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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/mafft">Debian Med / mafft</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mafft/-/commit/c8b1a350054f06c658f2596c29354b21005ac6e8">c8b1a350</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-07-31T01:39:48+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 7.487</pre>
</li>
</ul>
<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#171cea6c847639ec6a600b2378fe99ff36078c30">
core/Falign.c
</a>
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<li class="file-stats">
<a href="#bf392a27539c02d920458de76ae4ba00c5a3d6d0">
core/mafft.tmpl
</a>
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<li class="file-stats">
<a href="#fb792f1c5a19dfe68974be08a96f0756ba949034">
core/mltaln.h
</a>
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<li class="file-stats">
<a href="#f78a71af8bbf8cc2f6f313549d4da14bd3771359">
readme
</a>
</li>
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<h4>Changes:</h4>
<li id="171cea6c847639ec6a600b2378fe99ff36078c30">
<a href="https://salsa.debian.org/med-team/mafft/-/commit/c8b1a350054f06c658f2596c29354b21005ac6e8#171cea6c847639ec6a600b2378fe99ff36078c30"><strong>core/Falign.c</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">@@ -1553,6 +1553,23 @@ system( "less seqVec2 < /dev/tty > /dev/tty" );</td>
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1553
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<pre style="margin: 0;"> <span id="LC1553" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">chudanres</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">chudanres</span> <span class="p">)</span></span>
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1554
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1554
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<pre style="margin: 0;"> <span id="LC1554" class="line" lang="c"> <span class="p">{</span></span>
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1555
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<td class="new_line diff-line-num" data-linenumber="1555" 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">
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<pre style="margin: 0;"> <span id="LC1555" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// fprintf( stderr, "\n\n## CHUUDAN!!! at Falign_localhom\n" );</span></span>
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<pre style="margin: 0;">+<span id="LC1556" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// Added 2021/Jul/25.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1557" 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">
1557
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<pre style="margin: 0;">+<span id="LC1557" class="line" lang="c"> <span class="n" style="color: #333;">FreeCharMtx</span><span class="p">(</span> <span class="n" style="color: #333;">result1</span> <span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1558" 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">
1558
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<pre style="margin: 0;">+<span id="LC1558" class="line" lang="c"> <span class="n" style="color: #333;">FreeCharMtx</span><span class="p">(</span> <span class="n" style="color: #333;">result2</span> <span class="p">);</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="1559" 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">
1559
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<pre style="margin: 0;">+<span id="LC1559" class="line" lang="c"> <span class="n" style="color: #333;">FreeCharMtx</span><span class="p">(</span> <span class="n" style="color: #333;">tmpres1</span> <span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1560" 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">
1560
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<pre style="margin: 0;">+<span id="LC1560" class="line" lang="c"> <span class="n" style="color: #333;">FreeCharMtx</span><span class="p">(</span> <span class="n" style="color: #333;">tmpres2</span> <span class="p">);</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="1561" 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">
1561
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<pre style="margin: 0;">+<span id="LC1561" class="line" lang="c"> <span class="n" style="color: #333;">FreeCharMtx</span><span class="p">(</span> <span class="n" style="color: #333;">tmpseq1</span> <span class="p">);</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="1562" 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">
1562
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<pre style="margin: 0;">+<span id="LC1562" class="line" lang="c"> <span class="n" style="color: #333;">FreeCharMtx</span><span class="p">(</span> <span class="n" style="color: #333;">tmpseq2</span> <span class="p">);</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="1563" 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">
1563
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<pre style="margin: 0;">+<span id="LC1563" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">sgap1</span> <span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1564" 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">
1564
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<pre style="margin: 0;">+<span id="LC1564" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">egap1</span> <span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1565" 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">
1565
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<pre style="margin: 0;">+<span id="LC1565" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">sgap2</span> <span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1566" 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">
1566
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<pre style="margin: 0;">+<span id="LC1566" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">egap2</span> <span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1567" 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">
1567
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<pre style="margin: 0;">+<span id="LC1567" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">tmpptr1</span> <span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1568" 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">
1568
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<pre style="margin: 0;">+<span id="LC1568" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span> <span class="n" style="color: #333;">tmpptr2</span> <span class="p">);</span></span>
</pre>
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1569
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<pre style="margin: 0;">+<span id="LC1569" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if RND</span></span>
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1570
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<pre style="margin: 0;">+<span id="LC1570" class="line" lang="c"> <span class="n" style="color: #333;">FreeCharMtx</span><span class="p">(</span> <span class="n" style="color: #333;">rndseq1</span> <span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1571" 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">
1571
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<pre style="margin: 0;">+<span id="LC1571" class="line" lang="c"> <span class="n" style="color: #333;">FreeCharMtx</span><span class="p">(</span> <span class="n" style="color: #333;">rndseq2</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1572" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC1573" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">(</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1574" class="line" lang="c"> <span class="p">}</span></span>
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1558
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<pre style="margin: 0;"> <span id="LC1575" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<a href="https://salsa.debian.org/med-team/mafft/-/commit/c8b1a350054f06c658f2596c29354b21005ac6e8#bf392a27539c02d920458de76ae4ba00c5a3d6d0"><strong>core/mafft.tmpl</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#! /bin/bash </span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"><span class="nv" style="color: #008080;">er</span><span class="o" style="font-weight: 600;">=</span>0<span class="p">;</span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">myself</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">dirname</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$0</span><span class="s2" style="color: #d14;">"</span><span class="sb" style="color: #d14;">`</span>/<span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">basename</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$0</span><span class="s2" style="color: #d14;">"</span><span class="sb" style="color: #d14;">`</span><span class="p">;</span> <span class="nb" style="color: #0086b3;">export </span>myself</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"v7.48<span class="idiff left">6</span> (2021/Jul/<span class="idiff right">19</span>)"</span><span class="p">;</span> <span class="nb" style="color: #0086b3;">export </span>version</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"v7.48<span class="idiff left">7</span> (2021/Jul/<span class="idiff right">25</span>)"</span><span class="p">;</span> <span class="nb" style="color: #0086b3;">export </span>version</span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">LANG</span><span class="o" style="font-weight: 600;">=</span>C<span class="p">;</span> <span class="nb" style="color: #0086b3;">export </span>LANG</span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="nv" style="color: #008080;">os</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">uname</span><span class="sb" style="color: #d14;">`</span></span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">basename</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$0</span><span class="s2" style="color: #d14;">"</span><span class="sb" style="color: #d14;">`</span></span>
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<a href="https://salsa.debian.org/med-team/mafft/-/commit/c8b1a350054f06c658f2596c29354b21005ac6e8#fb792f1c5a19dfe68974be08a96f0756ba949034"><strong>core/mltaln.h</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">@@ -36,7 +36,7 @@</td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define VERSION "7.48<span class="idiff left right">6</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define VERSION "7.48<span class="idiff left right">7</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define SHOWVERSION reporterr( "%s (%s) Version " VERSION "\nalg=%c, model=%s, amax=%3.1f\n%d thread(s)\n\n", progName( argv[0] ), (dorp=='d')?"nuc":((nblosum==-2)?"text":"aa"), alg, modelname, specificityconsideration, nthread )</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define FFT_THRESHOLD 80</span></span>
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<a href="https://salsa.debian.org/med-team/mafft/-/commit/c8b1a350054f06c658f2596c29354b21005ac6e8#f78a71af8bbf8cc2f6f313549d4da14bd3771359"><strong>readme</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">-----------------------------------------------------------------------</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"> MAFFT: a multiple sequence alignment program</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> version 7.48<span class="idiff left">6</span>, 2021/Jul/<span class="idiff right">19</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> version 7.48<span class="idiff left">7</span>, 2021/Jul/<span class="idiff right">25</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> http://mafft.cbrc.jp/alignment/software/</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> katoh@ifrec.osaka-u.ac.jp</span>
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