diff --git a/DESCRIPTION b/DESCRIPTION
index 4b291b7f060475162d6145858302b6bbdfc8cb92..fee01df8ab96edaa92362bbf1bfc6e28e5d15160 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 77d195602ae87fd4fb2cc55ef6199a4f31a0af7e..b4b0a5a2234df7cc40ffb503eb2d125ab1b1be2f 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 48f7379e40343019aa1c83f70d5b97be3ca21721..22d916d200f366383314aa9affc5fc074cdda0bd 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 c515dcf84d7656f9aaa1d87f0e6971ff1b62d3b2..3f03c1af64d0f3cd72db02c561d1caeb47a437d1 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 56f62138cb12b79b1673451cf3b8c16637520fd5..14b77bb16146274166dec3367a6c2c02ce018a46 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 5aefc3769bf27d4a0a859cbd690a55af9c3d5279..6f39d7664afe614b0db14f9de6764891aa184736 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 3c571f4da0ee70b33e2d4dc6018e37c28458bc09..f11f3f4a3fce97c197e09664a6e1d16af7f321ae 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 bcc3fa44839a6a93b269e24b6474d1466607c897..7adcd733351fc47d61764dda7647eadfa46b3384 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 92e22df45dcc28e876264dfdab2fb5054f80b24e..daaf0337a9358bf4d321aeeb2320ec9f85e96f49 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 3f9e6aa316c6b0d1cd095561abf06c07be53fb67..df06082ca053a902f21457d1f15bf7a93d033230 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 cece4c392c989b59028eec7af8e4c3ef3d7d6cda..1b77b7216f8a07d6b494f6e24c16c6c29c4e3983 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 965c32af57549f0e94fba7f871a0a3ded1f620bc..73f43c541c545cac826e2a2e229af145864bc606 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 2082c37bdac084015ac13ff6173cb1c96bbd76d3..f1f98f9bd4ba394c7c3915d175fc0cba4d6bdb25 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 014c009d8f1a892e72e23d252938f3c59faf1618..78c5bb5a30586a5a8b4f3e8eb38760b2f9c68965 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 9f4cfa5ce2d871ffdae127db76c4a57f1704eaf2..b2185a9fc0fdf99d87193c6dfdc486008a111d1d 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 732136398c4eaae9e870b3ce387712f1f5636412..187e1ddfa47add1d8ff005d952abd90b1eb31db3 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 2852f301b0d4215b6cbb07f31c4260f107b549b9..353e74cd80098e2b1ff819cad9f20ed73ff9a486 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 913b0be83667c3e0785eadb64866e02f75cbdeb5..9e6089ef8e5da277e72675c81d1edbeb5fb7162d 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 2cf6110fda6317c15af9bbbaac5fd1508fb456f0..3f46bb504911c43f788f55e2bb985c9703720693 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 fc6fe46db9b06e3d59cd5c392d01392a4ef129ca..3f697e8eab4cc5a0e01413673bd878aaf16dd7a3 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 0818dae320df857bbbc27b25f01f9b5f383db739..b902622115cf67685e51ccb61c3c786b106f14ae 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 89a77d3ae983803ec3b25096ee0917af8c953190..3ac12c6d63ddc4ce92867c841d46ec3698d87aa4 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 5c71f0d585fc0cd8541b593f4b9887e93fd98216..4b90f0bbc193a1b2645c4135bda6b5b5b2d01cfe 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 21ccfd7c0a992200f3ce137ba8757e96196db9cf..a56ee34b16e85bf3f76caff244f4ff321f194e9e 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 8aa75b84c567d1d8d12c48883da71210fc84fb10..30005bd4619700a4511e60ac8df1ad1ab35a0140 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 eae69984e1d0c3d3400714fc1be7738144a301b8..65366fc81df83313300f6e6c4b62e9734093a252 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 69b1fd11a62bd9482a943bd0e28281cbb1250703..a492baa3db1a766bf69ec309585268bbbbf81513 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 d48897e6103822f60c562bcc9a66b2a666d4098a..c231aae13a698aeb9a562049be1b939a57dbdc61 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 3b63bc563e15b3176951e3f3ea49f611e38a6a2c..a4cb850b0ec86b63047c6a85cb18e4f68ae9b7b2 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 a863f325e05992b84bcd54baa212e89bd40ff572..64fa4d006dfc0341ee713edfce2d7f16738fde51 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 a5b165738f9d06d9f6a95537813902f615d8f454..bbb897b08d15fc16a0c604b87edb308eef0ec411 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 2b17d6256a4eb9fd2c9c79a9d941ea46bdcf379b..e06795bb003113f11358c790c2101424fca6cbf1 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 a178fb57e398fe85cbf498f6c81db70a73ffb006..645b28f5b70f831dd36136373e0a753f7ced4061 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 362b92663c7f07eec662a39d36b2ac226d333045..0013d82be1676f3da3f13d1950b4b9a252cc2211 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 d90bb04c8d5e110949bfd06e717f1593ed8800e2..56491f7cfc9344ef3ce183c560f4aa1ff9024377 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 ddb515f9334bfdb6fd1abcf35c023a62dbd2ba1e..0b7558507318d74793c3baafc809ba3d42e635b1 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 02935448dcd00bfa67e4f57c0b717cfa52c0ccdf..14dec31f79c8f478a401c02f687c4e4c1aeb5432 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 aa12a45ffdc1ea47d5412ccf7460102a47fdd8be..aa5a6005468b2ad82b7767d592c8366eb876c400 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 57af89caa05df6d1a45e11c681ef98244842d8d6..c0c61c3c3ce547560cf2503ab8ed270ea9033ece 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 7e81b92d2a81b592780ac29350cad9a0cb90c4c7..b70473316d8e0bdcf137b0cb8da66c259eb3946a 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 fe5c94721b6e1362727584329679277915fa6d69..93ff0b4e8bee4ce6a005eef63c2fdf9652a10f25 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 5f8938e744a0630d50686e436d873013d95a26f8..e59ec94b155d369f1cfafead0af3f145b4140e01 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 462c7da231942d51745afa1c137ca8930ef0ae12..4253e25ea8f3de91d52d363da5ea40bdf825338b 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 d6ca8a8a2e4462ad35316583b3838fd944227416..880e124a637a2536fa8dd78dd4deae95c11e07b5 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 fbe14ffd58842aaac76eb32c0132ed2c8abbc44c..395fd34ad7c4d7c84772ceed741c6e3d4a4923a5 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 deff85a03880178ffc6b36497fd53fd1be32f078..481756f901c2fe3823607f80dc98aed0d88ce4ff 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 0a59fdd57530396ddc90ddaee39f9c576be1f21c..09f461b233125db513e13ac0eaed35805cd828bb 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 36196559d36d70322ffd6fc9b1168eb946984b79..7e62c4aa3d949acad40707a6f35f0df4171d0138 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 6aefb5cb61a2920bf77b10506464181a45c37a1d..b54ca34ffab856d5f3d6cfd66c7c193fe373d6c2 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 a6125bbdf67da79af6a63982725b04821ddfee29..832a7940e7db42d1da903d108154af670211cbf6 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 816b6c96f7deb04cea2885be39b37b4edc0191b9..11e117651e11b1a4eb3751c946ced5a7c4c0a914 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 28d6a46f483703e65477a4872014bf313082cf1a..5464a8c7f7863aeceb45ef1690fa2b349dfa56fa 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 69c5c0c525add26099687a8792c74e1ab74c1bab..ddc9417052b6d70dc3022ebc77c8e80bc8c215a6 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 1fc17bf5d493c0a429ed7b842ecb5c4047c7fa5b..7736ee7d5b6e6781b524214862088a956459a0fb 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 5f5d62c5ac758a3c6d29f0f4775cf1c275eb49a3..0c754dab041281a966de25f3aa38382687901940 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 145c88bd2a09c15c5e44da4c61b9fe096d78f81c..beda740a074cbe7d308304d85ab0ffa0cb339411 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 3b6f8559d45b9c54ec302a5bf9ebabea2c5a1278..2b7c2e8aa76d128719cc20f5e5d3b9d9f6f5d36a 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 1ba8e5f230ad14faae5fb1ef2d7c089b56b3a068..edc96b6d38018bcdd45b869aaa9b629618e02691 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 62502d273aaf85a5445ff0238663d35dcb5dbde4..589c96654c8deb30f3f5b9a9723b80974c08f943 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 c2be3356fad7908ce7ddd9ea73e7dd2130980676..f5201029102fc0af8df6ce8074966e26352d6be0 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 769c907a173dfa23e40293985688ad2b9cd07ed3..beafed6d7a3642b0cd41f323427730e4101c7b4b 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 8176156ade8d74d2a6a2edd302a72a2c9545b265..921722125210f0efd015163e4fb0574a6511bf35 100644
--- a/public/reference/subString.html
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@@ -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 0a201fc3ddfa0205d57d19ecb2a66edcafae8d18..a8d580ca3c5ab7f6a904eb47d1aa82a97a3037a1 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>