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<h3>
Steffen Möller pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/pal2nal">Debian Med / pal2nal</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pal2nal/commit/4f7f0eac281f33e7937dc5cdc402246673c68984">4f7f0eac</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2018-05-10T00:58:29+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 14.1</pre>
</li>
</ul>
<h4>2 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#69e27356ef629022720d868ab0c0e3394775b6c1">
README
</a>
</li>
<li class="file-stats">
<a href="#992cdea45ca8371ef49c159900cfda7e41578fc1">
pal2nal.pl
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="69e27356ef629022720d868ab0c0e3394775b6c1">
<a href="https://salsa.debian.org/med-team/pal2nal/commit/4f7f0eac281f33e7937dc5cdc402246673c68984#69e27356ef629022720d868ab0c0e3394775b6c1"><strong>README</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,8 +14,9 @@</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"># version 12.2 September 9, 2009 #</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"># version 13.0 July 26, 2010 #</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"># version 14.0 December 2, 2011 #</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"># version 14.1 October 17, 2017 #</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"># #</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"># Mikita Suyama (mikita@<span class="idiff left right">genome.med.kyoto-u.ac.jp)</span> #</span>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"># Mikita Suyama (mikita@<span class="idiff left right">bioreg.kyushu-u.ac.jp) </span> #</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"># #</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">#=================================================================#</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -35,6 +36,9 @@ The resulting codon-based DNA alignment can further be subjected</td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">to the calculation of synonymous (Ks) and non-synonymous (Ka)</span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">substitution rates.</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">The script is licensed under GPL v2.</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">#-----------#</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"># Reference</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -176,7 +180,7 @@ Example:</td>
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="plaintext">http://www.bork.embl.de/pal2nal</span>
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="plaintext"> or</span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="plaintext">http://www.genome.med.kyoto-u.ac.jp/cgi-bin/suyama/pal2nal/index.cgi</span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext">http://www.genome.med.kyoto-u.ac.jp/cgi-bin/suyama/pal2nal/index.cgi<span class="idiff left right"> (not working)</span></span>
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180
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="plaintext"></span>
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181
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="plaintext"></span>
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182
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="plaintext">#---------#</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -186,10 +190,10 @@ http://www.genome.med.kyoto-u.ac.jp/cgi-bin/suyama/pal2nal/index.cgi</td>
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186
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="plaintext">If you have any questions or comments, please email me:</span>
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187
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="plaintext"></span>
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192
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC192" class="line" lang="plaintext"> Mikita Suyama</span>
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="plaintext"> <span class="idiff left right">Center for Genomic Medicine,</span></span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="plaintext"> <span class="idiff left right">Graduate School of Medicine, Kyoto</span> University,</span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="plaintext"> <span class="idiff left right">606-8501 Kyoto</span>, JAPAN</span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="plaintext"> tel: +81 <span class="idiff left right">75 753 4383</span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="plaintext"> fax: +81 <span class="idiff left right">75 753 438</span>2</span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="plaintext"> email: mikita@<span class="idiff left right">genome.med.kyoto</span>-u.ac.jp</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext"> <span class="idiff left right">Medical Institute of Bioregulation</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext"> <span class="idiff left right">Kyushu</span> University,</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext"> <span class="idiff left right">812-8582 Fukuoka</span>, JAPAN</span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext"> tel: +81 <span class="idiff left right">92 642 6384</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext"> fax: +81 <span class="idiff left right">92 642 656</span>2</span>
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext"> email: mikita@<span class="idiff left right">bioreg.kyushu</span>-u.ac.jp</span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/perl</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># pal2nal.pl (c) 2017 Mikita Suyama <mikita@bioreg.kyushu-u.ac.jp></span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># pal2nal.pl (v14) Mikita Suyama</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># #----------------------------------------#</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># This script is licensed under GPL v2.0</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># #----------------------------------------#</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># pal2nal.pl (v14.1) Mikita Suyama</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Usage: pal2nal.pl pep.aln nuc.fasta [nuc.fasta...] [options] > output</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -56,6 +63,10 @@</td>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># NUC1 GCTTGTGATGAATTTGGTGCTCGTCATG--GGG---TTTTAA</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># NUC2 GCGGG-GACGACTGG---GCGTAGCAC---GGGGG-TTTTGA</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># </span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># v14.1</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># - licensed under GPL v2.0</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># 2017/10/17</span></span>
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59
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># v14.</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># - NCBI GenBank codon table</span></span>
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61
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># 1 Universal code</span></span>
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