GENETIC_CODE_TCAG.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/aa2selfscore.html b/public/reference/aa2selfscore.html
index 7321363..187e1dd 100644
--- a/public/reference/aa2selfscore.html
+++ b/public/reference/aa2selfscore.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/aabin2aastring.html b/public/reference/aabin2aastring.html
index 2852f30..353e74c 100644
--- a/public/reference/aabin2aastring.html
+++ b/public/reference/aabin2aastring.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/aastring2aabin.html b/public/reference/aastring2aabin.html
index 913b0be..9e6089e 100644
--- a/public/reference/aastring2aabin.html
+++ b/public/reference/aastring2aabin.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/aastring2aln.html b/public/reference/aastring2aln.html
index 2cf6110..3f46bb5 100644
--- a/public/reference/aastring2aln.html
+++ b/public/reference/aastring2aln.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/aastring2dist.html b/public/reference/aastring2dist.html
index fc6fe46..3f697e8 100644
--- a/public/reference/aastring2dist.html
+++ b/public/reference/aastring2dist.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/addmask2string.html b/public/reference/addmask2string.html
index 0818dae..b902622 100644
--- a/public/reference/addmask2string.html
+++ b/public/reference/addmask2string.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/addpop2string.html b/public/reference/addpop2string.html
index 89a77d3..3ac12c6 100644
--- a/public/reference/addpop2string.html
+++ b/public/reference/addpop2string.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/addpos2string.html b/public/reference/addpos2string.html
index 5c71f0d..4b90f0b 100644
--- a/public/reference/addpos2string.html
+++ b/public/reference/addpos2string.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/addregion2string.html b/public/reference/addregion2string.html
index 21ccfd7..a56ee34 100644
--- a/public/reference/addregion2string.html
+++ b/public/reference/addregion2string.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/aln2aastring.html b/public/reference/aln2aastring.html
index 8aa75b8..30005bd 100644
--- a/public/reference/aln2aastring.html
+++ b/public/reference/aln2aastring.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/aln2dnastring.html b/public/reference/aln2dnastring.html
index eae6998..65366fc 100644
--- a/public/reference/aln2dnastring.html
+++ b/public/reference/aln2dnastring.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/cds2aa.html b/public/reference/cds2aa.html
index 69b1fd1..a492baa 100644
--- a/public/reference/cds2aa.html
+++ b/public/reference/cds2aa.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/cds2codonaln.html b/public/reference/cds2codonaln.html
index d48897e..c231aae 100644
--- a/public/reference/cds2codonaln.html
+++ b/public/reference/cds2codonaln.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/cdsstring2codonaln.html b/public/reference/cdsstring2codonaln.html
index 3b63bc5..a4cb850 100644
--- a/public/reference/cdsstring2codonaln.html
+++ b/public/reference/cdsstring2codonaln.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/codon2numberAMBIG.html b/public/reference/codon2numberAMBIG.html
index a863f32..64fa4d0 100644
--- a/public/reference/codon2numberAMBIG.html
+++ b/public/reference/codon2numberAMBIG.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/codon2numberTCAG.html b/public/reference/codon2numberTCAG.html
index a5b1657..bbb897b 100644
--- a/public/reference/codon2numberTCAG.html
+++ b/public/reference/codon2numberTCAG.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/codonmat2pnps.html b/public/reference/codonmat2pnps.html
index 2b17d62..e06795b 100644
--- a/public/reference/codonmat2pnps.html
+++ b/public/reference/codonmat2pnps.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/codonmat2xy.html b/public/reference/codonmat2xy.html
index a178fb5..645b28f 100644
--- a/public/reference/codonmat2xy.html
+++ b/public/reference/codonmat2xy.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/compareCodons.html b/public/reference/compareCodons.html
index 362b926..0013d82 100644
--- a/public/reference/compareCodons.html
+++ b/public/reference/compareCodons.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/dnabin2dnastring.html b/public/reference/dnabin2dnastring.html
index d90bb04..56491f7 100644
--- a/public/reference/dnabin2dnastring.html
+++ b/public/reference/dnabin2dnastring.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/dnastring2aln.html b/public/reference/dnastring2aln.html
index ddb515f..0b75585 100644
--- a/public/reference/dnastring2aln.html
+++ b/public/reference/dnastring2aln.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/dnastring2codonmat.html b/public/reference/dnastring2codonmat.html
index 0293544..14dec31 100644
--- a/public/reference/dnastring2codonmat.html
+++ b/public/reference/dnastring2codonmat.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/dnastring2dist.html b/public/reference/dnastring2dist.html
index aa12a45..aa5a600 100644
--- a/public/reference/dnastring2dist.html
+++ b/public/reference/dnastring2dist.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/dnastring2dnabin.html b/public/reference/dnastring2dnabin.html
index 57af89c..c0c61c3 100644
--- a/public/reference/dnastring2dnabin.html
+++ b/public/reference/dnastring2dnabin.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/dnastring2kaks.html b/public/reference/dnastring2kaks.html
index 7e81b92..b704733 100644
--- a/public/reference/dnastring2kaks.html
+++ b/public/reference/dnastring2kaks.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/getmask.html b/public/reference/getmask.html
index fe5c947..93ff0b4 100644
--- a/public/reference/getmask.html
+++ b/public/reference/getmask.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/getpos.html b/public/reference/getpos.html
index 5f8938e..e59ec94 100644
--- a/public/reference/getpos.html
+++ b/public/reference/getpos.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/gff2cds.html b/public/reference/gff2cds.html
index 462c7da..4253e25 100644
--- a/public/reference/gff2cds.html
+++ b/public/reference/gff2cds.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/globalDeletion.html b/public/reference/globalDeletion.html
index d6ca8a8..880e124 100644
--- a/public/reference/globalDeletion.html
+++ b/public/reference/globalDeletion.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/granthamMatrix.html b/public/reference/granthamMatrix.html
index fbe14ff..395fd34 100644
--- a/public/reference/granthamMatrix.html
+++ b/public/reference/granthamMatrix.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/hiv-data.html b/public/reference/hiv-data.html
index deff85a..481756f 100644
--- a/public/reference/hiv-data.html
+++ b/public/reference/hiv-data.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/index.html b/public/reference/index.html
index 0a59fdd..09f461b 100644
--- a/public/reference/index.html
+++ b/public/reference/index.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/indices2kaks.html b/public/reference/indices2kaks.html
index 3619655..7e62c4a 100644
--- a/public/reference/indices2kaks.html
+++ b/public/reference/indices2kaks.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/iupac-data.html b/public/reference/iupac-data.html
index 6aefb5c..b54ca34 100644
--- a/public/reference/iupac-data.html
+++ b/public/reference/iupac-data.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/iupacMatrix.html b/public/reference/iupacMatrix.html
index a6125bb..832a794 100644
--- a/public/reference/iupacMatrix.html
+++ b/public/reference/iupacMatrix.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/makePostalignedSeqs.html b/public/reference/makePostalignedSeqs.html
index 816b6c9..11e1176 100644
--- a/public/reference/makePostalignedSeqs.html
+++ b/public/reference/makePostalignedSeqs.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/pal2nal.html b/public/reference/pal2nal.html
index 28d6a46..5464a8c 100644
--- a/public/reference/pal2nal.html
+++ b/public/reference/pal2nal.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
@@ -72,6 +72,11 @@ the protein alignment into a codon alignment.</p>
<dt>nal</dt>
<dd><p><code>DNAStringSet</code> [mandatory]</p></dd>
+
+<dt>remove.gaps</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>
diff --git a/public/reference/popinteger.html b/public/reference/popinteger.html
index 69c5c0c..ddc9417 100644
--- a/public/reference/popinteger.html
+++ b/public/reference/popinteger.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/popnames.html b/public/reference/popnames.html
index 1fc17bf..7736ee7 100644
--- a/public/reference/popnames.html
+++ b/public/reference/popnames.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/rcpp_KaKs.html b/public/reference/rcpp_KaKs.html
index 5f5d62c..0c754da 100644
--- a/public/reference/rcpp_KaKs.html
+++ b/public/reference/rcpp_KaKs.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/rcpp_distSTRING.html b/public/reference/rcpp_distSTRING.html
index 145c88b..beda740 100644
--- a/public/reference/rcpp_distSTRING.html
+++ b/public/reference/rcpp_distSTRING.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/rcpp_pairwiseDeletionAA.html b/public/reference/rcpp_pairwiseDeletionAA.html
index 3b6f855..2b7c2e8 100644
--- a/public/reference/rcpp_pairwiseDeletionAA.html
+++ b/public/reference/rcpp_pairwiseDeletionAA.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/rcpp_pairwiseDeletionDNA.html b/public/reference/rcpp_pairwiseDeletionDNA.html
index 1ba8e5f..edc96b6 100644
--- a/public/reference/rcpp_pairwiseDeletionDNA.html
+++ b/public/reference/rcpp_pairwiseDeletionDNA.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/region.html b/public/reference/region.html
index 62502d2..589c966 100644
--- a/public/reference/region.html
+++ b/public/reference/region.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/regionused.html b/public/reference/regionused.html
index c2be335..f520102 100644
--- a/public/reference/regionused.html
+++ b/public/reference/regionused.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/string2region.html b/public/reference/string2region.html
index 769c907..beafed6 100644
--- a/public/reference/string2region.html
+++ b/public/reference/string2region.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/subString.html b/public/reference/subString.html
index 8176156..9217221 100644
--- a/public/reference/subString.html
+++ b/public/reference/subString.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
diff --git a/public/reference/uptriidx.html b/public/reference/uptriidx.html
index 0a201fc..a8d580c 100644
--- a/public/reference/uptriidx.html
+++ b/public/reference/uptriidx.html
@@ -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="">1.7.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7.4</span>
</span>
</div>
--
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