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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/proteinortho">Debian Med / proteinortho</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/proteinortho/-/commit/3746e15da8bc7609707daf904845cd274344cd8f">3746e15d</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-04-20T18:33:16+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 6.0.30+dfsg</pre>
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</ul>
<h4>9 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a">
CHANGELOG
</a>
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<li class="file-stats">
<a href="#ff6936350384213d6f693f4d604134188ce088c8">
CHANGEUID
</a>
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<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
</a>
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
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<li class="file-stats">
<a href="#36a872632d316444cc5323d30503cc0b7ef33071">
manual.html
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<li class="file-stats">
<a href="#c9e37a96ac72f9ef076d7a41a57470524d63b36e">
proteinortho6.pl
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<a href="#e6d14c79cd4fd6390fadb1ca94af0c36b0671d26">
proteinorthoHelper.html
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<li class="file-stats">
<a href="#d0cbc2488744231506d0c284dad99f8cc4078553">
src/proteinortho2xml.pl
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<li class="file-stats">
<a href="#3439148ea7017354388f7c55043cc84986c1c394">
src/proteinortho_grab_proteins.pl
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<h4>Changes:</h4>
<li id="1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a">
<a href="https://salsa.debian.org/med-team/proteinortho/-/commit/3746e15da8bc7609707daf904845cd274344cd8f#1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a"><strong>CHANGELOG</strong></a>
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="plaintext">    10. Jan (5379)</span>
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="plaintext">            last update introduced a bug that removes the *.blast-graph if --step=3 is used</span>
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="plaintext">    29. Jan (5399)</span>
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="plaintext">            fixed a bug (https://gitlab.com/paulklemm_PHD/proteinortho/-/issues/44) involving the --isoform=trinity option (search pattern was too strict), thanks to Sasha Sh !</span></pre>
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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">\ No newline at end of file</td>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="plaintext">            fixed a bug (https://gitlab.com/paulklemm_PHD/proteinortho/-/issues/44) involving the --isoform=trinity option (search pattern was too strict), thanks to Sasha Sh !</span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="plaintext">    3. Feb (5444)</span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="plaintext">            fixed another --isoform=uniprot bug + more STDERR output </span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="plaintext">    15. Feb (5544)</span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="plaintext">            new -step=4 : for each orthology group (of proteinortho.tsv) build a hmm profile and search in the input files to enrich the group.</span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="plaintext">            proteinortho_grab_proteins.pl now supports multiple cpu threads (-cpus)</span>
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="plaintext">    6. April (5584)</span>
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="plaintext">            fixed a bug, where generated databases are always overwritten (https://gitlab.com/paulklemm_PHD/proteinortho/-/issues/48). Thanks to Bjoern </span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="plaintext">            fixed another bug that caused the compilation of proteinortho_clustering to fail on CentOS (OMP_PROC_BIND=true) (https://gitlab.com/paulklemm_PHD/proteinortho/-/issues/39). </span></pre>
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<li id="ff6936350384213d6f693f4d604134188ce088c8">
<a href="https://salsa.debian.org/med-team/proteinortho/-/commit/3746e15da8bc7609707daf904845cd274344cd8f#ff6936350384213d6f693f4d604134188ce088c8"><strong>CHANGEUID</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">5<span class="idiff left right">399</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">5<span class="idiff left right">584</span></span></pre>
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</li>
<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
<a href="https://salsa.debian.org/med-team/proteinortho/-/commit/3746e15da8bc7609707daf904845cd274344cd8f#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</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">@@ -60,8 +60,12 @@ UNAME_S=$(shell uname -s)_$(shell uname -m)</td>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># output dir of make (make install moves these to PREFIX)</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="make"><span class="nv" style="color: #008080;">BUILDDIR</span><span class="o" style="font-weight: 600;">=</span>src/BUILD/<span class="nv" style="color: #008080;">$(UNAME_S)</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="make"><span class="k" style="font-weight: 600;">ifndef</span> <span class="nv" style="color: #008080;">CC</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="make"><span class="nv" style="color: #008080;">CC</span><span class="o" style="font-weight: 600;">=</span>cc</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="make"><span class="k" style="font-weight: 600;">ifndef</span> <span class="nv" style="color: #008080;">CXX</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="make"><span class="nv" style="color: #008080;">CXX</span><span class="o" style="font-weight: 600;">=</span>g++</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="make"><span class="nv" style="color: #008080;">IS_COLOR_COMPATIBLE</span><span class="o" style="font-weight: 600;">:=</span><span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> tput color 2>/dev/null<span class="nf" style="color: #900; font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="make"><span class="k" style="font-weight: 600;">ifdef</span> <span class="nv" style="color: #008080;">IS_COLOR_COMPATIBLE</span></span>
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</li>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/proteinortho/-/commit/3746e15da8bc7609707daf904845cd274344cd8f#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
<hr>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="42" 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">@@ -42,7 +42,7 @@ Connected components within this graph can be considered as putative co-ortholog</td>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="markdown"> <span class="nt" style="color: #000080;"><details><summary></span>6.0.13: (Click to expand)<span class="nt" style="color: #000080;"></summary></span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="markdown"><span class="p">  -</span> added -p=autoblast : this option alows the comparison of aminoacid and nucleotide sequences. E.g. Proteom-vs-Genome: find the protein that corresponds to a given gene (/cluster). </span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="markdown"><span class="p">  -</span> added -isoform={ncbi,uniprot,trinity} option : The reciprocal best hit graph is build using isoform information (isoforms are treated equivalent).</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="markdown"><span class="p">  -</span> added -isoform={ncbi,uniprot,trinity} option : The reciprocal best hit graph is build using isoform information (isoforms are treated equivalent).<span class="idiff left"> </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">more information about --isoform</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://gitlab.com/paulklemm_PHD/proteinortho/-/wikis/FAQ#how-does-the-isoform-work</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="markdown"><span class="p">6.</span>0.14 : public release to https://usegalaxy.eu/</span>
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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">@@ -93,7 +93,7 @@ If you need brew (see [here](https://brew.sh/index_de))</td>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### <span class="idiff left right">Easy installation</span> with docker [![install with docker](https://img.shields.io/badge/install%20with-docker-brightgreen.svg?style=flat)](https://quay.io/repository/biocontainers/proteinortho)</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### <span class="idiff left right">Deploy</span> with docker [![install with docker](https://img.shields.io/badge/install%20with-docker-brightgreen.svg?style=flat)](https://quay.io/repository/biocontainers/proteinortho)</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="markdown"><span class="sb" style="color: #d14;">    docker pull quay.io/biocontainers/proteinortho:TAG</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="137" 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="137" 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">@@ -137,14 +137,14 @@ Or you can integrate proteinortho into your own galaxy instance using: [proteino</td>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="markdown"><span class="sb" style="color: #d14;"><br></span></span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="markdown"><span class="sb" style="color: #d14;">#### <span class="idiff left right">Easy i</span>nstallation with dpkg (root privileges are required)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="140" 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="LC140" class="line" lang="markdown"><span class="sb" style="color: #d14;">#### <span class="idiff left right">I</span>nstallation with dpkg (root privileges are required)</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="markdown"><span class="sb" style="color: #d14;">The deb package can be downloaded here: [https://packages.debian.org/unstable/proteinortho](https://packages.debian.org/unstable/proteinortho).</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="markdown"><span class="sb" style="color: #d14;">Afterwards the deb package can be installed with `sudo dpkg -i proteinortho*deb`.</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="markdown"></span>
</pre>
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="markdown"><span class="sb" style="color: #d14;"><br></span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="146" 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">
146
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<td class="new_line diff-line-num" data-linenumber="146" 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">
146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="markdown"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
147
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<td class="new_line diff-line-num old" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="markdown"><span class="sb" style="color: #d14;">#### *(<span class="idiff left right">Easy i</span>nstallation with apt-get)*</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="148" 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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<td class="new_line diff-line-num new" data-linenumber="147" 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">
147
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC147" class="line" lang="markdown"><span class="sb" style="color: #d14;">#### *(<span class="idiff left right">I</span>nstallation with apt-get)*</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="148" 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">
148
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<td class="new_line diff-line-num" data-linenumber="148" 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">
148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="markdown"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="149" 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">
149
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<td class="new_line diff-line-num" data-linenumber="149" 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">
149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="markdown"><span class="sb" style="color: #d14;">**! Disclamer: Work in progress !**</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="150" 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">
150
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<td class="new_line diff-line-num" data-linenumber="150" 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="LC150" class="line" lang="markdown"><span class="sb" style="color: #d14;">*proteinortho will be released to stable with Debian 11 (~2021), then proteinortho can be installed with `apt-get install proteinortho` (currently this installes the outdated version v5.16b)*</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="375" 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="375" 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">@@ -375,8 +375,10 @@ Open `proteinorthoHelper.html` in your favorite browser or visit [lechnerlab.de/</td>
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="markdown">    </details>     </span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="377" 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="LC377" class="line" lang="markdown">        </span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC378" class="line" lang="markdown">  - **--isoform**={ncbi,uniprot,trinity}</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="379" 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="LC378" class="line" lang="markdown">  - **--isoform**={ncbi,uniprot,trinity}<span class="idiff left right"> [more information about --isoform](https://gitlab.com/paulklemm_PHD/proteinortho/-/wikis/FAQ#how-does-the-isoform-work)</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="379" 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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<td class="new_line diff-line-num" data-linenumber="379" 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="LC379" class="line" lang="markdown">   </span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="380" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="380" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC380" class="line" lang="markdown">    Merge isoforms to a single entity. </span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="380" 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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<td class="new_line diff-line-num new" data-linenumber="381" 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">
381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="markdown"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="380" 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">
380
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<td class="new_line diff-line-num" data-linenumber="382" 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">
382
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="markdown">    <details><summary>ncbi</summary> </span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="381" 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">
381
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<td class="new_line diff-line-num" data-linenumber="383" 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">
383
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="markdown">        </span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="382" 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">
382
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<td class="new_line diff-line-num" data-linenumber="384" 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="LC384" class="line" lang="markdown">        isoforms are specified in ncbi style </span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="419" 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="421" 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">@@ -419,16 +421,13 @@ Open `proteinorthoHelper.html` in your favorite browser or visit [lechnerlab.de/</td>
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419
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<td class="new_line diff-line-num" data-linenumber="421" 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="LC421" class="line" lang="markdown">        (...)</span>
</pre>
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="markdown">        ---</span>
</pre>
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="markdown">        </span>
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<pre style="margin: 0;">-<span id="LC422" class="line" lang="markdown">        The protein id is TRINITY_DN1000_c115_g5a and the isoform id is specified with <span class="idiff left right">_</span>i1</span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="markdown">        The protein id is TRINITY_DN1000_c115_g5a and the isoform id is specified with i1</span>
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="markdown">        </span>
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="markdown">    </details></span>
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC428" class="line" lang="markdown"> **Search options (step 1-2)**</span>
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="markdown">  (output: <myproject>.blast-graph)</span>
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430
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC429" class="line" lang="markdown"><details></span>
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<pre style="margin: 0;">-<span id="LC430" class="line" lang="markdown">  <summary>(Click to expand)</summary></span>
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<pre style="margin: 0;">-<span id="LC431" class="line" lang="markdown"></span>
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<td class="new_line diff-line-num" data-linenumber="431" 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="LC431" class="line" lang="markdown">  - **--p**=algorithm (default: diamond) </span>
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC433" class="line" lang="markdown">    <details></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="443" 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="442" 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">@@ -443,10 +442,9 @@ Open `proteinorthoHelper.html` in your favorite browser or visit [lechnerlab.de/</td>
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<pre style="margin: 0;"> <span id="LC442" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;"> <span id="LC443" class="line" lang="markdown">        - diamond : Only for protein files! standard diamond procedure and for</span>
</pre>
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<pre style="margin: 0;"> <span id="LC444" class="line" lang="markdown">        genes/proteins of length >40 with the additional --sensitive flag</span>
</pre>
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<td class="new_line diff-line-num old" data-linenumber="445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC446" class="line" lang="markdown">        Warning: Please use version 0.9.29 or later to avoid this known bug: <span class="idiff left right">https://gitlab.com/paulklemm_PHD/proteinortho/issues/</span>24</span>
</pre>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="markdown">        Warning: Please use version 0.9.29 or later to avoid this known bug: <span class="idiff left right">#</span>24</span>
</pre>
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<pre style="margin: 0;"> <span id="LC446" class="line" lang="markdown"></span>
</pre>
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<td class="new_line diff-line-num old" data-linenumber="447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC448" class="line" lang="markdown">        - lastn,lastp : lastal. -n : dna files, -p protein files (BLOSUM62</span>
</pre>
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<pre style="margin: 0;">-<span id="LC449" class="line" lang="markdown">        scoring matrix)!</span>
</pre>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="markdown">        - lastn,lastp : lastal. -n : dna files, -p protein files (BLOSUM62 scoring matrix)!</span>
</pre>
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<pre style="margin: 0;"> <span id="LC448" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;"> <span id="LC449" class="line" lang="markdown">        - rapsearch : Only for protein files!</span>
</pre>
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<pre style="margin: 0;"> <span id="LC450" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="463" 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="461" 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">@@ -463,15 +461,18 @@ Open `proteinorthoHelper.html` in your favorite browser or visit [lechnerlab.de/</td>
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="markdown">    </details></span>
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="markdown">    <br></span>
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<pre style="margin: 0;"> <span id="LC463" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="markdown">  - **--sim**=float (default: 0.95)</span>
</pre>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="markdown">    min. reciprocal similarity for additional hits. 1 : only the best reciprocal hits are reported, 0 : all possible reciprocal blast matches (within the -evalue) are reported.</span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="markdown"><details></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="468" 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="LC468" class="line" lang="markdown">  <summary>More (Click to expand)</summary></span>
</pre>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="markdown"></span>
</pre>
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<td class="new_line diff-line-num" data-linenumber="470" 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="LC470" class="line" lang="markdown">  - **--e**=evalue (default: 1e-05)</span>
</pre>
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<pre style="margin: 0;"> <span id="LC471" class="line" lang="markdown">    E-value for blast</span>
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<pre style="margin: 0;"> <span id="LC472" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;"> <span id="LC473" class="line" lang="markdown">  - **--selfblast**</span>
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<td class="new_line diff-line-num" data-linenumber="474" 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="LC474" class="line" lang="markdown">    apply selfblast, detects paralogs without orthologs</span>
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<pre style="margin: 0;"> <span id="LC475" class="line" lang="markdown"></span>
</pre>
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<td class="new_line diff-line-num old" data-linenumber="476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC472" class="line" lang="markdown">  - **--sim**=float (default: 0.95)</span>
</pre>
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<td class="new_line diff-line-num old" data-linenumber="476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC473" class="line" lang="markdown">    min. similarity for additional hits</span>
</pre>
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<pre style="margin: 0;">-<span id="LC474" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;"> <span id="LC476" class="line" lang="markdown">  - **--identity**=number (default: 25)</span>
</pre>
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<pre style="margin: 0;"> <span id="LC477" class="line" lang="markdown">    min. percent identity of best blast hits</span>
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478
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="488" 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="489" 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">@@ -488,7 +489,7 @@ Open `proteinorthoHelper.html` in your favorite browser or visit [lechnerlab.de/</td>
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<pre style="margin: 0;"> <span id="LC489" class="line" lang="markdown">  (output: <myproject>.ffadj-graph, <myproject>.poff.tsv (tab separated file)-graph)</span>
</pre>
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<pre style="margin: 0;"> <span id="LC490" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;"> <span id="LC491" class="line" lang="markdown"><details></span>
</pre>
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<td class="new_line diff-line-num old" data-linenumber="492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC491" class="line" lang="markdown">  <summary>(Click to expand)</summary></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="492" 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="LC492" class="line" lang="markdown">  <summary><span class="idiff left right">More </span>(Click to expand)</summary></span>
</pre>
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493
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<pre style="margin: 0;"> <span id="LC493" class="line" lang="markdown"></span>
</pre>
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<td class="new_line diff-line-num" data-linenumber="494" 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="LC494" class="line" lang="markdown">  - **--synteny**</span>
</pre>
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<td class="new_line diff-line-num" data-linenumber="495" 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="LC495" class="line" lang="markdown">    activate PoFF extension to separate similar by contextual adjacencies</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="509" 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="510" 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">@@ -509,8 +510,12 @@ Open `proteinorthoHelper.html` in your favorite browser or visit [lechnerlab.de/</td>
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509
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<td class="new_line diff-line-num" data-linenumber="510" 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="LC510" class="line" lang="markdown"> **Clustering options (step 3)**</span>
</pre>
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<td class="new_line diff-line-num" data-linenumber="511" 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">
511
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<pre style="margin: 0;"> <span id="LC511" class="line" lang="markdown">  (output: <myproject>.proteinortho.tsv, <myproject>.proteinortho.html, <myproject>.proteinortho-graph)</span>
</pre>
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<td class="new_line diff-line-num" data-linenumber="512" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC512" class="line" lang="markdown"></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="512" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="513" 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="LC513" class="line" lang="markdown">  - **--conn**=float (default: 0.1)</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="512" 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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<td class="new_line diff-line-num new" data-linenumber="514" 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="LC514" class="line" lang="markdown">    min. algebraic connectivity. <b>This is the main parameter for the clustering step.</b> Choose larger values then more splits are done, resulting in more and smaller clusters. (There are still cluster with an alg. conn. below this given threshold allowed if the protein to species ratio is good enough, see -minspecies option below)</span>
</pre>
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="markdown"></span>
</pre>
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512
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516
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<pre style="margin: 0;"> <span id="LC516" class="line" lang="markdown"><details></span>
</pre>
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513
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<td class="new_line diff-line-num old" data-linenumber="517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC513" class="line" lang="markdown">  <summary>(Click to expand)</summary></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="514" 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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<td class="new_line diff-line-num new" data-linenumber="517" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC517" class="line" lang="markdown"></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="514" 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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<td class="new_line diff-line-num new" data-linenumber="518" 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">
518
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC518" class="line" lang="markdown">  <summary>More (Click to expand)</summary></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="514" 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">
514
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<td class="new_line diff-line-num" data-linenumber="519" 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">
519
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC519" class="line" lang="markdown"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="515" 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">
515
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<td class="new_line diff-line-num" data-linenumber="520" 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">
520
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC520" class="line" lang="markdown">  - **--singles**</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="516" 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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<td class="new_line diff-line-num" data-linenumber="521" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC521" class="line" lang="markdown">    report singleton genes without any hit</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="518" 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="523" 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">@@ -518,9 +523,6 @@ Open `proteinorthoHelper.html` in your favorite browser or visit [lechnerlab.de/</td>
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<td class="new_line diff-line-num" data-linenumber="523" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC523" class="line" lang="markdown">  - **--purity**=float (default: 1e-7)</span>
</pre>
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<td class="new_line diff-line-num" data-linenumber="524" 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">
524
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<pre style="margin: 0;"> <span id="LC524" class="line" lang="markdown">    avoid spurious graph assignments</span>
</pre>
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<td class="new_line diff-line-num" data-linenumber="525" 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">
525
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC525" class="line" lang="markdown"></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC521" class="line" lang="markdown">  - **--conn**=float (default: 0.1)</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC522" class="line" lang="markdown">    min. algebraic connectivity. <b>This is the main parameter for the clustering step.</b> Choose larger values then more splits are done, resulting in more and smaller clusters.</span>
</pre>
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<td class="new_line diff-line-num old" data-linenumber="526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC523" class="line" lang="markdown"></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="524" 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">
524
</td>
<td class="new_line diff-line-num" data-linenumber="526" 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">
526
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC526" class="line" lang="markdown">  - **--minspecies**=float (default: 1, must be >=0)</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="525" 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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<td class="new_line diff-line-num" data-linenumber="527" 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="LC527" class="line" lang="markdown">    min. number of genes per species. If a group is found with up to (minspecies) genes/species, it wont be split again (regardless of the connectivity).</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="526" 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">
526
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<td class="new_line diff-line-num" data-linenumber="528" 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">
528
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC528" class="line" lang="markdown"></span>
</pre>
</td>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="547" 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="549" 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">@@ -547,15 +549,15 @@ Open `proteinorthoHelper.html` in your favorite browser or visit [lechnerlab.de/</td>
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<td class="old_line diff-line-num" data-linenumber="547" 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">
547
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<td class="new_line diff-line-num" data-linenumber="549" 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">
549
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC549" class="line" lang="markdown"></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="548" 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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<td class="new_line diff-line-num" data-linenumber="550" 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">
550
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC550" class="line" lang="markdown"> **Misc options**</span>
</pre>
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<td class="new_line diff-line-num" data-linenumber="551" 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">
551
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<pre style="margin: 0;"> <span id="LC551" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="markdown">  - **--checkfasta**</span>
</pre>
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="markdown">    checks input fasta files if the given algorithm can process the given fasta file.</span>
</pre>
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;"> <span id="LC555" class="line" lang="markdown"><details></span>
</pre>
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551
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<pre style="margin: 0;"> <span id="LC556" class="line" lang="markdown">  <summary>(Click to expand)</summary></span>
</pre>
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557
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<pre style="margin: 0;"> <span id="LC557" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;"> <span id="LC558" class="line" lang="markdown">  - **--cleanblast**</span>
</pre>
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<pre style="margin: 0;"> <span id="LC559" class="line" lang="markdown">    cleans blast-graph with proteinortho_cleanupblastgraph</span>
</pre>
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<pre style="margin: 0;"> <span id="LC560" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">-<span id="LC556" class="line" lang="markdown">  - **--checkfasta**</span>
</pre>
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<pre style="margin: 0;">-<span id="LC557" class="line" lang="markdown">    checks input fasta files if the given algorithm can process the given fasta file.</span>
</pre>
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<pre style="margin: 0;">-<span id="LC558" class="line" lang="markdown"></span>
</pre>
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559
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561
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<pre style="margin: 0;"> <span id="LC561" class="line" lang="markdown">  - **--desc**</span>
</pre>
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<pre style="margin: 0;"> <span id="LC562" class="line" lang="markdown">    write description files (for NCBI FASTA input only)</span>
</pre>
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<pre style="margin: 0;"> <span id="LC563" class="line" lang="markdown"></span>
</pre>
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</li>
<li id="36a872632d316444cc5323d30503cc0b7ef33071">
<a href="https://salsa.debian.org/med-team/proteinortho/-/commit/3746e15da8bc7609707daf904845cd274344cd8f#36a872632d316444cc5323d30503cc0b7ef33071"><strong>manual.html</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="html"><span class="nt" style="color: #000080;"><h1</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"proteinortho"</span><span class="nt" style="color: #000080;">></span>Proteinortho<span class="nt" style="color: #000080;"></h1></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="html"></span>
</pre>
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<td class="new_line diff-line-num old" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Proteinortho is a tool to detect orthologous genes within different species. For doing so, it compares similarities of given gene sequences and clusters them to find significant groups. The algorithm was designed to handle large-scale data and can be applied to hundreds of species at one. Details can be found in <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-124"</span><span class="nt" style="color: #000080;">></span>Lechner et al., BMC Bioinformatics. 2011 Apr 28;12:124.<span class="nt" style="color: #000080;"></a></span></span>
</pre>
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<td class="new_line diff-line-num old" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="html">To enhance the prediction accuracy, the relative order of genes (synteny) can be used as additional feature for the discrimination of orthologs. The corresponding extension, namely PoFF (manuscript in preparation), is already build in Proteinortho. The general workflow of proteinortho is depicted [<span class="nt" style="color: #000080;"><img</span> <span class="na" style="color: #008080;">src=</span><span class="s" style="color: #d14;">"https://www.dropbox.com/s/7ubl1ginn3fmf8k/proteinortho_workflow.jpg?dl=0"</span> <span class="na" style="color: #008080;">alt=</span><span class="s" style="color: #d14;">"here"</span> <span class="nt" style="color: #000080;">/></span>].<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="html"><span class="nt" style="color: #000080;"><h1</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"newfeaturesofproteinorthoversion6"</span><span class="nt" style="color: #000080;">></span>New Features of Proteinortho Version 6!<span class="nt" style="color: #000080;"></h1></span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Proteinortho is a tool to detect orthologous genes within different species.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>For doing so, it compares similarities of given gene sequences and clusters them to find significant groups. </span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="html">The algorithm was designed to handle large-scale data and can be applied to hundreds of species at one. </span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="html">Details can be found in (<span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-124"</span><span class="nt" style="color: #000080;">></span>doi:10.1186/1471-2105-12-124<span class="nt" style="color: #000080;"></a></span>).</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="html">To enhance the prediction accuracy, the relative order of genes (synteny) can be used as additional feature for the discrimination of orthologs. The corresponding extension, namely PoFF (<span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0105015"</span><span class="nt" style="color: #000080;">></span>doi:10.1371/journal.pone.0105015<span class="nt" style="color: #000080;"></a></span>), is already build in Proteinortho. The general workflow of proteinortho: <span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="html"><span class="nt" style="color: #000080;"><p><img</span> <span class="na" style="color: #008080;">src=</span><span class="s" style="color: #d14;">"https://www.uni-marburg.de/de/fb16/ipc/ag-lechner/graph.png/@@images/image/unimr_lead_image_sd"</span> <span class="na" style="color: #008080;">alt=</span><span class="s" style="color: #d14;">"proteinortho.workflow.png"</span> <span class="na" style="color: #008080;">height=</span><span class="s" style="color: #d14;">"250"</span><span class="nt" style="color: #000080;">></p></span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="html"><span class="nt" style="color: #000080;"><p><strong></span>Input<span class="nt" style="color: #000080;"></strong></span>: Multiple fasta files (orange boxes) with many proteins/genes (circles). <span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>First an initial all vs. all comparison between all proteins of all species is performed to determine protein similarities (upper right image). <span class="nt" style="color: #000080;"><br></span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="html">The second stage is the clustering of similar genes to meaningful co-orthologous groups (lower right image). <span class="nt" style="color: #000080;"><br></span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="html">Connected components within this graph can be considered as putative co-orthologous groups in theory and are returned in the output (lower left image).<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="html"><span class="nt" style="color: #000080;"><p><strong></span>Output<span class="nt" style="color: #000080;"></strong></span>: Groups (*.proteinortho) and pairs (*.proteinortho-graph) of orthologs proteins/genes.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="html"><span class="nt" style="color: #000080;"><h1</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"new-features-of-proteinortho-version-6"</span><span class="nt" style="color: #000080;">></span>New Features of Proteinortho Version 6<span class="nt" style="color: #000080;"></h1></span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="html"><span class="nt" style="color: #000080;"><ul></span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p></span>Implementation of various Blast alternatives for step (for -step=2 the -p= options): Diamond, MMseqs2, Last, Topaz, Rapsearch2, Blat, Ublast and Usearch<span class="nt" style="color: #000080;"></p></li></span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p></span>Multithreading support for the clustering step (-step=3)<span class="nt" style="color: #000080;"></p></li></span></span>
</pre>
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12
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<td class="new_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p></span>Integration of the LAPACK Fortran Library for a faster clustering step (-step=3)<span class="nt" style="color: #000080;"></p></li></span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC15" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p></span>Integration of the bitscore weights in the connectivity calculation for more data dependant splits (-step=3)</span>
</pre>
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<td class="new_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="html"><span class="nt" style="color: #000080;"><details></span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="html"><span class="nt" style="color: #000080;"><summary></span>Minor features: (Click to expand)<span class="nt" style="color: #000080;"></summary></p></li></span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p></span>Output now supports OrthoXML (-xml) and HTML.<span class="nt" style="color: #000080;"></p></li></span></span>
</pre>
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<td class="new_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p></span>Various test routines (make test).<span class="nt" style="color: #000080;"></p></li></span></span>
</pre>
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<td class="new_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="23" 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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<td class="new_line diff-line-num new" data-linenumber="15" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC15" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>Implementation of various Blast alternatives for step (for -step=2 the -p= options): Diamond, MMseqs2, Last, Topaz, Rapsearch2, Blat, Ublast and Usearch<span class="nt" style="color: #000080;"></li></span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="23" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="16" 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="LC16" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>Multithreading support for the clustering step (-step=3)<span class="nt" style="color: #000080;"></li></span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="23" 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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<td class="new_line diff-line-num new" data-linenumber="17" 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="LC17" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>Integration of the LAPACK Fortran Library for a faster clustering step (-step=3)<span class="nt" style="color: #000080;"></li></span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="23" 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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<td class="new_line diff-line-num new" data-linenumber="18" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC18" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>Integration of the bitscore weights in the connectivity calculation for more data dependant splits (-step=3)<span class="nt" style="color: #000080;"></li></span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="23" 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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<td class="new_line diff-line-num new" 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="html"><span class="nt" style="color: #000080;"><li><p></span>Continuous Integration <span class="ni" style="color: #800080;">&amp;</span> Continuous Development <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://gitlab.com/paulklemm_PHD/proteinortho/pipelines"</span><span class="nt" style="color: #000080;">><img</span> <span class="na" style="color: #008080;">src=</span><span class="s" style="color: #d14;">"https://gitlab.com/paulklemm_PHD/proteinortho/badges/master/pipeline.svg"</span> <span class="na" style="color: #008080;">alt=</span><span class="s" style="color: #d14;">"pipeline status"</span><span class="nt" style="color: #000080;">></a></span> </span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="23" 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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<td class="new_line diff-line-num new" data-linenumber="20" 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">
20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="html"><span class="nt" style="color: #000080;"><details></p></span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="21" 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">
21
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC21" class="line" lang="html"><span class="nt" style="color: #000080;"><summary></span>New minor features: (Click to expand)<span class="nt" style="color: #000080;"></summary></span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="22" 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="LC22" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p></span>Output now supports OrthoXML (-xml) and HTML.<span class="nt" style="color: #000080;"></p></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="25" 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="LC25" class="line" lang="html"><span class="nt" style="color: #000080;"><li><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Tools%20and%20additional%20programs"</span><span class="nt" style="color: #000080;">></span>proteinortho_history.pl<span class="nt" style="color: #000080;"></a></span> a new tool for tracking proteins (or pairs of proteins) in the workflow of proteinortho.<span class="nt" style="color: #000080;"></li></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="html"><span class="nt" style="color: #000080;"><li><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Tools%20and%20additional%20programs"</span><span class="nt" style="color: #000080;">></span>proteinortho_summary.pl<span class="nt" style="color: #000080;"></a></li></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>Various test routines (make test).<span class="nt" style="color: #000080;"></li></span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p></span>New heuristics for connectivity calculation (-step=3).</span>
</pre>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="html"><span class="nt" style="color: #000080;"></details></p></li></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="html"><span class="nt" style="color: #000080;"></details><details></p></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="html"><span class="nt" style="color: #000080;"><summary></span>6.0.12: (Click to expand)<span class="nt" style="color: #000080;"></summary></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p></span>improved <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Tools%20and%20additional%20programs"</span><span class="nt" style="color: #000080;">></span>proteinortho_history.pl<span class="nt" style="color: #000080;"></a></span> : now the program is <span class="ni" style="color: #800080;">&quot;</span>smarter<span class="ni" style="color: #800080;">&quot;</span> in detecting files automatically<span class="nt" style="color: #000080;"></p></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="34" 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="LC34" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>added <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Tools%20and%20additional%20programs"</span><span class="nt" style="color: #000080;">></span>proteinortho_summary.pl<span class="nt" style="color: #000080;"></a></span> : a tool for summarizing the proteinortho-graph on species level. With the output it is easy to identify weak connected species.   <span class="nt" style="color: #000080;"></li></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p></span>removed the diamond spam</span>
</pre>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="html"><span class="nt" style="color: #000080;"></details></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="html"><span class="nt" style="color: #000080;"><details><summary></span>6.0.13: (Click to expand)<span class="nt" style="color: #000080;"></summary></p></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p></span>added -p=autoblast : this option alows the comparison of aminoacid and nucleotide sequences. E.g. Proteom-vs-Genome: find the protein that corresponds to a given gene (/cluster). <span class="nt" style="color: #000080;"></p></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>added -isoform={ncbi,uniprot,trinity} option : The reciprocal best hit graph is build using isoform information (isoforms are treated equivalent).</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="html"><span class="nt" style="color: #000080;"></details></li></span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="html"><span class="nt" style="color: #000080;"></ul></span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="html"><span class="nt" style="color: #000080;"><h1</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"continuousintegration"</span><span class="nt" style="color: #000080;">></span>Continuous Integration<span class="nt" style="color: #000080;"></h1></span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>supports</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="html">The badge </span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="html"><span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://gitlab.com/paulklemm_PHD/proteinortho/commits/master"</span><span class="nt" style="color: #000080;">><img</span> <span class="na" style="color: #008080;">src=</span><span class="s" style="color: #d14;">"https://gitlab.com/paulklemm_PHD/proteinortho/badges/master/pipeline.svg"</span> <span class="na" style="color: #008080;">alt=</span><span class="s" style="color: #d14;">"pipeline status"</span> <span class="nt" style="color: #000080;">/></a></span> indicates the current status of the continuous integration (CI) among various platforms (ubuntu, centos, debian, fedora) and GNU c++ versions (5, 6, latest)</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="html">The whole git repository gets deployed on a clean docker imager (gcc:latest,gcc:5,ubuntu:latest,fedora:latest,debian:latest,centos:latest) and compiled (make all) and tested (make test). The badge is green only if all test are passed. For more information see <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Continuous%20Integration"</span><span class="nt" style="color: #000080;">></span>Continuous Integration (proteinortho wiki)<span class="nt" style="color: #000080;"></a></span>.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="html"><span class="nt" style="color: #000080;"><h1</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"tableofcontents"</span><span class="nt" style="color: #000080;">></span>Table of Contents<span class="nt" style="color: #000080;"></h1></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="html"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>6.0.14 : public release to <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://usegalaxy.eu/"</span><span class="nt" style="color: #000080;">></span>https://usegalaxy.eu/<span class="nt" style="color: #000080;"></a></p></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>A more detailed list of all changes: <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://gitlab.com/paulklemm_PHD/proteinortho/blob/master/CHANGELOG"</span><span class="nt" style="color: #000080;">></span>CHANGELOG<span class="nt" style="color: #000080;"></a></p></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="html"><span class="nt" style="color: #000080;"><h1</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"table-of-contents"</span><span class="nt" style="color: #000080;">></span>Table of Contents<span class="nt" style="color: #000080;"></h1></span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="html"><span class="nt" style="color: #000080;"><ol></span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="html"><span class="nt" style="color: #000080;"><li><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#installation"</span><span class="nt" style="color: #000080;">></span>Installation<span class="nt" style="color: #000080;"></a></li></span></span>
</pre>
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<td class="new_line diff-line-num old" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="39" 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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<td class="new_line diff-line-num" data-linenumber="49" 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="LC49" class="line" lang="html"><span class="nt" style="color: #000080;"><li><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#synopsis"</span><span class="nt" style="color: #000080;">></span>Synopsis and Description<span class="nt" style="color: #000080;"></a></li></span></span>
</pre>
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<td class="new_line diff-line-num old" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="41" 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="LC50" class="line" lang="html"><span class="nt" style="color: #000080;"><li><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#options"</span><span class="nt" style="color: #000080;">></span>Options/Parameters<span class="nt" style="color: #000080;"></a></li></span></span>
</pre>
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<td class="new_line diff-line-num old" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="43" 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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<td class="new_line diff-line-num" data-linenumber="51" 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="LC51" class="line" lang="html"><span class="nt" style="color: #000080;"><li><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#poff"</span><span class="nt" style="color: #000080;">></span>PoFF synteny extension<span class="nt" style="color: #000080;"></a></li></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="html"></span>
</pre>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="html"><span class="nt" style="color: #000080;"><li><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#output"</span><span class="nt" style="color: #000080;">></span>Output description<span class="nt" style="color: #000080;"></a></li></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="47" 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="LC53" class="line" lang="html"><span class="nt" style="color: #000080;"><li><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#examples"</span><span class="nt" style="color: #000080;">></span>Examples<span class="nt" style="color: #000080;"></a></li></span></span>
</pre>
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<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
49
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<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="html"><span class="nt" style="color: #000080;"><li><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error-Codes"</span><span class="nt" style="color: #000080;">></span>Error Codes and Troubleshooting<span class="nt" style="color: #000080;"></a></span> <span class="ni" style="color: #800080;">&lt;</span>- look here if you cannot compile/run (proteinortho wiki)<span class="nt" style="color: #000080;"></li></span></span>
</pre>
</td>
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50
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<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
51
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<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="html"><span class="nt" style="color: #000080;"><li><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Large-compute-jobs-(the--jobs-option)"</span><span class="nt" style="color: #000080;">></span>Large compute jobs example<span class="nt" style="color: #000080;"></a></span> (proteinortho wiki)<span class="nt" style="color: #000080;"></li></span></span>
</pre>
</td>
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<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC53" class="line" lang="html"><span class="nt" style="color: #000080;"><li><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://gitlab.com/paulklemm_PHD/proteinortho/wikis/biological-example"</span><span class="nt" style="color: #000080;">></span>Biological example<span class="nt" style="color: #000080;"></a></span> (proteinortho wiki)<span class="nt" style="color: #000080;"></li></span></span>
</pre>
</td>
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54
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54
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="html"><span class="nt" style="color: #000080;"></ol></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="html"></span>
</pre>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Bug reports: See chapter 7. or send a mail to incoming+paulklemm-phd-proteinortho-7278443-issue-@incoming.gitlab.com (Please include the 'Parameter-vector' that is printed for all errors)</span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="html">You can also send a mail to lechner@staff.uni-marburg.de.<span class="nt" style="color: #000080;"></p></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="html"><span class="nt" style="color: #000080;"><h1</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"-proteinortho-wiki-https-gitlab-com-paulklemm_phd-proteinortho-wikis-table-of-contents"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://gitlab.com/paulklemm_PHD/proteinortho/wikis/"</span><span class="nt" style="color: #000080;">></span>Proteinortho-Wiki<span class="nt" style="color: #000080;"></a></span> Table of Contents<span class="nt" style="color: #000080;"></h1></span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="html"><span class="nt" style="color: #000080;"><ol></span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="html"><span class="nt" style="color: #000080;"><li><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Tools%20and%20additional%20programs"</span><span class="nt" style="color: #000080;">></span>Tools and additional programs<span class="nt" style="color: #000080;"></a></li></span></span>
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<td class="new_line diff-line-num new" data-linenumber="58" 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="LC58" class="line" lang="html"><span class="nt" style="color: #000080;"><li><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error-Codes"</span><span class="nt" style="color: #000080;">></span>Error Codes and Troubleshooting<span class="nt" style="color: #000080;"></a></span> <span class="ni" style="color: #800080;">&lt;</span>- look here if you cannot compile/run proteinortho<span class="nt" style="color: #000080;"></li></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="html"><span class="nt" style="color: #000080;"><li><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Large-compute-jobs-(the--jobs-option"</span><span class="nt" style="color: #000080;">></span>Large compute jobs example<span class="nt" style="color: #000080;"></a></span>)<span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="html"><span class="nt" style="color: #000080;"><li><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://gitlab.com/paulklemm_PHD/proteinortho/wikis/FAQ"</span><span class="nt" style="color: #000080;">></span>FAQ<span class="nt" style="color: #000080;"></a></span> <span class="nt" style="color: #000080;"><br></span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="html"><span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://gitlab.com/paulklemm_PHD/proteinortho/wikis/"</span><span class="nt" style="color: #000080;">></span>(...)<span class="nt" style="color: #000080;"></a></li></span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="html"><span class="nt" style="color: #000080;"></ol></span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Bug reports: Please have a look at chapter <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error-Codes"</span><span class="nt" style="color: #000080;">></span>2.<span class="nt" style="color: #000080;"></a></span> first or send a mail to incoming+paulklemm-phd-proteinortho-7278443-issue-@incoming.gitlab.com. (please include the <span class="ni" style="color: #800080;">&#39;</span>parameter-vector<span class="ni" style="color: #800080;">&#39;</span> that is printed for all errors)</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="html">You can also send mails to lechner@staff.uni-marburg.de. Any suggestions, feedback and comments are welcome!<span class="nt" style="color: #000080;"></p></span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="html"><span class="nt" style="color: #000080;"><h1</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"installation"</span><span class="nt" style="color: #000080;">></span>Installation<span class="nt" style="color: #000080;"></h1></span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="html"><span class="nt" style="color: #000080;"><p><strong></span>Proteinortho comes with precompiled binaries of all executables (Linux/x86) so you should be able to run perl proteinortho6.pl in the downloaded directory.<span class="nt" style="color: #000080;"></strong></span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span> <span class="nt" style="color: #000080;"><strong></span>Proteinortho comes with precompiled binaries of all executables (Linux/x86) so you should be able to run perl proteinortho6.pl in the downloaded directory.<span class="nt" style="color: #000080;"></strong></span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="html">You could also move all executables to your favorite directory (e.g. with make install PREFIX=/home/paul/bin).</span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="html">If you cannot execute the src/BUILD/Linux<span class="nt" style="color: #000080;"><em></span>x86<span class="nt" style="color: #000080;"></em></span>64/proteinortho_clustering, then you have to recompile with make, see the section 2. Building and installing proteinortho from source.<span class="nt" style="color: #000080;"></p></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="html"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="html">If you cannot execute the src/BUILD/Linux_x86_64/proteinortho_clustering, then you have to recompile with make, see the section 2. Building and installing proteinortho from source.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="html"><span class="nt" style="color: #000080;"><p><br></p></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="html"><span class="nt" style="color: #000080;"><h4</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"easy-installation-with-bio-conda-for-linux-osx-install-with-bioconda-https-img-shields-io-badge-install-20with-bioconda-brightgreen-svg-style-flat-http-bioconda-github-io-recipes-proteinortho-readme-html-alt-https-img-shields-io-conda-dn-bioconda-proteinortho-svg-style-flat-https-bioconda-github-io-recipes-proteinortho-readme-html-"</span><span class="nt" style="color: #000080;">></span>Easy installation with (bio)conda (for Linux + OSX) <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"http://bioconda.github.io/recipes/proteinortho/README.html"</span><span class="nt" style="color: #000080;">><img</span> <span class="na" style="color: #008080;">src=</span><span class="s" style="color: #d14;">"https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat"</span> <span class="na" style="color: #008080;">alt=</span><span class="s" style="color: #d14;">"install with bioconda"</span><span class="nt" style="color: #000080;">></a></span> <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://bioconda.github.io/recipes/proteinortho/README.html"</span><span class="nt" style="color: #000080;">><img</span> <span class="na" style="color: #008080;">src=</span><span class="s" style="color: #d14;">"https://img.shields.io/conda/dn/bioconda/proteinortho.svg?style=flat"</span> <span class="na" style="color: #008080;">alt=</span><span class="s" style="color: #d14;">"alt"</span><span class="nt" style="color: #000080;">></a></h4></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="html"><span class="nt" style="color: #000080;"><pre><code></span>conda <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"hljs-keyword"</span><span class="nt" style="color: #000080;">></span>install<span class="nt" style="color: #000080;"></span></span> proteinortho</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="66" 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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<td class="new_line diff-line-num new" data-linenumber="72" 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="LC72" class="line" lang="html"><span class="nt" style="color: #000080;"></code></pre><p></span>If you need conda (see <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://docs.anaconda.com/anaconda/install/"</span><span class="nt" style="color: #000080;">></span>here<span class="nt" style="color: #000080;"></a></span>) and the bioconda channel: <span class="nt" style="color: #000080;"><code></span>conda config --add channels defaults <span class="ni" style="color: #800080;">&amp;&amp;</span> conda config --add channels bioconda <span class="ni" style="color: #800080;">&amp;&amp;</span> conda config --add channels conda-forge<span class="nt" style="color: #000080;"></code></span>.<span class="nt" style="color: #000080;"></p></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="html"><span class="nt" style="color: #000080;"><p><br></p></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="html"><span class="nt" style="color: #000080;"><h4</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"easy-installation-with-brew-for-osx-install-with-brew-https-img-shields-io-badge-install-20with-brew-brightgreen-svg-style-flat-https-formulae-brew-sh-formula-proteinortho-dl-https-img-shields-io-badge-dynamic-json-svg-label-downloads-query-27analytics-27-27install-27-27365d-27-27proteinortho-27-url-https-3a-2f-2fformulae-brew-sh-2fapi-2fformula-2fproteinortho-json-color-green-https-formulae-brew-sh-formula-proteinortho-"</span><span class="nt" style="color: #000080;">></span>Easy installation with brew (for OSX) <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://formulae.brew.sh/formula/proteinortho"</span><span class="nt" style="color: #000080;">><img</span> <span class="na" style="color: #008080;">src=</span><span class="s" style="color: #d14;">"https://img.shields.io/badge/install%20with-brew-brightgreen.svg?style=flat"</span> <span class="na" style="color: #008080;">alt=</span><span class="s" style="color: #d14;">"install with brew"</span><span class="nt" style="color: #000080;">></a></span> <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://formulae.brew.sh/formula/proteinortho"</span><span class="nt" style="color: #000080;">><img</span> <span class="na" style="color: #008080;">src=</span><span class="s" style="color: #d14;">"https://img.shields.io/badge/dynamic/json.svg?label=downloads&amp;query=$[%27analytics%27][%27install%27][%27365d%27][%27proteinortho%27]&amp;url=https%3A%2F%2Fformulae.brew.sh%2Fapi%2Fformula%2Fproteinortho.json&amp;color=green"</span> <span class="na" style="color: #008080;">alt=</span><span class="s" style="color: #d14;">"dl"</span><span class="nt" style="color: #000080;">></a></h4></span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="75" 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="LC75" class="line" lang="html"><span class="nt" style="color: #000080;"><pre><code><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"hljs-keyword"</span><span class="nt" style="color: #000080;">></span>brew <span class="nt" style="color: #000080;"></span><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"hljs-keyword"</span><span class="nt" style="color: #000080;">></span>install <span class="nt" style="color: #000080;"></span></span>proteinortho</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="76" 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="LC76" class="line" lang="html"><span class="nt" style="color: #000080;"></code></pre><p></span>If you need brew (see <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://brew.sh/index_de"</span><span class="nt" style="color: #000080;">></span>here<span class="nt" style="color: #000080;"></a></span>)<span class="nt" style="color: #000080;"></p></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="html"><span class="nt" style="color: #000080;"><p><br></p></span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="78" 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="LC78" class="line" lang="html"><span class="nt" style="color: #000080;"><h4</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"easy-installation-with-docker-install-with-docker-https-img-shields-io-badge-install-20with-docker-brightgreen-svg-style-flat-https-quay-io-repository-biocontainers-proteinortho-"</span><span class="nt" style="color: #000080;">></span>Easy installation with docker <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://quay.io/repository/biocontainers/proteinortho"</span><span class="nt" style="color: #000080;">><img</span> <span class="na" style="color: #008080;">src=</span><span class="s" style="color: #d14;">"https://img.shields.io/badge/install%20with-docker-brightgreen.svg?style=flat"</span> <span class="na" style="color: #008080;">alt=</span><span class="s" style="color: #d14;">"install with docker"</span><span class="nt" style="color: #000080;">></a></h4></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="html"><span class="nt" style="color: #000080;"><pre><code></span>docker pull quay.io<span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"hljs-regexp"</span><span class="nt" style="color: #000080;">></span>/biocontainers/<span class="nt" style="color: #000080;"></span><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"hljs-string"</span><span class="nt" style="color: #000080;">></span>proteinortho:<span class="nt" style="color: #000080;"></span></span>TAG</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="80" 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="LC80" class="line" lang="html"><span class="nt" style="color: #000080;"></code></pre><p></span>with TAG specified <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://quay.io/repository/biocontainers/proteinortho?tab=tags"</span><span class="nt" style="color: #000080;">></span>here<span class="nt" style="color: #000080;"></a></span> (e.g. 6.0.23--hfd40d39_0).<span class="nt" style="color: #000080;"></p></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="html"><span class="nt" style="color: #000080;"><details></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="html">  <span class="nt" style="color: #000080;"><summary></span>how to docker (Click to expand)<span class="nt" style="color: #000080;"></summary></span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="html"><span class="nt" style="color: #000080;"><h4</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"easyinstallationwithbiocondaforlinuxosx"</span><span class="nt" style="color: #000080;">></span>Easy installation with (bio)conda (for Linux + OSX)<span class="nt" style="color: #000080;"></h4></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="html"><span class="nt" style="color: #000080;"><pre><code></span>conda install proteinortho</span>
</pre>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="html"><span class="nt" style="color: #000080;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>If you need conda (see <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://docs.anaconda.com/anaconda/install/"</span><span class="nt" style="color: #000080;">></span>here<span class="nt" style="color: #000080;"></a></span>) and the bioconda channel: <span class="nt" style="color: #000080;"><code></span>conda config --add channels defaults <span class="ni" style="color: #800080;">&amp;&amp;</span> conda config --add channels bioconda <span class="ni" style="color: #800080;">&amp;&amp;</span> conda config --add channels conda-forge<span class="nt" style="color: #000080;"></code></span>.<span class="nt" style="color: #000080;"></p></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="html"><span class="nt" style="color: #000080;"><p><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"http://bioconda.github.io/recipes/proteinortho/README.html"</span><span class="nt" style="color: #000080;">><img</span> <span class="na" style="color: #008080;">src=</span><span class="s" style="color: #d14;">"https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat"</span> <span class="na" style="color: #008080;">alt=</span><span class="s" style="color: #d14;">"install with bioconda"</span> <span class="nt" style="color: #000080;">/></a></span> <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://bioconda.github.io/recipes/proteinortho/README.html"</span><span class="nt" style="color: #000080;">><img</span> <span class="na" style="color: #008080;">src=</span><span class="s" style="color: #d14;">"https://img.shields.io/conda/dn/bioconda/proteinortho.svg?style=flat"</span> <span class="na" style="color: #008080;">alt=</span><span class="s" style="color: #d14;">"alt"</span> <span class="nt" style="color: #000080;">/></a></p></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="html">  <span class="nt" style="color: #000080;"><br></span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left"><p><br></span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff right"></p></span></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="html"><span class="idiff left right">  To start a bash shell </span></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left"><h4</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">id=</span></span><span class="s" style="color: #d14;"><span class="idiff">"easyinstallationwithbrewforosx"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">Easy installation with brew (for OSX)</span><span class="nt" style="color: #000080;"><span class="idiff right"></h4</span>></span></span>
</pre>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="html"><span class="idiff left">  </span><span class="nt" style="color: #000080;"><span class="idiff"><code></span></span><span class="idiff">docker run --rm -it quay.io/biocontainers/proteinortho:6.0.22--hfd40d39_0 bash</span><span class="nt" style="color: #000080;"><span class="idiff right"></code</span>></span></span>
</pre>
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="html"></span>
</pre>
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<td class="new_line diff-line-num old" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left"><pre><code></span></span><span class="idiff right">brew install</span> proteinortho</span>
</pre>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left right"></code></pre></span></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="html"><span class="idiff left">  Here you can start/use</span> proteinortho<span class="idiff right">.</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="82" 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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<td class="new_line diff-line-num new" data-linenumber="91" 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">
91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="html"><span class="idiff left">  You can change </span><span class="ni" style="color: #800080;"><span class="idiff">&quot;</span></span><span class="idiff">6.0.22--hfd40d39_0</span><span class="ni" style="color: #800080;"><span class="idiff">&quot;</span></span><span class="idiff"> with any tag/version that is available </span><span class="nt" style="color: #000080;"><span class="idiff"><a</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">href=</span></span><span class="s" style="color: #d14;"><span class="idiff">"https://quay.io/repository/biocontainers/proteinortho?tab=tags"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">here</span><span class="nt" style="color: #000080;"><span class="idiff"></a></span></span><span class="idiff">. Sadly there is no </span><span class="ni" style="color: #800080;"><span class="idiff">&quot;</span></span><span class="idiff">:latest</span><span class="ni" style="color: #800080;"><span class="idiff">&quot;</span></span><span class="idiff right"> tag available ...</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="82" 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">
82
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left"><p></span></span><span class="idiff">If you need brew (see </span><span class="nt" style="color: #000080;"><span class="idiff"><a</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">href=</span></span><span class="s" style="color: #d14;"><span class="idiff">"https://brew.sh/index_de"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">here</span><span class="nt" style="color: #000080;"><span class="idiff"></a></span></span><span class="idiff">)</span><span class="nt" style="color: #000080;"><span class="idiff right"></p></span></span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="93" 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="LC93" class="line" lang="html"><span class="idiff left right">  ### Now lets try to mount your home in docker</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="84" 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">
84
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<td class="new_line diff-line-num" data-linenumber="94" 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">
94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left"><p><a</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">href=</span></span><span class="s" style="color: #d14;"><span class="idiff">"https://formulae.brew.sh/formula/proteinortho"</span></span><span class="nt" style="color: #000080;"><span class="idiff">><img</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">src=</span></span><span class="s" style="color: #d14;"><span class="idiff">"https://img.shields.io/badge/install%20with-brew-brightgreen.svg?style=flat"</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">alt=</span></span><span class="s" style="color: #d14;"><span class="idiff">"install with brew"</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">/></a></span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff"><a</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">href=</span></span><span class="s" style="color: #d14;"><span class="idiff">"https://formulae.brew.sh/formula/proteinortho"</span></span><span class="nt" style="color: #000080;"><span class="idiff">><img</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">src=</span></span><span class="s" style="color: #d14;"><span class="idiff">"https://img.shields.io/badge/dynamic/json.svg?label=downloads&amp;query=$[%27analytics%27][%27install%27][%27365d%27][%27proteinortho%27]&amp;url=https%3A%2F%2Fformulae.brew.sh%2Fapi%2Fformula%2Fproteinortho.json&amp;color=green"</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">alt=</span></span><span class="s" style="color: #d14;"><span class="idiff">"dl"</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff right">/></a></p></span></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="html"><span class="idiff left right">  This is neccessary if you want to access your local files:</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left right"><p><br></p</span>></span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="88" 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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<td class="new_line diff-line-num new" data-linenumber="97" 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="LC97" class="line" lang="html"><span class="idiff left">  </span><span class="nt" style="color: #000080;"><span class="idiff"><code></span></span><span class="idiff">docker run --rm --mount </span><span class="ni" style="color: #800080;"><span class="idiff">&quot;</span></span><span class="idiff">type=bind,src=/home/$(id -un),dst=/home/$(id -un)</span><span class="ni" style="color: #800080;"><span class="idiff">&quot;</span></span><span class="idiff"> -u $(id -u):$(id -g) -it quay.io/biocontainers/proteinortho:6.0.22--hfd40d39_0 bash</span><span class="nt" style="color: #000080;"><span class="idiff right"></code</span>></span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left"><h4</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">id=</span></span><span class="s" style="color: #d14;"><span class="idiff">"easyinstallationwithdocker"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">Easy installation</span> with docker<span class="nt" style="color: #000080;"><span class="idiff right"></h4></span></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="html"><span class="idiff left">  now you have your home directory mounted to /home/YOURNAME. (load your bashrc</span> with<span class="idiff">in</span> docker<span class="idiff"> : </span><span class="nt" style="color: #000080;"><span class="idiff"><code></span></span><span class="idiff">source /home/YOURNAME/.bashrc</span><span class="nt" style="color: #000080;"><span class="idiff"></code></span></span><span class="idiff right">)</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="html"><span class="nt" style="color: #000080;"><pre><code></span>docker pull quay.io/biocontainers/proteinortho</span>
</pre>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="html"><span class="nt" style="color: #000080;"></code></pre></span></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="html"><span class="nt" style="color: #000080;"><<span class="idiff left">p><a</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">href=</span></span><span class="s" style="color: #d14;"><span class="idiff">"https://quay.io/repository/biocontainers/proteinortho"</span></span><span class="nt" style="color: #000080;"><span class="idiff">><img</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">src=</span></span><span class="s" style="color: #d14;"><span class="idiff">"https://img.shields.io/badge/install%20with-docker-brightgreen.svg?style=flat"</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">alt=</span></span><span class="s" style="color: #d14;"><span class="idiff">"install with docker"</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff right">/></a></p</span>></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="html"><span class="nt" style="color: #000080;"><<span class="idiff left right">/details</span>></span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="html"></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="html"><span class="nt" style="color: #000080;"><p><br></p></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="html"><span class="nt" style="color: #000080;"><h4</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"easyinstallationwithdpkgrootprivilegesarerequired"</span><span class="nt" style="color: #000080;">></span>Easy installation with dpkg (root privileges are required)<span class="nt" style="color: #000080;"></h4></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="html"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="html"><span class="nt" style="color: #000080;"><h4</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"available-at-galaxy-europe"</span><span class="nt" style="color: #000080;">></span>Available at Galaxy Europe<span class="nt" style="color: #000080;"></h4></span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="106" 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="LC106" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Simply go to the european galaxy server and search for proteinortho:<span class="nt" style="color: #000080;"></p></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="html"><span class="nt" style="color: #000080;"><pre><code><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"hljs-symbol"</span><span class="nt" style="color: #000080;">></span>https:<span class="nt" style="color: #000080;"></span><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"hljs-comment"</span><span class="nt" style="color: #000080;">></span>//usegalaxy.eu<span class="nt" style="color: #000080;"></span></span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="108" 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="LC108" class="line" lang="html"><span class="nt" style="color: #000080;"></code></pre><p></span>Or you can integrate proteinortho into your own galaxy instance using: <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://toolshed.g2.bx.psu.edu/view/iuc/proteinortho/4850f0d15f01"</span><span class="nt" style="color: #000080;">></span>proteinortho (iuc repository)<span class="nt" style="color: #000080;"></a></p></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="html"><span class="nt" style="color: #000080;"><p><br></p></span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="html"><span class="nt" style="color: #000080;"><h4</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"easy-installation-with-dpkg-root-privileges-are-required-"</span><span class="nt" style="color: #000080;">></span>Easy installation with dpkg (root privileges are required)<span class="nt" style="color: #000080;"></h4></span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>The deb package can be downloaded here: <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://packages.debian.org/unstable/proteinortho"</span><span class="nt" style="color: #000080;">></span>https://packages.debian.org/unstable/proteinortho<span class="nt" style="color: #000080;"></a></span>.</span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="html">Afterwards the deb package can be installed with <span class="nt" style="color: #000080;"><code></span>sudo dpkg -i proteinortho*deb<span class="nt" style="color: #000080;"></code></span>.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="html"></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="html"><span class="nt" style="color: #000080;"><p><br></p></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="html"><span class="nt" style="color: #000080;"><h4</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"easyinstallationwithaptget"</span><span class="nt" style="color: #000080;">><em></span>(Easy installation with apt-get)<span class="nt" style="color: #000080;"></em></h4></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="html"><span class="nt" style="color: #000080;"><h4</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"-easy-installation-with-apt-get-"</span><span class="nt" style="color: #000080;">><em></span>(Easy installation with apt-get)<span class="nt" style="color: #000080;"></em></h4></span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="html"><span class="nt" style="color: #000080;"><p><strong></span>! Disclamer: Work in progress !<span class="nt" style="color: #000080;"></strong></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="html"><span class="nt" style="color: #000080;"><em></span>proteinortho will be released to stable with Debian 11 (~2021), then proteinortho can be installed with <span class="nt" style="color: #000080;"><code></span>sudo apt-get install proteinortho<span class="nt" style="color: #000080;"></code></span> (currently this installes the outdated version v5.16b)<span class="nt" style="color: #000080;"></em></p></span></span>
</pre>
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<td class="new_line diff-line-num old" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="html"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="html"><span class="nt" style="color: #000080;"><em></span>proteinortho will be released to stable with Debian 11 (~2021), then proteinortho can be installed with <span class="nt" style="color: #000080;"><code></span>apt-get install proteinortho<span class="nt" style="color: #000080;"></code></span> (currently this installes the outdated version v5.16b)<span class="nt" style="color: #000080;"></em></p></span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="html"><span class="nt" style="color: #000080;"><p><br></p></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="html"></span>
</pre>
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<td class="new_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="html"><span class="nt" style="color: #000080;"><h4</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"1prerequisites"</span><span class="nt" style="color: #000080;">></span>1. Prerequisites<span class="nt" style="color: #000080;"></h4></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="html"></span>
</pre>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Proteinortho uses standard software which is often installed already or is part of then package repositories and can thus easily be installed. The sources come with a precompiled version of Proteinortho for 64bit Linux.<span class="nt" style="color: #000080;"></p></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="html"></span>
</pre>
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<td class="new_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="html"><span class="nt" style="color: #000080;"><p><details></span></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
117
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<td class="new_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="html">  <span class="nt" style="color: #000080;"><summary></span>To <span class="nt" style="color: #000080;"><b></span>run<span class="nt" style="color: #000080;"></b></span> Proteinortho, you need: (Click to expand)<span class="nt" style="color: #000080;"></summary></p></span></span>
</pre>
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118
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<td class="new_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC118" class="line" lang="html"></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC119" class="line" lang="html"><span class="nt" style="color: #000080;"><ul></span></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
120
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<td class="new_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p></span>At least one of the following the following programs (default is diamond):<span class="nt" style="color: #000080;"></p></span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
121
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<td class="new_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC121" class="line" lang="html"></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
122
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<td class="new_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC122" class="line" lang="html"><span class="nt" style="color: #000080;"><ul></span></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
123
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<td class="new_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC123" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>NCBI BLAST+ or NCBI BLAST legacy (to test this, type tblastn. apt-get install ncbi-blast+)<span class="nt" style="color: #000080;"></li></span></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC124" class="line" lang="html"></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC125" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>Diamond (apt-get install diamond, brew install diamond, conda install diamond, https://github.com/bbuchfink/diamond)<span class="nt" style="color: #000080;"></li></span></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC126" class="line" lang="html"></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
127
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<td class="new_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC127" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>Last (http://last.cbrc.jp/)<span class="nt" style="color: #000080;"></li></span></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num old" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC128" class="line" lang="html"></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num old" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
129
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<td class="new_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC129" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>Rapsearch (https://github.com/zhaoyanswill/RAPSearch2)<span class="nt" style="color: #000080;"></li></span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC130" class="line" lang="html"></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num old" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC131" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>Topaz (https://github.com/ajm/topaz)<span class="nt" style="color: #000080;"></li></span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC132" class="line" lang="html"></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num old" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
133
</td>
<td class="new_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC133" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>usearch (https://www.drive5.com/usearch/download.html)<span class="nt" style="color: #000080;"></li></span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
134
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<td class="new_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC134" class="line" lang="html"></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num old" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
135
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<td class="new_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC135" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>ublast (is part of usearch)<span class="nt" style="color: #000080;"></li></span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="html"></span>
</pre>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>blat (http://hgdownload.soe.ucsc.edu/admin/)<span class="nt" style="color: #000080;"></li></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="html"></span>
</pre>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>mmseqs2 (conda install mmseqs2, https://github.com/soedinglab/MMseqs2)<span class="nt" style="color: #000080;"></li></ul></li></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="html"></span>
</pre>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p></span>Perl v5.08 or higher (to test this, type perl -v in the command line)<span class="nt" style="color: #000080;"></p></li></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p></span>Python v2.6.0 or higher to include synteny analysis (to test this, type 'python -V' in the command line) <span class="nt" style="color: #000080;"></p></li></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p></span>Perl standard modules (these should come with Perl): Thread::Queue, File::Basename, Pod::Usage, threads (if you miss one just install with <span class="nt" style="color: #000080;"><code></span>cpan install ...<span class="nt" style="color: #000080;"></code></span> )</span>
</pre>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="html"><span class="nt" style="color: #000080;"></details></p></li></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="html"><span class="nt" style="color: #000080;"></ul></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="html"></span>
</pre>
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="html"><span class="nt" style="color: #000080;"><p><br></span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="150" 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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<td class="new_line diff-line-num new" data-linenumber="118" 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="LC118" class="line" lang="html"><span class="nt" style="color: #000080;"><h4</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"prerequisites-for-compiling-proteinortho-from-source"</span><span class="nt" style="color: #000080;">></span>Prerequisites for compiling proteinortho from source<span class="nt" style="color: #000080;"></h4></span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="119" 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="LC119" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Proteinortho uses standard software which is often installed already or is part of then package repositories and can thus easily be installed. The sources come with a precompiled version of Proteinortho for 64bit Linux x86.<span class="nt" style="color: #000080;"></p></span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="html"><span class="nt" style="color: #000080;"><details></span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="html">  <span class="nt" style="color: #000080;"><summary></span>To <span class="nt" style="color: #000080;"><b></span>compile<span class="nt" style="color: #000080;"></b></span> Proteinortho (linux/osx), you need: (Click to expand)<span class="nt" style="color: #000080;"></summary></p></span></span>
</pre>
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</td>
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="html"></span>
</pre>
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</td>
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="html"><span class="nt" style="color: #000080;"><ul></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>GNU make (to test this, type 'make' in the command line)<span class="nt" style="color: #000080;"></li></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="html"></span>
</pre>
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>GNU g++ v4.1 or higher (to test this, type 'g++ --version' in the command line) <span class="nt" style="color: #000080;"></li></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="html"></span>
</pre>
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>openmp (to test this, type 'g++ -fopenmp' in the command line) <span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="html"></span>
</pre>
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>(optional) gfortran for compiling LAPACK (to test this, type 'whereis gfortran' in the command line)<span class="nt" style="color: #000080;"></li></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>(optional) CMake for compiling LAPACK (to test this, type 'cmake' in the command line), OR you can use your own compiled version of lapack (you can get this with 'apt-get install liblapack3') and run 'make USEPRECOMPILEDLAPACK=TRUE'<span class="nt" style="color: #000080;"></li></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="html"><span class="nt" style="color: #000080;"></ul></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="html"><span class="nt" style="color: #000080;"><p></details></p></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="html">  <span class="nt" style="color: #000080;"><summary></span>To <span class="nt" style="color: #000080;"><b></span>run<span class="nt" style="color: #000080;"></b></span> Proteinortho, you need: (Click to expand)<span class="nt" style="color: #000080;"></summary></span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="html"></span>
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<td class="old_line diff-line-num new" data-linenumber="166" 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="LC123" class="line" lang="html"></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="124" 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="LC124" class="line" lang="html">   - At least one of the following the following programs (default is diamond):</span>
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<td class="new_line diff-line-num new" data-linenumber="125" 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="LC125" class="line" lang="html"></span>
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<td class="old_line diff-line-num new" data-linenumber="166" 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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<td class="new_line diff-line-num new" data-linenumber="126" 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="LC126" class="line" lang="html">     - NCBI BLAST+ or NCBI BLAST legacy (to test this, type tblastn. apt-get install ncbi-blast+)</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="127" 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="LC127" class="line" lang="html">     - Diamond (apt-get install diamond, brew install diamond, conda install diamond, <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://github.com/bbuchfink/diamond"</span><span class="nt" style="color: #000080;">></span>https://github.com/bbuchfink/diamond<span class="nt" style="color: #000080;"></a></span>)</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="128" 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="LC128" class="line" lang="html">     - Last (<span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"http://last.cbrc.jp/"</span><span class="nt" style="color: #000080;">></span>http://last.cbrc.jp/<span class="nt" style="color: #000080;"></a></span>)</span>
</pre>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="html">     - Rapsearch (<span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://github.com/zhaoyanswill/RAPSearch2"</span><span class="nt" style="color: #000080;">></span>https://github.com/zhaoyanswill/RAPSearch2<span class="nt" style="color: #000080;"></a></span>)</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="130" 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">
130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="html">     - Topaz (<span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://github.com/ajm/topaz"</span><span class="nt" style="color: #000080;">></span>https://github.com/ajm/topaz<span class="nt" style="color: #000080;"></a></span>)</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="131" 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">
131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="html">     - usearch (<span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://www.drive5.com/usearch/download.html"</span><span class="nt" style="color: #000080;">></span>https://www.drive5.com/usearch/download.html<span class="nt" style="color: #000080;"></a></span>)</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="132" 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">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="html">     - ublast (is part of usearch)</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="133" 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">
133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="html">     - blat (<span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"http://hgdownload.soe.ucsc.edu/admin/"</span><span class="nt" style="color: #000080;">></span>http://hgdownload.soe.ucsc.edu/admin/<span class="nt" style="color: #000080;"></a></span>)</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="134" 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">
134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="html">     - mmseqs2 (conda install mmseqs2, <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://github.com/soedinglab/MMseqs2"</span><span class="nt" style="color: #000080;">></span>https://github.com/soedinglab/MMseqs2<span class="nt" style="color: #000080;"></a></span>)</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="135" 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="LC135" class="line" lang="html">   - Perl v5.08 or higher (to test this, type perl -v in the command line)</span>
</pre>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="html">   - (optional) Python v3.0 or higher to include synteny analysis (to test this, type <span class="ni" style="color: #800080;">&#39;</span>python -V<span class="ni" style="color: #800080;">&#39;</span> in the command line)</span>
</pre>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="html">   - Perl standard modules (these should come with Perl): Thread::Queue, File::Basename, Pod::Usage, threads (if you miss one just install with <span class="nt" style="color: #000080;"><code></span>cpan install ...<span class="nt" style="color: #000080;"></code></span> )</span>
</pre>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="html"><span class="nt" style="color: #000080;"></details></span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="html"></span>
</pre>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="html"><span class="nt" style="color: #000080;"><p><br></p></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="html"><span class="nt" style="color: #000080;"><details></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="html">  <span class="nt" style="color: #000080;"><summary></span>To <span class="nt" style="color: #000080;"><b></span>compile<span class="nt" style="color: #000080;"></b></span> Proteinortho (linux/osx), you need: (Click to expand)<span class="nt" style="color: #000080;"></summary></span></span>
</pre>
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="html"></span>
</pre>
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<td class="new_line diff-line-num old" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="html"><span class="nt" style="color: #000080;"><h4</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"2buildingandinstallingproteinorthofromsourcelinuxandosx"</span><span class="nt" style="color: #000080;">></span>2. Building and installing proteinortho from source (linux and osx)<span class="nt" style="color: #000080;"></h4></span></span>
</pre>
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170
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<td class="new_line diff-line-num old" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="html"></span>
</pre>
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Here you can use a working lapack library, check this with 'dpkg --get-selections | grep lapack'. Install lapack e.g. with 'apt-get install libatlas3-base' or liblapack3.<span class="nt" style="color: #000080;"></p></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>If you dont have Lapack, then 'make' will automatically compiles Lapack v3.8.0 for you !<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="html"></span>
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<td class="old_line diff-line-num old" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Fetch the latest source code archive downloaded from <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://gitlab.com/paulklemm_PHD/proteinortho/-/archive/master/proteinortho-master.zip"</span><span class="nt" style="color: #000080;">></span>here<span class="nt" style="color: #000080;"></a></span> </span>
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<td class="new_line diff-line-num old" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="html"><span class="nt" style="color: #000080;"><details></span> <span class="nt" style="color: #000080;"><summary></span>or from here (Click to expand)<span class="nt" style="color: #000080;"></summary></p></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="html"><span class="nt" style="color: #000080;"><blockquote></span></span>
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="html">  <span class="nt" style="color: #000080;"><p></span>git clone https://gitlab.com/paulklemm_PHD/proteinortho<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="html">  </span>
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="html">  <span class="nt" style="color: #000080;"><p></span>wget https://gitlab.com/paulklemm_PHD/proteinortho/-/archive/master/proteinortho-master.zip</span>
</pre>
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="html">  <span class="nt" style="color: #000080;"></details></span></span>
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="html">  <span class="nt" style="color: #000080;"><br></p></span></span>
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="html"><span class="nt" style="color: #000080;"></blockquote></span></span>
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="html"></span>
</pre>
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="html"><span class="nt" style="color: #000080;"><ul></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code></span>tar -xzvf proteinortho*.tar.gz<span class="nt" style="color: #000080;"></code></span> or <span class="nt" style="color: #000080;"><code></span>unzip proteinortho*.zip<span class="nt" style="color: #000080;"></code></span> : Extract the files<span class="nt" style="color: #000080;"></li></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code></span>cd proteinortho*<span class="nt" style="color: #000080;"></code></span> : Change directory into the extracted folder<span class="nt" style="color: #000080;"></li></span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="144" 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="LC144" class="line" lang="html">   - GNU make (to test this, type <span class="ni" style="color: #800080;">&#39;</span>make<span class="ni" style="color: #800080;">&#39;</span> in the command line)</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="190" 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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<td class="new_line diff-line-num new" data-linenumber="145" 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="LC145" class="line" lang="html">   - GNU g++ v4.1 or higher (to test this, type <span class="ni" style="color: #800080;">&#39;</span>g++ --version<span class="ni" style="color: #800080;">&#39;</span> in the command line)</span>
</pre>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="html">   - openmp (to test this, type <span class="ni" style="color: #800080;">&#39;</span>g++ -fopenmp<span class="ni" style="color: #800080;">&#39;</span> in the command line)</span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="html">   - (optional) gfortran for compiling LAPACK (to test this, type <span class="ni" style="color: #800080;">&#39;</span>whereis gfortran<span class="ni" style="color: #800080;">&#39;</span> in the command line)</span>
</pre>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="html">   - (optional) CMake for compiling LAPACK (to test this, type <span class="ni" style="color: #800080;">&#39;</span>cmake<span class="ni" style="color: #800080;">&#39;</span> in the command line), OR you can use your own compiled version of lapack (you can get this with <span class="ni" style="color: #800080;">&#39;</span>apt-get install liblapack3<span class="ni" style="color: #800080;">&#39;</span>) and run <span class="ni" style="color: #800080;">&#39;</span>make USEPRECOMPILEDLAPACK=TRUE<span class="ni" style="color: #800080;">&#39;</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="html"></span>
</pre>
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<td class="new_line diff-line-num old" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="html"><span class="nt" style="color: #000080;"><<span class="idiff left">li></span></span><span class="idiff">You can now run proteinortho6.pl directly (linux only).</span><span class="nt" style="color: #000080;"><span class="idiff right"></li</span>></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="html"><span class="nt" style="color: #000080;"><<span class="idiff left right">/details</span>></span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="html"></span>
</pre>
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code></span>make clean <span class="ni" style="color: #800080;">&amp;&amp;</span> make<span class="nt" style="color: #000080;"></code></span> : If you want to recompile Proteinortho. (For osx you need a newer g++ compiler to support multithreading, see below)<span class="nt" style="color: #000080;"></li></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="html"><span class="nt" style="color: #000080;"><p><br></p></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="html"><span class="nt" style="color: #000080;"><h4</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"building-and-installing-proteinortho-from-source-linux-and-osx-"</span><span class="nt" style="color: #000080;">></span>Building and installing proteinortho from source (linux and osx)<span class="nt" style="color: #000080;"></h4></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>  Here you can use a working lapack library, check this with <span class="ni" style="color: #800080;">&#39;</span>dpkg --get-selections | grep lapack<span class="ni" style="color: #800080;">&#39;</span>. Install lapack e.g. with <span class="ni" style="color: #800080;">&#39;</span>apt-get install libatlas3-base<span class="ni" style="color: #800080;">&#39;</span> or liblapack3.<span class="nt" style="color: #000080;"></p></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>  If you dont have Lapack, then <span class="ni" style="color: #800080;">&#39;</span>make<span class="ni" style="color: #800080;">&#39;</span> will automatically compiles Lapack v3.8.0 for you !<span class="nt" style="color: #000080;"></p></span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="156" 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="LC156" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>  Fetch the latest source code archive downloaded from <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://gitlab.com/paulklemm_PHD/proteinortho/-/archive/master/proteinortho-master.zip"</span><span class="nt" style="color: #000080;">></span>here<span class="nt" style="color: #000080;"></a></p></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="html"><span class="nt" style="color: #000080;"><details></span> <span class="nt" style="color: #000080;"><summary></span>or from here (Click to expand)<span class="nt" style="color: #000080;"></summary></span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left"><li><code></span></span><span class="idiff">make install</span><span class="nt" style="color: #000080;"><span class="idiff"></code></span></span><span class="idiff"> or </span><span class="nt" style="color: #000080;"><span class="idiff"><code></span></span><span class="idiff">make install PREFIX=~/bin</span><span class="nt" style="color: #000080;"><span class="idiff"></code></span></span><span class="idiff"> if you dont have root privileges. </span><span class="nt" style="color: #000080;"><span class="idiff right"></li</span>></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="html"><span class="idiff left">  </span><span class="ni" style="color: #800080;"><span class="idiff">&gt;</span></span><span class="idiff"> git clone </span><span class="nt" style="color: #000080;"><span class="idiff"><a</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">href=</span></span><span class="s" style="color: #d14;"><span class="idiff">"https://gitlab.com/paulklemm_PHD/proteinortho"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">https://gitlab.com/paulklemm_PHD/proteinortho</span><span class="nt" style="color: #000080;"><span class="idiff right"></a</span>></span></span>
</pre>
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="html"></span>
</pre>
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197
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<td class="new_line diff-line-num old" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="html"><span class="nt" style="color: #000080;"><li><code></span>make test<span class="nt" style="color: #000080;"></code></span> : To make sure Proteinortho works as expected. The output should look like below (3. Make test output).<span class="nt" style="color: #000080;"></li></span></span>
</pre>
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198
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<td class="new_line diff-line-num old" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC198" class="line" lang="html"><span class="nt" style="color: #000080;"></ul></span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="199" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="161" 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">
161
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC161" class="line" lang="html">  <span class="ni" style="color: #800080;">&gt;</span> wget <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://gitlab.com/paulklemm_PHD/proteinortho/-/archive/master/proteinortho-master.zip"</span><span class="nt" style="color: #000080;">></span>https://gitlab.com/paulklemm_PHD/proteinortho/-/archive/master/proteinortho-master.zip<span class="nt" style="color: #000080;"></a></span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="199" 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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<td class="new_line diff-line-num new" data-linenumber="162" 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">
162
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC162" class="line" lang="html"><span class="nt" style="color: #000080;"></details></span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="199" 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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<td class="new_line diff-line-num new" data-linenumber="163" 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">
163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="html"><span class="nt" style="color: #000080;"><br></span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="199" 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">
199
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<td class="new_line diff-line-num" data-linenumber="164" 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">
164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="html"><span class="nt" style="color: #000080;"><p><details></span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
201
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<td class="new_line diff-line-num old" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC201" class="line" lang="html">  <span class="nt" style="color: #000080;"><summary><b></span>OSX additional informations (the -fopenmp error)<span class="nt" style="color: #000080;"></b></summary></p></span></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="202" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="165" 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">
165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="html">  - <span class="nt" style="color: #000080;"><code></span>tar -xzvf proteinortho*.tar.gz<span class="nt" style="color: #000080;"></code></span> or <span class="nt" style="color: #000080;"><code></span>unzip proteinortho*.zip<span class="nt" style="color: #000080;"></code></span> : Extract the files</span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="202" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="166" 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">
166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="html">  - <span class="nt" style="color: #000080;"><code></span>cd proteinortho*<span class="nt" style="color: #000080;"></code></span> : Change directory into the extracted folder</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="202" 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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<td class="new_line diff-line-num new" data-linenumber="167" 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">
167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="html">  - You can now run proteinortho6.pl directly (linux only).</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="202" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="168" 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">
168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="html">  - <span class="nt" style="color: #000080;"><code></span>make clean <span class="ni" style="color: #800080;">&amp;&amp;</span> make<span class="nt" style="color: #000080;"></code></span> : If you want to recompile Proteinortho. (For osx you need a newer g++ compiler to support multithreading, see below)</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="202" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="169" 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">
169
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC169" class="line" lang="html">  - <span class="nt" style="color: #000080;"><code></span>make install<span class="nt" style="color: #000080;"></code></span> or <span class="nt" style="color: #000080;"><code></span>make install PREFIX=~/bin<span class="nt" style="color: #000080;"></code></span> if you dont have root privileges.</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="202" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="170" 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">
170
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC170" class="line" lang="html">  - <span class="nt" style="color: #000080;"><code></span>make test<span class="nt" style="color: #000080;"></code></span> : To make sure Proteinortho works as expected. The output should look like below (3. Make test output).</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num" data-linenumber="202" 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">
202
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<td class="new_line diff-line-num" data-linenumber="171" 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">
171
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC171" class="line" lang="html"></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="203" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="172" 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">
172
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC172" class="line" lang="html"><span class="nt" style="color: #000080;"><details></span></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="203" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="173" 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">
173
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC173" class="line" lang="html">  <span class="nt" style="color: #000080;"><summary><b></span>OSX additional informations (the -fopenmp error)<span class="nt" style="color: #000080;"></b></summary></span></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num" data-linenumber="203" 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">
203
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<td class="new_line diff-line-num" data-linenumber="174" 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">
174
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC174" class="line" lang="html"><span class="nt" style="color: #000080;"><pre></span></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num old" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
204
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<td class="new_line diff-line-num old" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="html">Install a newer g++ compiler for -fopenmp support (multithreading) with brew (get brew here https://brew.sh/index_de)</span>
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="html"><span class="nt" style="color: #000080;"><pre><code></span>brew install gcc --without-multilib</span>
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="html"><span class="nt" style="color: #000080;"></code></pre></span></span>
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="html">Install a newer g++ compiler for -fopenmp support (multithreading) with brew (get brew here <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://brew.sh/index_de"</span><span class="nt" style="color: #000080;">></span>https://brew.sh/index_de<span class="nt" style="color: #000080;"></a></span>)</span>
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="html"></span>
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<td class="new_line diff-line-num old" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="html">Then you should have a g++-7 or whatever newer version that there is (g++-8,9,...). </span>
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="html">Next you have to tell make to use this new compiler with one of the following:<span class="nt" style="color: #000080;"><pre><code></span>ln -s /usr/local/bin/gcc-7 /usr/local/bin/gcc</span>
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<td class="new_line diff-line-num old" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="html">ln -s /usr/local/bin/g++-7 /usr/local/bin/g++</span>
</pre>
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="html"><span class="nt" style="color: #000080;"></code></pre></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="html"><span class="nt" style="color: #000080;"><code></span>brew install gcc --without-multilib<span class="nt" style="color: #000080;"></code></span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="html"></span>
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<td class="old_line diff-line-num old" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="html"><span class="idiff left right">OR(!) specify the new g++ in 'make CXX=/usr/local/bin/g++-7 all'</span></span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left right"></pre></span></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="html"></span>
</pre>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left right"><p></details></p</span>></span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="217" 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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<td class="new_line diff-line-num new" data-linenumber="179" 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="LC179" class="line" lang="html"><span class="idiff left right">Then you should have a g++-7 or whatever newer version that there is (g++-8,9,...).</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="217" 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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<td class="new_line diff-line-num new" data-linenumber="180" 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="LC180" class="line" lang="html"><span class="idiff left right">Next you have to tell make to use this new compiler with one of the following:</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="217" 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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<td class="new_line diff-line-num new" data-linenumber="181" 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="LC181" class="line" lang="html"><span class="nt" style="color: #000080;"><code></span>ln -s /usr/local/bin/gcc-7 /usr/local/bin/gcc</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="182" 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="LC182" class="line" lang="html"><span class="idiff left">ln -s /usr/local/bin/g++-7 /usr/local/bin/g++</span><span class="nt" style="color: #000080;"><span class="idiff right"></code</span>></span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="html"></span>
</pre>
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<td class="new_line diff-line-num old" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="html"><span class="nt" style="color: #000080;"><p><details></span></span>
</pre>
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219
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<td class="new_line diff-line-num old" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="html">  <span class="nt" style="color: #000080;"><summary></span>'make' successful output (Click to expand)<span class="nt" style="color: #000080;"></summary></p></span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="220" 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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<td class="new_line diff-line-num new" data-linenumber="184" 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">
184
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC184" class="line" lang="html">OR(!) specify the new g++ in <span class="ni" style="color: #800080;">&#39;</span>make CXX=/usr/local/bin/g++-7 all<span class="ni" style="color: #800080;">&#39;</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="220" 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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<td class="new_line diff-line-num new" data-linenumber="185" 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">
185
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC185" class="line" lang="html"><span class="nt" style="color: #000080;"></pre></span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="220" 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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<td class="new_line diff-line-num new" data-linenumber="186" 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">
186
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC186" class="line" lang="html"><span class="nt" style="color: #000080;"></details></span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="220" 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">
220
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<td class="new_line diff-line-num" data-linenumber="187" 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">
187
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC187" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="221" 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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<td class="new_line diff-line-num new" data-linenumber="188" 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">
188
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC188" class="line" lang="html"><span class="nt" style="color: #000080;"><details></span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="221" 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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<td class="new_line diff-line-num new" data-linenumber="189" 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">
189
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC189" class="line" lang="html">  <span class="nt" style="color: #000080;"><summary></span><span class="ni" style="color: #800080;">&#39;</span>make<span class="ni" style="color: #800080;">&#39;</span> successful output (Click to expand)<span class="nt" style="color: #000080;"></summary></span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="221" 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">
221
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<td class="new_line diff-line-num" data-linenumber="190" 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">
190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="html"><span class="nt" style="color: #000080;"><pre></span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="222" 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">
222
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<td class="new_line diff-line-num" data-linenumber="191" 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">
191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="html">[  0%] Prepare proteinortho_clustering ...</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
223
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<td class="new_line diff-line-num old" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="html">[ 20%] Building <span class="idiff left">**</span>proteinortho_clustering<span class="idiff right">**</span> with LAPACK (static/dynamic linking)</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
224
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<td class="new_line diff-line-num old" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC224" class="line" lang="html">[ 25%] Building <span class="idiff left">**</span>graphMinusRemovegraph<span class="idiff right">**</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
225
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<td class="new_line diff-line-num old" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC225" class="line" lang="html">[ 50%] Building <span class="idiff left">**</span>cleanupblastgraph<span class="idiff right">**</span></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
226
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<td class="new_line diff-line-num old" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC226" class="line" lang="html">[ 75%] Building <span class="idiff left right">**po_tree**</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="227" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="192" 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">
192
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC192" class="line" lang="html">[ 20%] Building <span class="nt" style="color: #000080;"><span class="idiff left"><strong></span></span>proteinortho_clustering<span class="nt" style="color: #000080;"><span class="idiff right"></strong></span></span> with LAPACK (static/dynamic linking)</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="227" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="193" 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">
193
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC193" class="line" lang="html">[ 25%] Building <span class="nt" style="color: #000080;"><span class="idiff left"><strong></span></span>graphMinusRemovegraph<span class="nt" style="color: #000080;"><span class="idiff right"></strong></span></span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="227" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="194" 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">
194
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC194" class="line" lang="html">[ 50%] Building <span class="nt" style="color: #000080;"><span class="idiff left"><strong></span></span>cleanupblastgraph<span class="nt" style="color: #000080;"><span class="idiff right"></strong></span></span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="227" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="195" 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">
195
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC195" class="line" lang="html">[ 75%] Building <span class="nt" style="color: #000080;"><span class="idiff left"><strong></span></span><span class="idiff">po_tree</span><span class="nt" style="color: #000080;"><span class="idiff right"></strong></span></span></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num" data-linenumber="227" 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">
227
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<td class="new_line diff-line-num" data-linenumber="196" 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">
196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="html">[100%] Everything is compiled with no errors.</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="228" 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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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="html"><span class="nt" style="color: #000080;"></pre></span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="229" 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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<td class="new_line diff-line-num" data-linenumber="198" 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">
198
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC198" class="line" lang="html"></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>The compilation of proteinortho_clustering has multiple fall-back routines. If everything fails please look here <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Codes"</span><span class="nt" style="color: #000080;">></span>Troubleshooting (proteinortho wiki)<span class="nt" style="color: #000080;"></a></span>.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="html"><span class="nt" style="color: #000080;"><p></details></p></span></span>
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="html">The compilation of proteinortho_clustering has multiple fall-back routines. If everything fails please look here <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Codes"</span><span class="nt" style="color: #000080;">></span>Troubleshooting (proteinortho wiki)<span class="nt" style="color: #000080;"></a></span>.</span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="html"><span class="nt" style="color: #000080;"><h4</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"3maketestoutput"</span><span class="nt" style="color: #000080;">></span>3. Make test output<span class="nt" style="color: #000080;"></h4></span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="html"><span class="nt" style="color: #000080;"><p><details></span></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="html">  <span class="nt" style="color: #000080;"><summary></span>'make test' successful output (Click to expand)<span class="nt" style="color: #000080;"></summary></p></span></span>
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="html"><span class="nt" style="color: #000080;"></details></span></span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="html"><span class="nt" style="color: #000080;"><h4</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"3-make-test-output"</span><span class="nt" style="color: #000080;">></span>3. Make test output<span class="nt" style="color: #000080;"></h4></span></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="html"><span class="nt" style="color: #000080;"><details></span></span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="html">  <span class="nt" style="color: #000080;"><summary></span><span class="ni" style="color: #800080;">&#39;</span>make test<span class="ni" style="color: #800080;">&#39;</span> successful output (Click to expand)<span class="nt" style="color: #000080;"></summary></span></span>
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="html">Everything is compiled with no errors.</span>
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="html">[TEST] 1. basic proteinortho6.pl -step=2 tests</span>
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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">@@ -252,42 +219,23 @@ Everything is compiled with no errors.</td>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="html"> [11/11] -p=mmseqsp (mmseqs) test: passed</span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="html">[TEST] 2. -step=3 tests (proteinortho_clustering)</span>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="html"> [1/2] various test functions of proteinortho_clustering (-test): passed</span>
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="html"> [2/2] Compare results of <span class="idiff left">'</span>with lapack<span class="idiff">' and '</span>without lapack<span class="idiff right">'</span>: passed</span>
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<td class="new_line diff-line-num new" data-linenumber="222" 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="LC222" class="line" lang="html"> [2/2] Compare results of <span class="ni" style="color: #800080;"><span class="idiff left">&#39;</span></span>with lapack<span class="ni" style="color: #800080;"><span class="idiff">&#39;</span></span><span class="idiff"> and </span><span class="ni" style="color: #800080;"><span class="idiff">&#39;</span></span>without lapack<span class="ni" style="color: #800080;"><span class="idiff right">&#39;</span></span>: passed</span>
</pre>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="html">[TEST] Clean up all test files...</span>
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<td class="old_line diff-line-num" data-linenumber="257" 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="LC224" class="line" lang="html">[TEST] All tests passed</span>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="html"><span class="nt" style="color: #000080;"></pre></span></span>
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="html"><span class="nt" style="color: #000080;"><p></details></p></span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="html"><span class="nt" style="color: #000080;"></details></span></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="html"></span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>If you have problems compiling/running the program go to <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Codes"</span><span class="nt" style="color: #000080;">></span>Troubleshooting (proteinortho wiki)<span class="nt" style="color: #000080;"></a></span>.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="html"></span>
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="html"><span class="nt" style="color: #000080;"><p><br></p></span></span>
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="html"></span>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="html"><span class="nt" style="color: #000080;"><h1</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"synopsis"</span><span class="nt" style="color: #000080;">></span>SYNOPSIS<span class="nt" style="color: #000080;"></h1></span></span>
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="html"><span class="nt" style="color: #000080;"><blockquote></span></span>
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="html">  <span class="nt" style="color: #000080;"><p><strong></span>proteinortho6.pl [options] \<span class="nt" style="color: #000080;"><fasta</span> <span class="na" style="color: #008080;">file</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">s</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)\</span><span class="nt" style="color: #000080;">></strong></span> (one fasta for each species, at least 2)<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="html"><span class="nt" style="color: #000080;"></blockquote></span></span>
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>OR<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="html"></span>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="html"><span class="nt" style="color: #000080;"><blockquote></span></span>
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="html"><span class="idiff left right">  </span><span class="nt" style="color: #000080;"><p><strong></span>proteinortho [options] \<span class="nt" style="color: #000080;"><fasta</span> <span class="na" style="color: #008080;">file</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">s</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)\</span><span class="nt" style="color: #000080;">></strong></p></span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="html"><span class="nt" style="color: #000080;"><p><strong></span>proteinortho [options] \<span class="nt" style="color: #000080;"><fasta</span> <span class="na" style="color: #008080;">file</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">s</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)\</span><span class="nt" style="color: #000080;">></strong></p></span></span>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="html"><span class="nt" style="color: #000080;"></blockquote></span></span>
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>   one fasta for each species; at least 2<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="html"><span class="nt" style="color: #000080;"><h1</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"description"</span><span class="nt" style="color: #000080;">></span>DESCRIPTION<span class="nt" style="color: #000080;"></h1></span></span>
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="html"><span class="nt" style="color: #000080;"><p><strong></span>proteinortho<span class="nt" style="color: #000080;"></strong></span> is a tool to detect orthologous genes within different</span>
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="html">  species. For doing so, it compares similarities of given gene sequences</span>
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="html">  and clusters them to find significant groups. The algorithm was designed</span>
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="html">  to handle large-scale data and can be applied to hundreds of species at</span>
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="html">  one. Details can be found in Lechner et al., BMC Bioinformatics. 2011 Apr</span>
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="html">  28;12:124. To enhance the prediction accuracy, the relative order of genes</span>
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="html">  (synteny) can be used as additional feature for the discrimination of</span>
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="html">  orthologs. The corresponding extension, namely PoFF (manuscript in</span>
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="html">  preparation), is already build in Proteinortho.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Proteinortho assumes, that you have all your gene sequences in FASTA</span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>  <span class="nt" style="color: #000080;"><strong></span>proteinortho<span class="nt" style="color: #000080;"></strong></span> is a tool to detect orthologous genes within different</span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="html">  species. <span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>  Proteinortho assumes, that you have all your gene sequences in FASTA</span>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="html">  format either represented as amino acids or as nucleotides. The source</span>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="html">  code archive contains some examples, namely C.faa, E.faa, L.faa, M.faa</span>
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="html">  located in the test/ directory. <span class="nt" style="color: #000080;"><strong></span>By default Proteinortho assumes amino<span class="nt" style="color: #000080;"></strong></span></span>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="html">  -p=blastn+ (or some other algorithm). (In case you have only have NCBI</span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="html">  BLAST legacy installed, you need to tell this too - either by adding</span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="html">  -p=blastp or -p=blastn respectively.) The full command for the example</span>
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="html">  files would thus be <span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="html">  files would thus be<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="html"><span class="nt" style="color: #000080;"><blockquote></span></span>
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="html"><span class="idiff left right">  </span><span class="nt" style="color: #000080;"><p></span>proteinortho6.pl -project=test test/C.faa test/E.faa<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>proteinortho6.pl -project=test test/C.faa test/E.faa<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="html"><span class="nt" style="color: #000080;"></blockquote></span></span>
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>test/L.faa test/M.faa. Instead of naming the FASTA files one by one, you</span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>  test/L.faa test/M.faa. Instead of naming the FASTA files one by one, you</span>
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="html">  could also use test/*.faa. Please note that the parameter</span>
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="html">  -project=test is optional, for naming the output. With this, you can set the prefix of the output</span>
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="html">  files generated by Proteinortho. If you skip the project parameter, the</span>
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="html">  default project name will be myproject.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="html"><span class="nt" style="color: #000080;"><h1</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"optionsgraphicaluserinterface"</span><span class="nt" style="color: #000080;">></span>OPTIONS graphical user interface<span class="nt" style="color: #000080;"></h1></span></span>
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="html"><span class="nt" style="color: #000080;"><h1</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"options-graphical-user-interface"</span><span class="nt" style="color: #000080;">></span>OPTIONS graphical user interface<span class="nt" style="color: #000080;"></h1></span></span>
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Open <span class="nt" style="color: #000080;"><code></span>proteinorthoHelper.html<span class="nt" style="color: #000080;"></code></span> in your favorite browser or visit <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"http://lechnerlab.de/proteinortho/"</span><span class="nt" style="color: #000080;">></span>lechnerlab.de/proteinortho<span class="nt" style="color: #000080;"></a></span> online for an interactiv exploration of the different options of proteinortho.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="html"></span>
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="html"><span class="nt" style="color: #000080;"><h1</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"options"</span><span class="nt" style="color: #000080;">></span>OPTIONS<span class="nt" style="color: #000080;"></h1></span></span>
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="html"><span class="nt" style="color: #000080;"><p><strong></span>Main parameters<span class="nt" style="color: #000080;"></strong></span> (can be used with -- or -)<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span> <span class="nt" style="color: #000080;"><strong></span>Main parameters<span class="nt" style="color: #000080;"></strong></span> (can be used with -- or -)<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="html"><span class="nt" style="color: #000080;"><ul></span></span>
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p><strong></span>--project<span class="nt" style="color: #000080;"></strong></span>=name (default: myproject)</span>
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="html">prefix for all resulting file names<span class="nt" style="color: #000080;"></p><span class="idiff left right"></li></span></span></span>
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="html">prefix for all resulting file names<span class="nt" style="color: #000080;"></p></span></span>
</pre>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
</pre>
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323
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<td class="new_line diff-line-num" data-linenumber="264" 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">
264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p><strong></span>--cpus<span class="nt" style="color: #000080;"></strong></span>=number (default: all available)</span>
</pre>
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324
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<td class="new_line diff-line-num" data-linenumber="265" 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">
265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="html">the number of processors to use (multicore/processor support)<span class="nt" style="color: #000080;"></p></span></span>
</pre>
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325
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<td class="new_line diff-line-num old" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="html"></span>
</pre>
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326
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266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="html"><span class="nt" style="color: #000080;"><ul></span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="327" 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">
327
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<td class="new_line diff-line-num" data-linenumber="267" 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">
267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p><strong></span>--ram<span class="nt" style="color: #000080;"></strong></span>=number (default: 90% of free memory)</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
328
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<td class="new_line diff-line-num old" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="html">maximal used ram threshold for LAPACK and the input graph in MB<span class="nt" style="color: #000080;"></p><span class="idiff left right"></li></span></span></span>
</pre>
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329
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="330" 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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<td class="new_line diff-line-num new" data-linenumber="268" 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">
268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="html">maximal used ram threshold for LAPACK and the input graph in MB<span class="nt" style="color: #000080;"></p></span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="269" 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">
269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
</pre>
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330
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<td class="new_line diff-line-num" data-linenumber="270" 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">
270
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p><strong></span>--verbose<span class="nt" style="color: #000080;"></strong></span>={0,1,2} (default: 1)</span>
</pre>
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331
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<td class="new_line diff-line-num old" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="html">verbose level. 1:keeps you informed about the progress<span class="nt" style="color: #000080;"></p><span class="idiff left right"></li></span></span></span>
</pre>
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332
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<td class="new_line diff-line-num old" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="333" 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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<td class="new_line diff-line-num new" data-linenumber="271" 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">
271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="html">verbose level. 1:keeps you informed about the progress<span class="nt" style="color: #000080;"></p></span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="272" 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">
272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
</pre>
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333
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<td class="new_line diff-line-num" data-linenumber="273" 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">
273
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p><strong></span>--silent<span class="nt" style="color: #000080;"></strong></span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
334
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<td class="new_line diff-line-num old" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="html">sets verbose level to 0.<span class="nt" style="color: #000080;"></p><span class="idiff left right"></li></span></span></span>
</pre>
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335
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<td class="new_line diff-line-num old" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC335" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="336" 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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<td class="new_line diff-line-num new" data-linenumber="274" 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">
274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="html">sets verbose level to 0.<span class="nt" style="color: #000080;"></p></span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="336" 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="LC275" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p><strong></span>--temp<span class="nt" style="color: #000080;"></strong></span>=directory(.)</span>
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337
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="html">path to the temporary files<span class="nt" style="color: #000080;"></p><span class="idiff left right"></li></span></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="html"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="html">path to the temporary files<span class="nt" style="color: #000080;"></p></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p><strong></span>--force<span class="nt" style="color: #000080;"></strong></span></span>
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="html">forces the recalculation of the blast results in any case in step=2. Also forces the recreation of the database generation in step=1<span class="nt" style="color: #000080;"></p><span class="idiff left right"></li></span></span></span>
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341
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="html"></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="html">forces the recalculation of the blast results in any case in step=2. Also forces the recreation of the database generation in step=1<span class="nt" style="color: #000080;"></p></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
</pre>
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342
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p><strong></span>--clean<span class="nt" style="color: #000080;"></strong></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="html">removes all database-index-files generated by the -p algorithm afterwards<span class="nt" style="color: #000080;"></p><span class="idiff left right"></li></span></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="html"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="html">removes all database-index-files generated by the -p algorithm afterwards<span class="nt" style="color: #000080;"></p></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p><strong></span>--step<span class="nt" style="color: #000080;"></strong></span>={0,1,2,3} (default: 0)</span>
</pre>
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="html">0 -> all. 1 -> prepare blast (build db). 2 -> run all-versus-all</span>
</pre>
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<pre style="margin: 0;">-<span id="LC347" class="line" lang="html">blast. 3 -> run the clustering.<span class="nt" style="color: #000080;"></p></li></ul></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC348" class="line" lang="html"></span>
</pre>
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="html"><span class="nt" style="color: #000080;"><p><strong></span>Search options (step 1-2)<span class="nt" style="color: #000080;"></strong></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="html">(output: <span class="nt" style="color: #000080;"><myproject></span>.blast-graph)<span class="nt" style="color: #000080;"></p></li></span></span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="html">0 -<span class="ni" style="color: #800080;">&gt;</span> all. 1 -<span class="ni" style="color: #800080;">&gt;</span> prepare blast (build db). 2 -<span class="ni" style="color: #800080;">&gt;</span> run all-versus-all</span>
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="html">blast. 3 -<span class="ni" style="color: #800080;">&gt;</span> run the clustering.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="html"><span class="nt" style="color: #000080;"></ul></span></span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="html"><span class="nt" style="color: #000080;"><details></span></span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="html"> <span class="nt" style="color: #000080;"><summary></span>(Show more information)<span class="nt" style="color: #000080;"></summary></span></span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="html">   proteinortho test/<span class="nt" style="color: #000080;"><em></span>faa </span>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC353" class="line" lang="html"><span class="nt" style="color: #000080;"><p><details></span></span>
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="html">  <span class="nt" style="color: #000080;"><summary></span>(Click to expand)<span class="nt" style="color: #000080;"></summary></p></span></span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="html">   # the following 3 commands are producing the same results as the command above</span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="html">   proteinortho -step=1 test/<span class="nt" style="color: #000080;"></em></span>faa </span>
</pre>
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="html">   proteinortho -step=2 test/*faa </span>
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="html">   proteinortho -step=3</span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="html"><span class="nt" style="color: #000080;"></details></span>   </span>
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="html"></span>
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="html"><span class="nt" style="color: #000080;"><ul></span></span>
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p><strong></span>--p<span class="nt" style="color: #000080;"></strong></span>=algorithm (default: diamond)<span class="nt" style="color: #000080;"></p></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="html"><span class="nt" style="color: #000080;"><li><strong></span>--keep<span class="nt" style="color: #000080;"></strong></span></span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="html">stores temporary blast results for reuse (same -project= name is mandatory)<span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="html"><span class="nt" style="color: #000080;"></ul></span></span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="html"><span class="nt" style="color: #000080;"><details></span></span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="html"> <span class="nt" style="color: #000080;"><summary></span>(Show more information)<span class="nt" style="color: #000080;"></summary></span></span>
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="html"><span class="nt" style="color: #000080;"><p><details></span></span>
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="html">  <span class="nt" style="color: #000080;"><summary></span>show all algorithms (Click to expand)<span class="nt" style="color: #000080;"></summary></p></span></span>
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="html">   # 1. generate db files</span>
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left"><pre><code></span></span><span class="idiff right">- autoblast,blastn_legacy,blastp_legacy,tblastx_legacy : legacy blast family (shell commands: blastall -) family. The suffix 'n' or 'p' indicates nucleotide or protein input files.</span></span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="html"><span class="idiff left">   proteinortho -step=1 -project=test -keep infile/</span><span class="nt" style="color: #000080;"><span class="idiff"><em></span></span><span class="idiff right">fasta</span></span>
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="html">- autoblast : standard blast+ family </span>
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<pre style="margin: 0;">-<span id="LC365" class="line" lang="html">automatically detects: blastn,blastp,tblastx,blastx depending on the input (can also be mixed together!)</span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="html">   # 2. run the all-versus-all blast of some input files (infile/) </span>
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="html">- blastn+,blastp+,tblastx+ : standard blast+ family (shell commands: blastn,blastp,tblastx)</span>
</pre>
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<pre style="margin: 0;">-<span id="LC368" class="line" lang="html">family. The suffix 'n' or 'p' indicates nucleotide or protein input files.</span>
</pre>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="html">   proteinortho -step=2 -project=test -keep infile/<span class="nt" style="color: #000080;"></em></span>fasta</span>
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="html"></span>
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<td class="new_line diff-line-num old" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC370" class="line" lang="html">- diamond : Only for protein files! standard diamond procedure and for</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
371
</td>
<td class="new_line diff-line-num old" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC371" class="line" lang="html">genes/proteins of length <span class="ni" style="color: #800080;">&gt;</span>40 with the additional --sensitive flag</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="372" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="317" 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">
317
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC317" class="line" lang="html">   # now you can insert more fasta files to infile/ and reuse everything computed </span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="372" 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">
372
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<td class="new_line diff-line-num" data-linenumber="318" 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">
318
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC318" class="line" lang="html"></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
373
</td>
<td class="new_line diff-line-num old" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC373" class="line" lang="html">- lastn,lastp : lastal. -n : dna files, -p protein files (BLOSUM62</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
374
</td>
<td class="new_line diff-line-num old" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC374" class="line" lang="html">scoring matrix)!</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="375" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="319" 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">
319
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC319" class="line" lang="html">   proteinortho -step=2 -project=test -keep infile/*fasta</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num" data-linenumber="375" 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">
375
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<td class="new_line diff-line-num" data-linenumber="320" 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">
320
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC320" class="line" lang="html"></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
376
</td>
<td class="new_line diff-line-num old" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC376" class="line" lang="html"><span class="idiff left">- rapsearch : Only for pro</span>tein<span class="idiff right"> files! </span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="377" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="321" 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">
321
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC321" class="line" lang="html"><span class="idiff left">   # finally run clus</span>te<span class="idiff">r</span>in<span class="idiff right">g</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="377" 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">
377
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<td class="new_line diff-line-num" data-linenumber="322" 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">
322
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC322" class="line" lang="html"></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num old" data-linenumber="378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
378
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<td class="new_line diff-line-num old" data-linenumber="323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC378" class="line" lang="html"><span class="idiff left right">- mmseqsp,mmseqsn : mmseqs2. -n : dna files, -p protein files</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="379" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="323" 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">
323
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC323" class="line" lang="html"><span class="idiff left right">   proteinortho -step=3 -project=test -keep</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="379" 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">
379
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<td class="new_line diff-line-num" data-linenumber="324" 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">
324
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC324" class="line" lang="html"></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
380
</td>
<td class="new_line diff-line-num old" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC380" class="line" lang="html"><span class="idiff left right">- topaz : Only for protein files!</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="381" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="325" 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">
325
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC325" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left"></details></span></span><span class="idiff right">     </span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="381" 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">
381
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<td class="new_line diff-line-num" data-linenumber="326" 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">
326
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC326" class="line" lang="html"></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
382
</td>
<td class="new_line diff-line-num old" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC382" class="line" lang="html">- usearch : usearch_local procedure with -id 0 (minimum identity</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
383
</td>
<td class="new_line diff-line-num old" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC383" class="line" lang="html">percentage).</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="384" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="327" 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">
327
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC327" class="line" lang="html"><span class="nt" style="color: #000080;"><ul></span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="384" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="328" 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">
328
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC328" class="line" lang="html"><span class="nt" style="color: #000080;"><li><strong></span>--isoform<span class="nt" style="color: #000080;"></strong></span>={ncbi,uniprot,trinity}<span class="nt" style="color: #000080;"></li></span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="384" 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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<td class="new_line diff-line-num new" data-linenumber="329" 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">
329
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC329" class="line" lang="html"><span class="nt" style="color: #000080;"></ul></span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="384" 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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<td class="new_line diff-line-num new" data-linenumber="330" 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">
330
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC330" class="line" lang="html"><span class="nt" style="color: #000080;"><details><summary></span>ncbi<span class="nt" style="color: #000080;"></summary></span> </span>
</pre>
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384
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331
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC331" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
385
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<td class="new_line diff-line-num old" data-linenumber="332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC385" class="line" lang="html"><span class="idiff left right">- ublast : usearch_ublast procedure.</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="386" 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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<td class="new_line diff-line-num new" data-linenumber="332" 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">
332
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC332" class="line" lang="html"><span class="idiff left right">   isoforms are specified in ncbi style </span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="386" 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">
386
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333
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC333" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
387
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<td class="new_line diff-line-num old" data-linenumber="334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC387" class="line" lang="html">- blatp,blatn : blat. -n : dna files, -p protein files</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
388
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<td class="new_line diff-line-num old" data-linenumber="334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC388" class="line" lang="html"><span class="nt" style="color: #000080;"></code></pre></span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="389" 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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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="html">   ---</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="389" 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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<td class="new_line diff-line-num new" data-linenumber="335" 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">
335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="html">   <span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"><strong></span>ENSMUSP00000021091.8<span class="nt" style="color: #000080;"></strong></span> pep chromosome:GRCm38:11:74673949:74724670:-1 <span class="nt" style="color: #000080;"><strong></span>gene:ENSMUSG00000020745.15<span class="nt" style="color: #000080;"></strong></span> transcript:ENSMUST00000021091.14 gene_biotype:protein_coding transcript_biotype:protein_coding gene_symbol:Pafah1b1 description:platelet-activating factor acetylhydrolase, <span class="nt" style="color: #000080;"><strong></span>isoform<span class="nt" style="color: #000080;"></strong></span> 1b, subunit 1 [Source:MGI Symbol;Acc:MGI:109520]</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="389" 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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<td class="new_line diff-line-num new" data-linenumber="336" 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">
336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="html">   <span class="ni" style="color: #800080;">&gt;</span><span class="nt" style="color: #000080;"><strong></span>ENSMUSP00000099578.2<span class="nt" style="color: #000080;"></strong></span> pep chromosome:GRCm38:11:74673950:74723858:-1 <span class="nt" style="color: #000080;"><strong></span>gene:ENSMUSG00000020745.15<span class="nt" style="color: #000080;"></strong></span> transcript:ENSMUST00000102520.8 gene_biotype:protein_coding transcript_biotype:protein_coding gene_symbol:Pafah1b1 description:platelet-activating factor acetylhydrolase, <span class="nt" style="color: #000080;"><strong></span>isoform<span class="nt" style="color: #000080;"></strong></span> 1b, subunit 1 [Source:MGI Symbol;Acc:MGI:109520]<span class="nt" style="color: #000080;"><br></span>   ---</span>
</pre>
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389
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337
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC337" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
390
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<td class="new_line diff-line-num old" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
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<pre style="margin: 0;">-<span id="LC390" class="line" lang="html"><span class="nt" style="color: #000080;"><p></details></span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
391
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<td class="new_line diff-line-num old" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC391" class="line" lang="html"><span class="nt" style="color: #000080;"><br></p></li></span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="392" 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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<td class="new_line diff-line-num new" data-linenumber="338" 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">
338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="html">   Different protein identifier (ENSMUSP00000021091.8, ENSMUSP00000099578.2) but the same gene id (ENSMUSG00000020745.15). The word <span class="ni" style="color: #800080;">&#39;</span>isoform<span class="ni" style="color: #800080;">&#39;</span> is also mandatory!</span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="392" 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">
392
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<td class="new_line diff-line-num" data-linenumber="339" 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">
339
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC339" class="line" lang="html"></span>
</pre>
</td>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
393
</td>
<td class="new_line diff-line-num old" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC393" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p><strong></span>--e<span class="nt" style="color: #000080;"></strong></span>=evalue (default: 1e-05)</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
394
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<td class="new_line diff-line-num old" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC394" class="line" lang="html">E-value for blast<span class="nt" style="color: #000080;"></p></li></span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="395" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="340" 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">
340
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC340" class="line" lang="html"><span class="nt" style="color: #000080;"></details></span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="395" 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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<td class="new_line diff-line-num new" data-linenumber="341" 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">
341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="html"><span class="nt" style="color: #000080;"><details><summary></span>uniprot<span class="nt" style="color: #000080;"></summary></span> </span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="395" 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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<td class="new_line diff-line-num new" data-linenumber="342" 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">
342
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC342" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="395" 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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<td class="new_line diff-line-num new" data-linenumber="343" 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">
343
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC343" class="line" lang="html">   isoforms are specified in uniprot style using the <span class="ni" style="color: #800080;">&#39;</span><span class="nt" style="color: #000080;"><em></span>_additional.fa<span class="ni" style="color: #800080;">&#39;</span> files </span>
</pre>
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395
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<td class="new_line diff-line-num" data-linenumber="344" 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">
344
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC344" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
396
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<td class="new_line diff-line-num old" data-linenumber="345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC396" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p><strong></span>--selfblast<span class="nt" style="color: #000080;"></strong></span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
397
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<td class="new_line diff-line-num old" data-linenumber="345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="html">apply selfblast, detects paralogs without orthologs<span class="nt" style="color: #000080;"></p></li></span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="398" 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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345
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC345" class="line" lang="html">   E.g. C.fa: </span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="398" 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">
398
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346
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
399
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<td class="new_line diff-line-num old" data-linenumber="347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p><strong></span>--sim<span class="nt" style="color: #000080;"></strong></span>=float (default: 0.95)</span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
400
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<td class="new_line diff-line-num old" data-linenumber="347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC400" class="line" lang="html">min. similarity for additional hits<span class="nt" style="color: #000080;"></p></li></span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="401" 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="LC347" class="line" lang="html">   ---</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="401" 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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<td class="new_line diff-line-num new" data-linenumber="348" 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">
348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="html">   <span class="ni" style="color: #800080;">&gt;</span>tr|ADHA2|R4GDP1_DANRE Gamma-aminobutyric</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="401" 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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<td class="new_line diff-line-num new" data-linenumber="349" 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">
349
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC349" class="line" lang="html">   (...)</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="401" 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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<td class="new_line diff-line-num new" data-linenumber="350" 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">
350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="html">   ---</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="401" 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">
401
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<td class="new_line diff-line-num" data-linenumber="351" 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">
351
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC351" class="line" lang="html"></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num old" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
402
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<td class="new_line diff-line-num old" data-linenumber="352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC402" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p><strong></span>--identity<span class="nt" style="color: #000080;"></strong></span>=number (default: 25)</span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
403
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<td class="new_line diff-line-num old" data-linenumber="352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC403" class="line" lang="html">min. percent identity of best blast hits<span class="nt" style="color: #000080;"></p></li></span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="404" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="352" 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">
352
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC352" class="line" lang="html">   C_additional.fa: </span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="404" 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">
404
</td>
<td class="new_line diff-line-num" data-linenumber="353" 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">
353
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC353" class="line" lang="html"></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
405
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<td class="new_line diff-line-num old" data-linenumber="354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC405" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p><strong></span>--cov<span class="nt" style="color: #000080;"></strong></span>=number (default: 50)</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
406
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<td class="new_line diff-line-num old" data-linenumber="354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC406" class="line" lang="html">min. coverage of best blast alignments in %<span class="nt" style="color: #000080;"></p></li></span></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="407" 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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<td class="new_line diff-line-num new" data-linenumber="354" 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="LC354" class="line" lang="html">   ---</span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="html">   <span class="ni" style="color: #800080;">&gt;</span>tr|QDHQ4|R4GDP1_DANRE isoform of ADHA2</span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="html">   (...)</span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="html">   ---</span>
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="html">   QDHQ4 is the isoform of ADHA2. Please simply add the <span class="nt" style="color: #000080;"></em></span>_additional.fa files to the proteinortho call!</span>
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p><strong></span>--subparaBlast<span class="nt" style="color: #000080;"></strong></span>='options'</span>
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="html">additional parameters for the search tool (-p=blastp+,diamond,...) example -subpara='-seg no'</span>
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<pre style="margin: 0;">-<span id="LC410" class="line" lang="html">or -subpara='--more-sensitive' for diamond</span>
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="html"><span class="nt" style="color: #000080;"></details></span></span>
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<pre style="margin: 0;">-<span id="LC412" class="line" lang="html"><span class="nt" style="color: #000080;"><<span class="idiff left right">br></p></span></span></span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="html"><span class="nt" style="color: #000080;"><<span class="idiff left">details><summary></span></span><span class="idiff">trinity</span><span class="nt" style="color: #000080;"><span class="idiff"></summary></span></span><span class="idiff right"> </span></span>
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<pre style="margin: 0;">-<span id="LC414" class="line" lang="html"><span class="nt" style="color: #000080;"><p><strong></span>Synteny options (optional, step 2)<span class="nt" style="color: #000080;"></strong></span></span>
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="html">(output: <span class="nt" style="color: #000080;"><myproject></span>.ffadj-graph, <span class="nt" style="color: #000080;"><myproject></span>.poff.tsv (tab separated file)-graph)<span class="nt" style="color: #000080;"></p></li></span></span>
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<pre style="margin: 0;">-<span id="LC416" class="line" lang="html"><span class="nt" style="color: #000080;"></ul></span></span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="html">   isoforms are specified in trinity style:</span>
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<pre style="margin: 0;">-<span id="LC418" class="line" lang="html"><span class="nt" style="color: #000080;"><p><details></span></span>
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<pre style="margin: 0;">-<span id="LC419" class="line" lang="html">  <span class="nt" style="color: #000080;"><summary></span>(Click to expand)<span class="nt" style="color: #000080;"></summary></p></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="html">   ---</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="420" 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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<td class="new_line diff-line-num new" data-linenumber="367" 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">
367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="html">   <span class="ni" style="color: #800080;">&gt;</span>TRINITY_DN1000_c115_g5_i1 len=247 path=[31015:0-148 23018:149-246]</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="420" 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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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="html">   (...)</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="420" 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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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="html">   ---</span>
</pre>
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420
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370
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC370" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
421
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<td class="new_line diff-line-num old" data-linenumber="371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC421" class="line" lang="html"><span class="nt" style="color: #000080;"><ul></span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
422
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<td class="new_line diff-line-num old" data-linenumber="371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC422" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p><strong></span>--synteny<span class="nt" style="color: #000080;"></strong></span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
423
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<td class="new_line diff-line-num old" data-linenumber="371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC423" class="line" lang="html">activate PoFF extension to separate similar by contextual adjacencies</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
424
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<td class="new_line diff-line-num old" data-linenumber="371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC424" class="line" lang="html">(requires .gff for each .fasta)<span class="nt" style="color: #000080;"></p></li></span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="425" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="371" 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">
371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="html">   The protein id is TRINITY_DN1000_c115_g5a and the isoform id is specified with i1</span>
</pre>
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425
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<td class="new_line diff-line-num" data-linenumber="372" 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">
372
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC372" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
426
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<td class="new_line diff-line-num old" data-linenumber="373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC426" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p><strong></span>--dups<span class="nt" style="color: #000080;"></strong></span>=number (default: 0)</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
427
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<td class="new_line diff-line-num old" data-linenumber="373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC427" class="line" lang="html">PoFF: number of reiterations for adjacencies heuristic, to determine</span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
428
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<td class="new_line diff-line-num old" data-linenumber="373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC428" class="line" lang="html">duplicated regions<span class="nt" style="color: #000080;"></p></li></span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="429" 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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<td class="new_line diff-line-num new" data-linenumber="373" 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">
373
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC373" class="line" lang="html"><span class="nt" style="color: #000080;"></details></span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="429" 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">
429
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<td class="new_line diff-line-num" data-linenumber="374" 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">
374
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC374" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
430
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<td class="new_line diff-line-num old" data-linenumber="375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC430" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p><strong></span>--cs<span class="nt" style="color: #000080;"></strong></span>=number (default: 3)</span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
431
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<td class="new_line diff-line-num old" data-linenumber="375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC431" class="line" lang="html">PoFF: Size of a maximum common substring (MCS) for adjacency matches<span class="nt" style="color: #000080;"></p></li></span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="432" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="375" 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">
375
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC375" class="line" lang="html"><span class="nt" style="color: #000080;"><p><strong></span>Search options (step 1-2)<span class="nt" style="color: #000080;"></strong></span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="432" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="376" 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">
376
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC376" class="line" lang="html">(output: <span class="nt" style="color: #000080;"><myproject></span>.blast-graph)<span class="nt" style="color: #000080;"></p></span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="432" 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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<td class="new_line diff-line-num new" data-linenumber="377" 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">
377
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC377" class="line" lang="html"><span class="nt" style="color: #000080;"><ul></span></span>
</pre>
</td>
</tr>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="html"><span class="nt" style="color: #000080;"><li><strong></span>--p<span class="nt" style="color: #000080;"></strong></span>=algorithm (default: diamond) <span class="nt" style="color: #000080;"></li></span></span>
</pre>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="html"><span class="nt" style="color: #000080;"></ul></span></span>
</pre>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="html"><span class="nt" style="color: #000080;"><p><details></p></span></span>
</pre>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="html"> <span class="nt" style="color: #000080;"><summary></span>show all options (Click to expand)<span class="nt" style="color: #000080;"></summary></span></span>
</pre>
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432
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382
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="html"></span>
</pre>
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433
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<pre style="margin: 0;">-<span id="LC433" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p><strong></span>--alpha<span class="nt" style="color: #000080;"></strong></span>=number (default: .5)</span>
</pre>
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434
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<pre style="margin: 0;">-<span id="LC434" class="line" lang="html">PoFF: weight of adjacencies vs. sequence similarity</span>
</pre>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="html"><span class="nt" style="color: #000080;"><ul></span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="384" 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">
384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p></span>autoblast : automatically detects the blast+ program (blastp,blastn,tblastn,blastx) depending on the input (can also be mixed together!)<span class="nt" style="color: #000080;"></p></span></span>
</pre>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="386" 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">
386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p></span>blastn_legacy,blastp_legacy,tblastx_legacy : legacy blast family (shell commands: blastall -) family. The suffix <span class="ni" style="color: #800080;">&#39;</span>n<span class="ni" style="color: #800080;">&#39;</span> or <span class="ni" style="color: #800080;">&#39;</span>p<span class="ni" style="color: #800080;">&#39;</span> indicates nucleotide or protein input files.<span class="nt" style="color: #000080;"></p></span></span>
</pre>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="388" 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">
388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p></span>blastn+,blastp+,tblastx+ : standard blast family (shell commands: blastn,blastp,tblastx)</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="389" 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">
389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="html">family. The suffix <span class="ni" style="color: #800080;">&#39;</span>n<span class="ni" style="color: #800080;">&#39;</span> or <span class="ni" style="color: #800080;">&#39;</span>p<span class="ni" style="color: #800080;">&#39;</span> indicates nucleotide or protein input files.<span class="nt" style="color: #000080;"></p></span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="390" 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">
390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="391" 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">
391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p></span>diamond : Only for protein files! standard diamond procedure and for</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="392" 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">
392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="html">genes/proteins of length <span class="ni" style="color: #800080;">&gt;</span>40 with the additional --sensitive flag</span>
</pre>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="html">Warning: Please use version 0.9.29 or later to avoid this known bug: #24<span class="nt" style="color: #000080;"></p></span></span>
</pre>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
</pre>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p></span>lastn,lastp : lastal. -n : dna files, -p protein files (BLOSUM62 scoring matrix)!<span class="nt" style="color: #000080;"></p></span></span>
</pre>
</td>
</tr>
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<td class="new_line diff-line-num new" data-linenumber="396" 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">
396
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC396" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="435" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="397" 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">
397
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC397" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p></span>rapsearch : Only for protein files!<span class="nt" style="color: #000080;"></p></span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="435" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="398" 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">
398
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC398" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="435" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="399" 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">
399
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC399" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p></span>mmseqsp,mmseqsn : mmseqs2. -n : dna files, -p protein files<span class="nt" style="color: #000080;"></p></span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="435" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="400" 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">
400
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC400" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="435" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="401" 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">
401
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC401" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p></span>topaz : Only for protein files!<span class="nt" style="color: #000080;"></p></span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="435" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="402" 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">
402
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC402" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="435" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="403" 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">
403
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC403" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p></span>usearch : usearch_local procedure with -id 0 (minimum identity</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="435" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="404" 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">
404
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC404" class="line" lang="html">percentage).<span class="nt" style="color: #000080;"></p></span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="435" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="405" 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">
405
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC405" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="435" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="406" 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">
406
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC406" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p></span>ublast : usearch_ublast procedure.<span class="nt" style="color: #000080;"></p></span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="435" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="407" 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">
407
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC407" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="435" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="408" 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">
408
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC408" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p></span>blatp,blatn : blat. -n : dna files, -p protein files</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="435" 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">
435
</td>
<td class="new_line diff-line-num" data-linenumber="409" 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">
409
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC409" class="line" lang="html"><span class="nt" style="color: #000080;"></details></span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="436" 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">
436
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<td class="new_line diff-line-num" data-linenumber="410" 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">
410
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC410" class="line" lang="html"><span class="nt" style="color: #000080;"><br></p></span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
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437
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<td class="new_line diff-line-num old" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC437" class="line" lang="html"></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
438
</td>
<td class="new_line diff-line-num old" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC438" class="line" lang="html"><span class="nt" style="color: #000080;"><p><strong></span>Clustering options (step 3)<span class="nt" style="color: #000080;"></strong></span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
439
</td>
<td class="new_line diff-line-num old" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC439" class="line" lang="html">(output: <span class="nt" style="color: #000080;"><myproject></span>.proteinortho.tsv, <span class="nt" style="color: #000080;"><myproject></span>.proteinortho.html, <span class="nt" style="color: #000080;"><myproject></span>.proteinortho-graph)<span class="nt" style="color: #000080;"></p></li></span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="440" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="411" 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">
411
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC411" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="440" 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">
440
</td>
<td class="new_line diff-line-num" data-linenumber="412" 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">
412
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC412" class="line" lang="html"><span class="nt" style="color: #000080;"></ul></span></span>
</pre>
</td>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="html"><span class="nt" style="color: #000080;"><ul></span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="414" 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">
414
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC414" class="line" lang="html"><span class="nt" style="color: #000080;"><li><strong></span>--sim<span class="nt" style="color: #000080;"></strong></span>=float (default: 0.95)</span>
</pre>
</td>
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<td class="new_line diff-line-num new" data-linenumber="415" 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">
415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="html">min. reciprocal similarity for additional hits. 1 : only the best reciprocal hits are reported, 0 : all possible reciprocal blast matches (within the -evalue) are reported.<span class="nt" style="color: #000080;"></li></span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="416" 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">
416
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC416" class="line" lang="html"><span class="nt" style="color: #000080;"></ul></span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="417" 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">
417
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC417" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
</pre>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="html"><span class="nt" style="color: #000080;"></ul></span></span>
</pre>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="html"><span class="nt" style="color: #000080;"><details></span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="420" 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">
420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="html">  <span class="nt" style="color: #000080;"><summary></span>More (Click to expand)<span class="nt" style="color: #000080;"></summary></span></span>
</pre>
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421
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="html"></span>
</pre>
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442
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC442" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left right"><p><details></span></span></span>
</pre>
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443
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</td>
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<pre style="margin: 0;">-<span id="LC443" class="line" lang="html">  <span class="nt" style="color: #000080;"><span class="idiff left"><summary></span></span><span class="idiff">(Click to expand)</span><span class="nt" style="color: #000080;"><span class="idiff right"></summary></p></span></span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="444" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="422" 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">
422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="html"><span class="idiff left">  - </span><span class="nt" style="color: #000080;"><span class="idiff"><strong></span></span><span class="idiff">--e</span><span class="nt" style="color: #000080;"><span class="idiff"></strong></span></span><span class="idiff right">=evalue (default: 1e-05)</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="423" 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">
423
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC423" class="line" lang="html">  <span class="idiff left right">  E-value for blast</span></span>
</pre>
</td>
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444
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<td class="new_line diff-line-num" data-linenumber="424" 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">
424
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC424" class="line" lang="html"></span>
</pre>
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445
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<td class="new_line diff-line-num old" data-linenumber="425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC445" class="line" lang="html"><span class="nt" style="color: #000080;"><ul></span></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num old" data-linenumber="446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
446
</td>
<td class="new_line diff-line-num old" data-linenumber="425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC446" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p><strong></span>--singles<span class="nt" style="color: #000080;"></strong></span></span>
</pre>
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447
</td>
<td class="new_line diff-line-num old" data-linenumber="425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC447" class="line" lang="html">report singleton genes without any hit<span class="nt" style="color: #000080;"></p></li></span></span>
</pre>
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</td>
<td class="new_line diff-line-num new" data-linenumber="425" 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">
425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="html">  - <span class="nt" style="color: #000080;"><strong></span>--selfblast<span class="nt" style="color: #000080;"></strong></span></span>
</pre>
</td>
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</td>
<td class="new_line diff-line-num new" data-linenumber="426" 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">
426
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC426" class="line" lang="html">    apply selfblast, detects paralogs without orthologs</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="427" 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">
427
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC427" class="line" lang="html"></span>
</pre>
</td>
</tr>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="html">  - <span class="nt" style="color: #000080;"><strong></span>--identity<span class="nt" style="color: #000080;"></strong></span>=number (default: 25)</span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="html">    min. percent identity of best blast hits</span>
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="html"></span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="html">  - <span class="nt" style="color: #000080;"><strong></span>--cov<span class="nt" style="color: #000080;"></strong></span>=number (default: 50)</span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="html">    min. coverage of best blast alignments in %</span>
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433
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<pre style="margin: 0;"> <span id="LC433" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC449" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p><strong></span>--purity<span class="nt" style="color: #000080;"></strong></span>=float (default: 1e-7)</span>
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<pre style="margin: 0;">-<span id="LC450" class="line" lang="html">avoid spurious graph assignments<span class="nt" style="color: #000080;"></p></li></span></span>
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="html">  - <span class="nt" style="color: #000080;"><strong></span>--subparaBlast<span class="nt" style="color: #000080;"></strong></span>=<span class="ni" style="color: #800080;">&#39;</span>options<span class="ni" style="color: #800080;">&#39;</span></span>
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="html">    additional parameters for the search tool (-p=blastp+,diamond,...) example -subpara=<span class="ni" style="color: #800080;">&#39;</span>-seg no<span class="ni" style="color: #800080;">&#39;</span></span>
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="html">    or -subpara=<span class="ni" style="color: #800080;">&#39;</span>--more-sensitive<span class="ni" style="color: #800080;">&#39;</span> for diamond</span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="html"><span class="nt" style="color: #000080;"></details></span></span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="html"><span class="nt" style="color: #000080;"><br></span></span>
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439
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<pre style="margin: 0;"> <span id="LC439" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC452" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left"><li><p></span><strong></span><span class="idiff">--conn</span><span class="nt" style="color: #000080;"><span class="idiff"></strong></span></span><span class="idiff right">=float (default: 0.1)</span></span>
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<pre style="margin: 0;">-<span id="LC453" class="line" lang="html"><span class="idiff left">min. algebraic connectivity. </span><span class="nt" style="color: #000080;"><span class="idiff"><b></span></span><span class="idiff">This is the main parameter for the clustering step.</span><span class="nt" style="color: #000080;"><span class="idiff"></b></span></span><span class="idiff"> Choose larger values then more splits are done, resulting in more and smaller clusters.</span><span class="nt" style="color: #000080;"><span class="idiff right"></p></li></span></span></span>
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="html"><span class="idiff left"> </span><span class="nt" style="color: #000080;"><strong></span><span class="idiff">Synteny options (optional, step 2)</span><span class="nt" style="color: #000080;"><span class="idiff right"></strong></span></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="html"><span class="idiff left">  (output: </span><span class="nt" style="color: #000080;"><span class="idiff"><myproject></span></span><span class="idiff">.ffadj-graph, </span><span class="nt" style="color: #000080;"><span class="idiff"><myproject></span></span><span class="idiff right">.poff.tsv (tab separated file)-graph)</span></span>
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<pre style="margin: 0;"> <span id="LC442" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC455" class="line" lang="html"><span class="nt" style="color: #000080;"><<span class="idiff left">li><p><strong></span></span><span class="idiff">--minspecies</span><span class="nt" style="color: #000080;"><span class="idiff"></strong></span></span><span class="idiff right">=float (default: 1, must be >=0)</span></span>
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<pre style="margin: 0;">-<span id="LC456" class="line" lang="html"><span class="idiff left">min. number of genes per species. If a group is found with up to (minspecies) genes/species, it wont be split again (regardless of the connectivity).</span><span class="nt" style="color: #000080;"><span class="idiff right"></p></li</span>></span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="html"><span class="nt" style="color: #000080;"><<span class="idiff left right">details></span></span></span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="html"><span class="idiff left">  </span><span class="nt" style="color: #000080;"><span class="idiff"><summary></span></span><span class="idiff">More (Click to expand)</span><span class="nt" style="color: #000080;"><span class="idiff right"></summary</span>></span></span>
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<pre style="margin: 0;"> <span id="LC445" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC458" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p><strong></span>--nograph<span class="nt" style="color: #000080;"></strong></span></span>
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<pre style="margin: 0;">-<span id="LC459" class="line" lang="html">do not generate *-graph file (pairwise orthology relations)<span class="nt" style="color: #000080;"></p></li></span></span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="html">  - <span class="nt" style="color: #000080;"><strong></span>--synteny<span class="nt" style="color: #000080;"></strong></span></span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="html">    activate PoFF extension to separate similar by contextual adjacencies</span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="html">    (requires .gff for each .fasta)</span>
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<pre style="margin: 0;"> <span id="LC449" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC461" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left"><li><p></span><strong></span>--<span class="idiff">subparaCluster</span><span class="nt" style="color: #000080;"><span class="idiff"></strong></span></span><span class="idiff right">='options'</span></span>
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<pre style="margin: 0;">-<span id="LC462" class="line" lang="html"><span class="idiff left right">additional parameters for the clustering algorithm (proteinortho_clustering) example -subparaCluster='-maxnodes 10000'. </span></span>
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<pre style="margin: 0;">-<span id="LC463" class="line" lang="html"><span class="idiff left">Note: -rmgraph cannot be set. All other parameters of subparaCluster are replacing the default values (like -cpus or -minSpecies)</span><span class="nt" style="color: #000080;"><span class="idiff right"></p></li></span></span></span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="html"><span class="idiff left">  - </span><span class="nt" style="color: #000080;"><strong></span>--<span class="idiff">dups</span><span class="nt" style="color: #000080;"><span class="idiff"></strong></span></span><span class="idiff right">=number (default: 0)</span></span>
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="html"><span class="idiff left right">    PoFF: number of reiterations for adjacencies heuristic, to determine</span></span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="html"><span class="idiff left right">    duplicated regions</span></span>
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC465" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left"><li><p></span><strong></span>--<span class="idiff right">xml</span><span class="nt" style="color: #000080;"></strong></span></span>
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<pre style="margin: 0;">-<span id="LC466" class="line" lang="html"><span class="idiff left">do generate an orthologyXML file (see http://www.orthoxml.org for more information). You can also use proteinortho2xml.pl </span><span class="nt" style="color: #000080;"><span class="idiff"><myproject.proteinortho></span></span><span class="idiff">.</span><span class="nt" style="color: #000080;"><span class="idiff right"></p></li></span></span></span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="html"><span class="idiff left">  - </span><span class="nt" style="color: #000080;"><strong></span>--<span class="idiff">cs</span><span class="nt" style="color: #000080;"></strong></span><span class="idiff right">=number (default: 3)</span></span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="html"><span class="idiff left right">    PoFF: Size of a maximum common substring (MCS) for adjacency matches</span></span>
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC468" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p><strong></span>--exactstep3<span class="nt" style="color: #000080;"></strong></span></span>
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<pre style="margin: 0;">-<span id="LC469" class="line" lang="html">perform step 3 without the k-mere heuristic (much slower for huge</span>
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<pre style="margin: 0;">-<span id="LC470" class="line" lang="html">datasets but more precise)<span class="nt" style="color: #000080;"></p></li></span></span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="html">  - <span class="nt" style="color: #000080;"><strong></span>--alpha<span class="nt" style="color: #000080;"></strong></span>=number (default: .5)</span>
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="html">    PoFF: weight of adjacencies vs. sequence similarity</span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="html"><span class="nt" style="color: #000080;"></details></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="html"><span class="nt" style="color: #000080;"><br></span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC472" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p><strong></span>--mcl<span class="nt" style="color: #000080;"></strong></span></span>
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<pre style="margin: 0;">-<span id="LC473" class="line" lang="html">perform the clustering without the k-mere heuristic. The k-mere heuristic is only applied for very large connected components (>1e+6 nodes) and if the algorithm would start to iteratate very slowly<span class="nt" style="color: #000080;"></p></li></span></span>
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<pre style="margin: 0;">-<span id="LC474" class="line" lang="html"><span class="nt" style="color: #000080;"></ul></span></span>
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="html"> <span class="nt" style="color: #000080;"><strong></span>Clustering options (step 3)<span class="nt" style="color: #000080;"></strong></span></span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="html">  (output: <span class="nt" style="color: #000080;"><myproject></span>.proteinortho.tsv, <span class="nt" style="color: #000080;"><myproject></span>.proteinortho.html, <span class="nt" style="color: #000080;"><myproject></span>.proteinortho-graph)</span>
</pre>
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="html"></span>
</pre>
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<pre style="margin: 0;">-<span id="LC476" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left right"><p></details></span></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC477" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left right"><br></p></span></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="html"><span class="idiff left">  - </span><span class="nt" style="color: #000080;"><span class="idiff"><strong></span></span><span class="idiff">--conn</span><span class="nt" style="color: #000080;"><span class="idiff"></strong></span></span><span class="idiff right">=float (default: 0.1)</span></span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="html"><span class="idiff left">    min. algebraic connectivity. </span><span class="nt" style="color: #000080;"><span class="idiff"><b></span></span><span class="idiff">This is the main parameter for the clustering step.</span><span class="nt" style="color: #000080;"><span class="idiff"></b></span></span><span class="idiff right"> Choose larger values then more splits are done, resulting in more and smaller clusters. (There are still cluster with an alg. conn. below this given threshold allowed if the protein to species ratio is good enough, see -minspecies option below)</span></span>
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<pre style="margin: 0;"> <span id="LC467" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC479" class="line" lang="html"><span class="nt" style="color: #000080;"><<span class="idiff left">p><strong></span></span><span class="idiff">Misc options</span><span class="nt" style="color: #000080;"><span class="idiff right"></strong></p</span>></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="html"><span class="nt" style="color: #000080;"><<span class="idiff left right">details</span>></span></span>
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<pre style="margin: 0;"> <span id="LC469" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC481" class="line" lang="html"><span class="nt" style="color: #000080;"><p><details></span></span>
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<pre style="margin: 0;">-<span id="LC482" class="line" lang="html">  <span class="nt" style="color: #000080;"><summary></span>(Click to expand)<span class="nt" style="color: #000080;"></summary></p></span></span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="html">  <span class="nt" style="color: #000080;"><summary></span>More (Click to expand)<span class="nt" style="color: #000080;"></summary></span></span>
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<pre style="margin: 0;"> <span id="LC471" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC484" class="line" lang="html"><span class="nt" style="color: #000080;"><ul></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC485" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p><strong></span>--cleanblast<span class="nt" style="color: #000080;"></strong></span></span>
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<td class="new_line diff-line-num old" data-linenumber="472" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC486" class="line" lang="html">cleans blast-graph with proteinortho_cleanupblastgraph<span class="nt" style="color: #000080;"></p></li></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="html">  - <span class="nt" style="color: #000080;"><strong></span>--singles<span class="nt" style="color: #000080;"></strong></span></span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="html">    report singleton genes without any hit</span>
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474
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<pre style="margin: 0;"> <span id="LC474" class="line" lang="html"></span>
</pre>
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<td class="new_line diff-line-num old" data-linenumber="475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC488" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left"><li><p></span><strong></span>--<span class="idiff">checkfasta</span><span class="nt" style="color: #000080;"><span class="idiff right"></strong></span></span></span>
</pre>
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489
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<pre style="margin: 0;">-<span id="LC489" class="line" lang="html"><span class="idiff left">checks input fasta files if the given algorithm can process the given fasta file.</span><span class="nt" style="color: #000080;"><span class="idiff right"></p></li></span></span></span>
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<td class="new_line diff-line-num new" data-linenumber="475" 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">
475
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="html"><span class="idiff left">  - </span><span class="nt" style="color: #000080;"><strong></span>--<span class="idiff">purity</span><span class="nt" style="color: #000080;"><span class="idiff"></strong></span></span><span class="idiff right">=float (default: 1e-7)</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="html"><span class="idiff left right">    avoid spurious graph assignments</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC477" class="line" lang="html"></span>
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491
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<pre style="margin: 0;">-<span id="LC491" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left"><li><p></span><strong></span>--<span class="idiff">desc</span><span class="nt" style="color: #000080;"><span class="idiff right"></strong></span></span></span>
</pre>
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492
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<td class="new_line diff-line-num old" data-linenumber="478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC492" class="line" lang="html"><span class="idiff left">write description files (for NCBI FASTA input only)</span><span class="nt" style="color: #000080;"><span class="idiff right"></p></li></span></span></span>
</pre>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="html"><span class="idiff left">  - </span><span class="nt" style="color: #000080;"><strong></span>--<span class="idiff">minspecies</span><span class="nt" style="color: #000080;"><span class="idiff"></strong></span></span><span class="idiff">=float (default: 1, must be </span><span class="ni" style="color: #800080;"><span class="idiff">&gt;</span></span><span class="idiff right">=0)</span></span>
</pre>
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479
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="html"><span class="idiff left right">    min. number of genes per species. If a group is found with up to (minspecies) genes/species, it wont be split again (regardless of the connectivity).</span></span>
</pre>
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493
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480
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<pre style="margin: 0;"> <span id="LC480" class="line" lang="html"></span>
</pre>
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494
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<td class="new_line diff-line-num old" data-linenumber="481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC494" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left"><li><p></span><strong></span>--<span class="idiff">binpat</span>h<span class="nt" style="color: #000080;"></strong></span><span class="idiff right">=directory (default: PATH)</span></span>
</pre>
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495
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<td class="new_line diff-line-num old" data-linenumber="481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC495" class="line" lang="html"><span class="idiff left">path to your local executab</span>le<span class="idiff">s</span> (<span class="idiff">blast, diamond, mcl, ...)</span><span class="nt" style="color: #000080;"><span class="idiff right"></p></li></span></span></span>
</pre>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="html"><span class="idiff left">  - </span><span class="nt" style="color: #000080;"><strong></span>--<span class="idiff right">nograp</span>h<span class="nt" style="color: #000080;"></strong></span></span>
</pre>
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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="html"><span class="idiff left">    do not generate </span><span class="nt" style="color: #000080;"><span class="idiff"><em></span></span><span class="idiff">-graph fi</span>le (<span class="idiff right">pairwise orthology relations)</span></span>
</pre>
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496
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483
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="html"></span>
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497
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<pre style="margin: 0;">-<span id="LC497" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left"><li><p></span><strong></span>--<span class="idiff">debug</span><span class="nt" style="color: #000080;"><span class="idiff right"></strong></span></span></span>
</pre>
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498
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<td class="new_line diff-line-num old" data-linenumber="484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC498" class="line" lang="html"><span class="idiff left">gives detailed information for bug tracking</span><span class="nt" style="color: #000080;"><span class="idiff right"></p></li></span></span></span>
</pre>
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499
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<pre style="margin: 0;">-<span id="LC499" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left right"></ul></span></span></span>
</pre>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="html"><span class="idiff left">  - </span><span class="nt" style="color: #000080;"><strong></span>--<span class="idiff">subparaCluster</span><span class="nt" style="color: #000080;"><span class="idiff"></strong></span></span><span class="idiff">=</span><span class="ni" style="color: #800080;"><span class="idiff">&#39;</span></span><span class="idiff">options</span><span class="ni" style="color: #800080;"><span class="idiff right">&#39;</span></span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="485" 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">
485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="html"><span class="idiff left">    additional parameters for the clustering algorithm (proteinortho_clustering) example -subparaCluster=</span><span class="ni" style="color: #800080;"><span class="idiff">&#39;</span></span><span class="idiff">-maxnodes 10000</span><span class="ni" style="color: #800080;"><span class="idiff">&#39;</span></span><span class="idiff right">.</span></span>
</pre>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="html"><span class="idiff left right">    Note: -rmgraph cannot be set. All other parameters of subparaCluster are replacing the default values (like -cpus or -minSpecies)</span></span>
</pre>
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500
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487
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<pre style="margin: 0;"> <span id="LC487" class="line" lang="html"></span>
</pre>
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501
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<pre style="margin: 0;">-<span id="LC501" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left right"><p></details</span>></span></span>
</pre>
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502
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<pre style="margin: 0;">-<span id="LC502" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left right"><br></p></span></span></span>
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="html"><span class="idiff left">  - </span><span class="nt" style="color: #000080;"><span class="idiff"><strong></span></span><span class="idiff">--xml</span><span class="nt" style="color: #000080;"><span class="idiff right"></strong</span>></span></span>
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="html"><span class="idiff left">    do generate an orthologyXML file (see </span><span class="nt" style="color: #000080;"><span class="idiff"><a</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">href=</span></span><span class="s" style="color: #d14;"><span class="idiff">"http://www.orthoxml.org"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">http://www.orthoxml.org</span><span class="nt" style="color: #000080;"><span class="idiff"></a></span></span><span class="idiff"> for more information). You can also use proteinortho2xml.pl </span><span class="nt" style="color: #000080;"><span class="idiff"><myproject.proteinortho></span></span><span class="idiff right">.</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC490" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC504" class="line" lang="html"><span class="nt" style="color: #000080;"><p><strong></span>Large compute jobs<span class="nt" style="color: #000080;"></strong></p></span></span>
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="html">  - <span class="nt" style="color: #000080;"><strong></span>--exactstep3<span class="nt" style="color: #000080;"></strong></span></span>
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="html">    perform step 3 without the k-mere heuristic (much slower for huge</span>
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="html">    datasets but more precise)</span>
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<pre style="margin: 0;"> <span id="LC494" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC506" class="line" lang="html"><span class="nt" style="color: #000080;"><ul></span></span>
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<pre style="margin: 0;">-<span id="LC507" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p><strong></span>--jobs<span class="nt" style="color: #000080;"></strong></span>=M/N</span>
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<pre style="margin: 0;">-<span id="LC508" class="line" lang="html">If you want to involve multiple machines or separate a Proteinortho</span>
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<pre style="margin: 0;">-<span id="LC509" class="line" lang="html">run into smaller chunks, use the -jobs=<span class="nt" style="color: #000080;"><strong></span>M<span class="nt" style="color: #000080;"></strong></span>/<span class="nt" style="color: #000080;"><strong></span>N<span class="nt" style="color: #000080;"></strong></span> option. First, run</span>
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<pre style="margin: 0;">-<span id="LC510" class="line" lang="html">'proteinortho6.pl -steps=1 ...' to generate the indices. Then you can</span>
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<pre style="margin: 0;">-<span id="LC511" class="line" lang="html">run 'proteinortho6.pl -steps=2 -jobs=<span class="nt" style="color: #000080;"><strong></span>M<span class="nt" style="color: #000080;"></strong></span>/<span class="nt" style="color: #000080;"><strong></span>N<span class="nt" style="color: #000080;"></strong></span> ...' to run small chunks</span>
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<pre style="margin: 0;">-<span id="LC512" class="line" lang="html">separately. Instead of <span class="nt" style="color: #000080;"><strong></span>M<span class="nt" style="color: #000080;"></strong></span> and <span class="nt" style="color: #000080;"><strong></span>N<span class="nt" style="color: #000080;"></strong></span> numbers must be set representing the</span>
</pre>
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<pre style="margin: 0;">-<span id="LC513" class="line" lang="html">number of jobs you want to divide the run into (<span class="nt" style="color: #000080;"><strong></span>M<span class="nt" style="color: #000080;"></strong></span>) and the job</span>
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<pre style="margin: 0;">-<span id="LC514" class="line" lang="html">division to be performed by the process. E.g. to divide a Proteinortho</span>
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<pre style="margin: 0;">-<span id="LC515" class="line" lang="html">run into 4 jobs to run on several machines, use 'proteinortho6.pl -steps=2 -jobs=1/4', 'proteinortho6.pl -steps=2 -jobs=1/4', 'proteinortho6.pl -steps=2 -jobs=2/4', 'proteinortho6.pl -steps=2 -jobs=3/4', 'proteinortho6.pl -steps=2 -jobs=4/4'.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC516" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC517" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>See <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Large-compute-jobs-(the--jobs-option)"</span><span class="nt" style="color: #000080;">></span>Large compute jobs, the --jobs option (proteinortho wiki)<span class="nt" style="color: #000080;"></a></span> for more details.<span class="nt" style="color: #000080;"></p></li></span></span>
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<pre style="margin: 0;">-<span id="LC518" class="line" lang="html"><span class="nt" style="color: #000080;"></ul></span></span>
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="html">  - <span class="nt" style="color: #000080;"><strong></span>--mcl<span class="nt" style="color: #000080;"></strong></span></span>
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="html">    perform the clustering without the k-mere heuristic. The k-mere heuristic is only applied for very large connected components (<span class="ni" style="color: #800080;">&gt;</span>1e+6 nodes) and if the algorithm would start to iteratate very slowly</span>
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<pre style="margin: 0;"> <span id="LC497" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC520" class="line" lang="html"><span class="nt" style="color: #000080;"><p><br></p></span></span>
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<pre style="margin: 0;"> <span id="LC498" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC522" class="line" lang="html"><span class="nt" style="color: #000080;"><h1</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"poff"</span><span class="nt" style="color: #000080;">></span>PoFF<span class="nt" style="color: #000080;"></h1></span></span>
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="html"><span class="nt" style="color: #000080;"></details></span></span>
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="html"><span class="nt" style="color: #000080;"><br></span></span>
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="html"> <span class="nt" style="color: #000080;"><strong></span>Misc options<span class="nt" style="color: #000080;"></strong></span></span>
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<pre style="margin: 0;"> <span id="LC503" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC524" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>The PoFF extension allows you to use the relative order of genes (synteny)</span>
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="html">  - <span class="nt" style="color: #000080;"><strong></span>--checkfasta<span class="nt" style="color: #000080;"></strong></span></span>
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="html">    checks input fasta files if the given algorithm can process the given fasta file.</span>
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="html"><span class="nt" style="color: #000080;"><details></span></span>
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="html">  <span class="nt" style="color: #000080;"><summary></span>(Click to expand)<span class="nt" style="color: #000080;"></summary></span></span>
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="html"></span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="html">  - <span class="nt" style="color: #000080;"><strong></span>--cleanblast<span class="nt" style="color: #000080;"></strong></span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="511" 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">
511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="html">    cleans blast-graph with proteinortho_cleanupblastgraph</span>
</pre>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="html"></span>
</pre>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="html">  - <span class="nt" style="color: #000080;"><strong></span>--desc<span class="nt" style="color: #000080;"></strong></span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="514" 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">
514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="html">    write description files (for NCBI FASTA input only)</span>
</pre>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="html"></span>
</pre>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="html">  - <span class="nt" style="color: #000080;"><strong></span>--binpath<span class="nt" style="color: #000080;"></strong></span>=directory (default: $PATH)</span>
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<td class="new_line diff-line-num new" data-linenumber="517" 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">
517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="html">    path to your local executables (blast, diamond, mcl, ...)</span>
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="html">  - <span class="nt" style="color: #000080;"><strong></span>--debug<span class="nt" style="color: #000080;"></strong></span></span>
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="html">    gives detailed information for bug tracking</span>
</pre>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="html"></span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="html"><span class="nt" style="color: #000080;"></details></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="html"><span class="nt" style="color: #000080;"><br></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="html"></span>
</pre>
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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="html"> <span class="nt" style="color: #000080;"><strong></span>Large compute jobs<span class="nt" style="color: #000080;"></strong></span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="526" 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="LC526" class="line" lang="html">  - <span class="nt" style="color: #000080;"><strong></span>--jobs<span class="nt" style="color: #000080;"></strong></span>=M/N</span>
</pre>
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="html">    If you want to involve multiple machines or separate a Proteinortho</span>
</pre>
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="html">    run into smaller chunks, use the -jobs=<span class="nt" style="color: #000080;"><strong></span>M<span class="nt" style="color: #000080;"></strong></span>/<span class="nt" style="color: #000080;"><strong></span>N<span class="nt" style="color: #000080;"></strong></span> option. First, run</span>
</pre>
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="html">    <span class="ni" style="color: #800080;">&#39;</span>proteinortho6.pl -steps=1 ...<span class="ni" style="color: #800080;">&#39;</span> to generate the indices. Then you can</span>
</pre>
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="html">    run <span class="ni" style="color: #800080;">&#39;</span>proteinortho6.pl -steps=2 -jobs=<span class="nt" style="color: #000080;"><strong></span>M<span class="nt" style="color: #000080;"></strong></span>/<span class="nt" style="color: #000080;"><strong></span>N<span class="nt" style="color: #000080;"></strong></span> ...<span class="ni" style="color: #800080;">&#39;</span> to run small chunks</span>
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="html">    separately. Instead of <span class="nt" style="color: #000080;"><strong></span>M<span class="nt" style="color: #000080;"></strong></span> and <span class="nt" style="color: #000080;"><strong></span>N<span class="nt" style="color: #000080;"></strong></span> numbers must be set representing the</span>
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="html">    number of jobs you want to divide the run into (<span class="nt" style="color: #000080;"><strong></span>M<span class="nt" style="color: #000080;"></strong></span>) and the job</span>
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="html">    division to be performed by the process. E.g. to divide a Proteinortho</span>
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="html">    run into 4 jobs to run on several machines, use <span class="ni" style="color: #800080;">&#39;</span>proteinortho6.pl -steps=2 -jobs=1/4<span class="ni" style="color: #800080;">&#39;</span>, <span class="ni" style="color: #800080;">&#39;</span>proteinortho6.pl -steps=2 -jobs=1/4<span class="ni" style="color: #800080;">&#39;</span>, <span class="ni" style="color: #800080;">&#39;</span>proteinortho6.pl -steps=2 -jobs=2/4<span class="ni" style="color: #800080;">&#39;</span>, <span class="ni" style="color: #800080;">&#39;</span>proteinortho6.pl -steps=2 -jobs=3/4<span class="ni" style="color: #800080;">&#39;</span>, <span class="ni" style="color: #800080;">&#39;</span>proteinortho6.pl -steps=2 -jobs=4/4<span class="ni" style="color: #800080;">&#39;</span>.</span>
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="html">    See <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Large-compute-jobs-(the--jobs-option"</span><span class="nt" style="color: #000080;">></span>Large compute jobs, the --jobs option (proteinortho wiki)<span class="nt" style="color: #000080;"></a></span>) for more details.</span>
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="html"><span class="nt" style="color: #000080;"><br></span></span>
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="html"># PoFF</span>
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="html">  The PoFF extension allows you to use the relative order of genes (synteny)</span>
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<pre style="margin: 0;"> <span id="LC543" class="line" lang="html">  as an additional criterion to disentangle complex co-orthology relations.</span>
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<pre style="margin: 0;"> <span id="LC544" class="line" lang="html">  To do so, add the parameter -synteny. You can use it to either come closer</span>
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<pre style="margin: 0;"> <span id="LC545" class="line" lang="html">  to one-to-one orthology relations by preferring synthetically conserved</span>
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<pre style="margin: 0;"> <span id="LC546" class="line" lang="html">  copies in the presence of two very similar paralogs (default), or just to</span>
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<pre style="margin: 0;"> <span id="LC547" class="line" lang="html">  reduce noise in the predictions by detecting multiple copies of genomic</span>
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<pre style="margin: 0;"> <span id="LC548" class="line" lang="html">  areas (add the parameter -dups=3). Please note that you need additional</span>
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<pre style="margin: 0;">-<span id="LC531" class="line" lang="html">  data to include synteny, namely the gene positions in GFF3 format.<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="html">  data to include synteny, namely the gene positions in GFF3 format.</span>
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<pre style="margin: 0;"> <span id="LC550" class="line" lang="html">  AsProteinortho is primarily made for proteins, it will only accept GFF</span>
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<pre style="margin: 0;"> <span id="LC551" class="line" lang="html">  entries of type CDS (column #3 in the GFF-file). The attributes column</span>
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<pre style="margin: 0;"> <span id="LC552" class="line" lang="html">  (#9) must contain Name=GENE IDENTIFIER where GENE IDENTIFIER corresponds</span>
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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">@@ -537,268 +555,244 @@ run into 4 jobs to run on several machines, use 'proteinortho6.pl -steps=2 -jobs</td>
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<pre style="margin: 0;"> <span id="LC555" class="line" lang="html">  files are provided in the source code archive. Hence, we can run</span>
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<pre style="margin: 0;"> <span id="LC556" class="line" lang="html">  proteinortho6.pl -project=test -synteny test/A1.faa test/B1.faa test/E1.faa</span>
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<pre style="margin: 0;"> <span id="LC557" class="line" lang="html">  test/F1.faa to add synteny information to the calculations. Of course,</span>
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<pre style="margin: 0;">-<span id="LC540" class="line" lang="html">  this only makes sense if species are sufficiently similar. You won<span class="idiff left right">'</span>t gain</span>
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="html">  this only makes sense if species are sufficiently similar. You won<span class="ni" style="color: #800080;"><span class="idiff left right">&#39;</span></span>t gain</span>
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<pre style="margin: 0;"> <span id="LC559" class="line" lang="html">  much when comparing e.g. bacteria with fungi. When the analysis is done</span>
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<pre style="margin: 0;"> <span id="LC560" class="line" lang="html">  you will find an additional file in your current working directory, namely</span>
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<pre style="margin: 0;"> <span id="LC561" class="line" lang="html">  test.poff.tsv (tab separated file). This file is equivalent to the test.proteinortho.tsv file (above) but</span>
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<pre style="margin: 0;"> <span id="LC562" class="line" lang="html">  can be considered more accurate as synteny was involved for its</span>
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<pre style="margin: 0;">-<span id="LC545" class="line" lang="html">  construction.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC546" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC547" class="line" lang="html"><span class="nt" style="color: #000080;"><h1</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"output"</span><span class="nt" style="color: #000080;">></span>Output<span class="nt" style="color: #000080;"></h1></span></span>
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<pre style="margin: 0;">-<span id="LC548" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC549" class="line" lang="html"><span class="nt" style="color: #000080;"><p><strong></span>BLAST Search (step 1-2)<span class="nt" style="color: #000080;"></strong></p></span></span>
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<pre style="margin: 0;">-<span id="LC550" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC551" class="line" lang="html"><span class="nt" style="color: #000080;"><p><details></span></span>
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552
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<pre style="margin: 0;">-<span id="LC552" class="line" lang="html">  <span class="nt" style="color: #000080;"><summary></span>myproject.blast-graph (Click to expand)<span class="nt" style="color: #000080;"></summary></p></span></span>
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553
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<pre style="margin: 0;">-<span id="LC553" class="line" lang="html"></span>
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554
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<pre style="margin: 0;">-<span id="LC554" class="line" lang="html"><span class="nt" style="color: #000080;"><pre><code></span>filtered raw blast data based on adaptive reciprocal best blast</span>
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555
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<pre style="margin: 0;">-<span id="LC555" class="line" lang="html">matches (= reciprocal best match plus all reciprocal matches within a</span>
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556
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<pre style="margin: 0;">-<span id="LC556" class="line" lang="html">range of 95% by default) The first two rows are just comments</span>
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<pre style="margin: 0;">-<span id="LC557" class="line" lang="html">explaining the meaning of each row. Whenever a further comment line (starting</span>
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558
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<pre style="margin: 0;">-<span id="LC558" class="line" lang="html">with #) follows, it indicates results comparing the two species is</span>
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559
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<pre style="margin: 0;">-<span id="LC559" class="line" lang="html">about to follow. E.g. # M.faa L.faa tells that the next lines representing</span>
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<pre style="margin: 0;">-<span id="LC560" class="line" lang="html">results for species M and L. All matches are reciprocal matches. If</span>
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561
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<td class="new_line diff-line-num old" data-linenumber="563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC561" class="line" lang="html">e.g. a match for M_15 L_15 is shown, L_15 M_15 exists implicitly.</span>
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<pre style="margin: 0;">-<span id="LC562" class="line" lang="html">E-Values and bit scores for both directions are given behind each</span>
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<pre style="margin: 0;">-<span id="LC563" class="line" lang="html">match.</span>
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<pre style="margin: 0;">-<span id="LC564" class="line" lang="html">The 4 comment numbers ('# 3.8e-124        434.9...') are representing the median values of  </span>
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<pre style="margin: 0;">-<span id="LC565" class="line" lang="html">evalue_ab, bitscore_ab, evalue_ba and bitscore_ba.</span>
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566
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<pre style="margin: 0;">-<span id="LC566" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC567" class="line" lang="html">  # file_a    file_b</span>
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568
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<pre style="margin: 0;">-<span id="LC568" class="line" lang="html">  # a   b     evalue_ab     bitscore_ab   evalue_ba     bitscore_ba </span>
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569
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<pre style="margin: 0;">-<span id="LC569" class="line" lang="html">  # E.faa     C.faa   </span>
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<pre style="margin: 0;">-<span id="LC570" class="line" lang="html">  # 3.8e-124        434.9   2.8e-126        442.2</span>
</pre>
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<pre style="margin: 0;">-<span id="LC571" class="line" lang="html">  E_11  C_11  5.9e-51 190.7   5.6e-50 187.61</span>
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572
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<pre style="margin: 0;">-<span id="LC572" class="line" lang="html">  E_10  C_10  3.8e-124    434.9   2.8e-126    442.2</span>
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<pre style="margin: 0;">-<span id="LC573" class="line" lang="html">  ...</span>
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574
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<pre style="margin: 0;">-<span id="LC574" class="line" lang="html"><span class="nt" style="color: #000080;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC575" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC576" class="line" lang="html"><span class="nt" style="color: #000080;"><p></details></span></span>
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577
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<pre style="margin: 0;">-<span id="LC577" class="line" lang="html"> <span class="nt" style="color: #000080;"><br></p></span></span>
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<pre style="margin: 0;">-<span id="LC578" class="line" lang="html"></span>
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579
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<pre style="margin: 0;">-<span id="LC579" class="line" lang="html"><span class="nt" style="color: #000080;"><p><strong></span>Clustering (step 3)<span class="nt" style="color: #000080;"></strong></p></span></span>
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<pre style="margin: 0;">-<span id="LC580" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC581" class="line" lang="html"><span class="nt" style="color: #000080;"><p><details></span></span>
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="html">  construction.</span>
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="html"># Output</span>
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<td class="new_line diff-line-num new" data-linenumber="566" 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">
566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="html"> <span class="nt" style="color: #000080;"><strong></span>BLAST Search (step 1-2)<span class="nt" style="color: #000080;"></strong></span></span>
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="html"><span class="nt" style="color: #000080;"><details></span></span>
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<td class="new_line diff-line-num new" data-linenumber="569" 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="LC569" class="line" lang="html">  <span class="nt" style="color: #000080;"><summary></span>myproject.blast-graph (Click to expand)<span class="nt" style="color: #000080;"></summary></span></span>
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="html">    filtered raw blast data based on adaptive reciprocal best blast</span>
</pre>
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="html">    matches (= reciprocal best match matches within a range of 95% by default) </span>
</pre>
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="html">    A line starting with # indicates the two species that are analysed below. E.g. <span class="ni" style="color: #800080;">&#39;</span># M.faa L.faa<span class="ni" style="color: #800080;">&#39;</span> tells that the next lines are for species M versus species L.</span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="html"></span>
</pre>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="html">    All matches are reciprocal matches. If</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="577" 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">
577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="html">    e.g. a match for M_15 L_15 is shown, L_15 M_15 exists implicitly.</span>
</pre>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="582" 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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<td class="new_line diff-line-num new" data-linenumber="579" 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">
579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="html">    E-Values and bit scores for both directions are given behind each</span>
</pre>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="html">    match. </span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="581" 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">
581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="html"></span>
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<td class="new_line diff-line-num new" data-linenumber="582" 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">
582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="html">    The 4 numbers below the species (e.g. <span class="ni" style="color: #800080;">&#39;</span># 3.8e-124        434.9...<span class="ni" style="color: #800080;">&#39;</span>) are representing the median values for this comparison.</span>
</pre>
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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="html"></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="584" 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">
584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="html">      # file_a    file_b</span>
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<td class="new_line diff-line-num new" data-linenumber="585" 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">
585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="html">      # a   b     evalue_ab     bitscore_ab   evalue_ba     bitscore_ba</span>
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<td class="new_line diff-line-num new" data-linenumber="586" 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">
586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="html">      # E.faa     C.faa<span class="nt" style="color: #000080;"><br></span>      # 3.8e-124        434.9   2.8e-126        442.2</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="587" 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">
587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="html">      E_11  C_11  5.9e-51 190.7   5.6e-50 187.61</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="588" 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">
588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="html">      E_10  C_10  3.8e-124    434.9   2.8e-126    442.2</span>
</pre>
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="html">      ...</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="590" 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">
590
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC590" class="line" lang="html"> <span class="nt" style="color: #000080;"></details></span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="591" 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">
591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="html"> <span class="nt" style="color: #000080;"><br></span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="592" 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">
592
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC592" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="582" 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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<td class="new_line diff-line-num new" data-linenumber="593" 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">
593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="html"> <span class="nt" style="color: #000080;"><strong></span>Clustering (step 3)<span class="nt" style="color: #000080;"></strong></span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="594" 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">
594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="html"></span>
</pre>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="html"><span class="nt" style="color: #000080;"><details></span></span>
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582
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<pre style="margin: 0;"> <span id="LC596" class="line" lang="html">  <span class="nt" style="color: #000080;"><summary></span>myproject.proteinortho-graph (Click to expand)<span class="nt" style="color: #000080;"></summary></span></span>
</pre>
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<td class="new_line diff-line-num old" data-linenumber="597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC583" class="line" lang="html">    clustered myproject.blast-graph. Its connected components are represented in myproject.proteinortho.tsv / myproject.proteinortho.html. The format of myproject.blast-graph is the same as the</span>
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<pre style="margin: 0;">-<span id="LC584" class="line" lang="html">    blast-graph (see above).<span class="nt" style="color: #000080;"></p></span></span>
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585
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<pre style="margin: 0;"> <span id="LC597" class="line" lang="html"></span>
</pre>
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<pre style="margin: 0;">-<span id="LC586" class="line" lang="html"><span class="nt" style="color: #000080;"><pre><code></span>  # file_a    file_b</span>
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587
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<td class="new_line diff-line-num old" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC587" class="line" lang="html">  # a   b     evalue_ab     bitscore_ab   evalue_ba     bitscore_ba</span>
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588
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<td class="new_line diff-line-num old" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC588" class="line" lang="html">  # E.faa     C.faa</span>
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589
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<pre style="margin: 0;">-<span id="LC589" class="line" lang="html">  E_10  C_10  3.8e-124    434.9   2.8e-126    442.2</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
590
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<td class="new_line diff-line-num old" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC590" class="line" lang="html">  E_11  C_11  5.9e-51 190.7   5.6e-50 187.6</span>
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591
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<td class="new_line diff-line-num old" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC591" class="line" lang="html"><span class="nt" style="color: #000080;"></code></pre></span></span>
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="html">    clustered version of the myproject.blast-graph.</span>
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<pre style="margin: 0;"> <span id="LC599" class="line" lang="html"></span>
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<td class="new_line diff-line-num old" data-linenumber="600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC593" class="line" lang="html"><span class="nt" style="color: #000080;"><p></details></span></span>
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<td class="new_line diff-line-num old" data-linenumber="600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC594" class="line" lang="html"> <span class="nt" style="color: #000080;"><br></p></span></span>
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<td class="old_line diff-line-num new" data-linenumber="595" 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="LC600" class="line" lang="html">    Its connected components are represented in myproject.proteinortho.tsv / myproject.proteinortho.html.</span>
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<pre style="margin: 0;"> <span id="LC601" class="line" lang="html"></span>
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<td class="new_line diff-line-num old" data-linenumber="602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC596" class="line" lang="html"><span class="nt" style="color: #000080;"><p><details></span></span>
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="html">    The format of myproject.blast-graph is the equivalent to the myproject.blast-graph (see above).</span>
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="html"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="html">      # file_a    file_b</span>
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="html">      # a   b     evalue_ab     bitscore_ab   evalue_ba     bitscore_ba</span>
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="html">      # E.faa     C.faa</span>
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="html">      E_10  C_10  3.8e-124    434.9   2.8e-126    442.2</span>
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="html">      E_11  C_11  5.9e-51 190.7   5.6e-50 187.6</span>
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="html">      ...</span>
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="html"> <span class="nt" style="color: #000080;"></details></span></span>
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="html"> <span class="nt" style="color: #000080;"><br></span></span>
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="html"> <span class="nt" style="color: #000080;"><details></span></span>
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<pre style="margin: 0;"> <span id="LC614" class="line" lang="html">  <span class="nt" style="color: #000080;"><summary></span> myproject.proteinortho.tsv (Click to expand)<span class="nt" style="color: #000080;"></summary></span></span>
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<pre style="margin: 0;">-<span id="LC598" class="line" lang="html">    The connected components. The first line starting with #is a comment</span>
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<pre style="margin: 0;">-<span id="LC599" class="line" lang="html">    line indicating the meaning of each column for each of the following</span>
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<pre style="margin: 0;">-<span id="LC600" class="line" lang="html">    lines which represent an orthologous group each. The very first column</span>
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<pre style="margin: 0;">-<span id="LC601" class="line" lang="html">    indicates the number of species covered by this group. The second</span>
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<pre style="margin: 0;">-<span id="LC602" class="line" lang="html">    column indicates the number of genes included in the group. Often,</span>
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<pre style="margin: 0;">-<span id="LC603" class="line" lang="html">    this number will equal the number of species, meaning that there is a</span>
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<pre style="margin: 0;">-<span id="LC604" class="line" lang="html">    single ortholog in each species. If the number of genes is bigger than</span>
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<pre style="margin: 0;">-<span id="LC605" class="line" lang="html">    the number of species, there are co-orthologs present. The third</span>
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<pre style="margin: 0;">-<span id="LC606" class="line" lang="html">    column gives rise to the algebraic connectivity of the respective</span>
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<pre style="margin: 0;">-<span id="LC607" class="line" lang="html">    group. Basically, this indicates how densely the genes are connected</span>
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<pre style="margin: 0;">-<span id="LC608" class="line" lang="html">    in the orthology graph that was used for clustering. A connectivity of</span>
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<pre style="margin: 0;">-<span id="LC609" class="line" lang="html">    1 indicates a perfect dense cluster with each gene similar to each</span>
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<pre style="margin: 0;">-<span id="LC610" class="line" lang="html">    other gene. By default, Proteinortho splits each group into two more</span>
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<pre style="margin: 0;">-<span id="LC611" class="line" lang="html">    dense subgroups when the connectivity is below 0.1 (can be user defined).</span>
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<pre style="margin: 0;">-<span id="LC612" class="line" lang="html">    Hint: you can open this file in Excel / Numbers / Open Office.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC613" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC614" class="line" lang="html"><span class="nt" style="color: #000080;"><pre><code></span>  # Species   Genes   Alg.-Conn.    C.faa   C2.faa  E.faa   L.faa   M.faa</span>
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<pre style="margin: 0;">-<span id="LC615" class="line" lang="html">  2   5     0.16  *     *     *     L_643,L_641   M_649,M_640,M_642</span>
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<pre style="margin: 0;">-<span id="LC616" class="line" lang="html">  3   6     0.138   C_164,C_166,C_167,C_2   *     *     L_2   M_2</span>
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<pre style="margin: 0;">-<span id="LC617" class="line" lang="html">  2   4     0.489   *     *     *     L_645,L_647   M_644,M_646</span>
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<pre style="margin: 0;">-<span id="LC618" class="line" lang="html"><span class="nt" style="color: #000080;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC619" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC620" class="line" lang="html"><span class="nt" style="color: #000080;"><p></details></span></span>
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<pre style="margin: 0;">-<span id="LC621" class="line" lang="html"> <span class="nt" style="color: #000080;"><br></p></span></span>
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<pre style="margin: 0;">-<span id="LC622" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC623" class="line" lang="html"><span class="nt" style="color: #000080;"><p><details></span></span>
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="html">    The connected components of myproject.proteinortho-graph. </span>
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="html">    The very first column indicates the number of species covered by this group. </span>
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="html">    The second column indicates the number of genes included in this group. </span>
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="html">    If the number of genes is bigger than the number of species, there are co-orthologs present. </span>
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="html">    The third column gives the algebraic connectivity of the respective group. This indicates how densely the genes are connected</span>
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="html">    in the orthology graph that was used for clustering. </span>
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625
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="html">    A connectivity of 1 indicates a perfect dense cluster with each gene beeing connected/orthologous to each</span>
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="html">    other gene. </span>
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627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="html"></span>
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628
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="html">    By default, Proteinortho splits each group into two more dense subgroups when the connectivity is below 0.1 (can be user defined).</span>
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629
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="html">    Hint: you can open this file in Excel / Numbers / Open Office.</span>
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631
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="html">      # Species   Genes   Alg.-Conn.    C.faa   C2.faa  E.faa   L.faa   M.faa</span>
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="html">      2   5     0.16  <span class="nt" style="color: #000080;"></em></span>     <span class="nt" style="color: #000080;"><em></span>     <span class="nt" style="color: #000080;"></em></span>     L_643,L_641   M_649,M_640,M_642</span>
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634
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="html">      3   6     0.138   C_164,C_166,C_167,C_2   <span class="nt" style="color: #000080;"><em></span>     <span class="nt" style="color: #000080;"></em></span>     L_2   M_2</span>
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<td class="new_line diff-line-num new" data-linenumber="635" 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">
635
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="html">      2   4     0.489   <span class="nt" style="color: #000080;"><em></span>     <span class="nt" style="color: #000080;"></em></span>     <span class="nt" style="color: #000080;"><em></span>     L_645,L_647   M_644,M_646</span>
</pre>
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636
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="html"> <span class="nt" style="color: #000080;"></details></span></span>
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="html"> <span class="nt" style="color: #000080;"><br></span></span>
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639
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="html"><span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Tools-and-additional-programs#proteinortho-graphblast-graph-species-summary-table"</span><span class="nt" style="color: #000080;">></span>myproject.proteinortho-graph.summary<span class="nt" style="color: #000080;"></a></span></span>
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641
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="html"></span>
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642
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="html"> <span class="nt" style="color: #000080;"><br></span></span>
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643
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="html"> <span class="nt" style="color: #000080;"><details></span></span>
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624
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<pre style="margin: 0;"> <span id="LC644" class="line" lang="html">  <span class="nt" style="color: #000080;"><summary></span> myproject.proteinortho.html (Click to expand)<span class="nt" style="color: #000080;"></summary></span></span>
</pre>
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625
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645
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<pre style="margin: 0;"> <span id="LC645" class="line" lang="html">    The html version of the myproject.proteinortho.tsv file</span>
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626
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646
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<pre style="margin: 0;"> <span id="LC646" class="line" lang="html"> <span class="nt" style="color: #000080;"></details></span></span>
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<pre style="margin: 0;">-<span id="LC627" class="line" lang="html"> <span class="nt" style="color: #000080;"><br><span class="idiff left right"></p></span></span></span>
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647
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="html"> <span class="nt" style="color: #000080;"><br></span></span>
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628
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648
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<pre style="margin: 0;"> <span id="LC648" class="line" lang="html"></span>
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629
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<td class="new_line diff-line-num old" data-linenumber="649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC629" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left"><p></span><strong></span>POFF (-synteny)<span class="nt" style="color: #000080;"></strong><span class="idiff right"></p></span></span></span>
</pre>
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649
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="html"><span class="idiff left right"> </span><span class="nt" style="color: #000080;"><strong></span>POFF (-synteny)<span class="nt" style="color: #000080;"></strong></span></span>
</pre>
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630
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650
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<pre style="margin: 0;"> <span id="LC650" class="line" lang="html"></span>
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631
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<pre style="margin: 0;">-<span id="LC631" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left right"><p></span></span>The synteny based graph files (myproject.ffadj-graph and</span>
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651
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="html"><span class="idiff left right">  </span>The synteny based graph files (myproject.ffadj-graph and</span>
</pre>
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<pre style="margin: 0;"> <span id="LC652" class="line" lang="html">  myproject.poff.tsv (tab separated file)-graph) have two additional columns: same_strand and</span>
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653
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<pre style="margin: 0;"> <span id="LC653" class="line" lang="html">  simscore. The first one indicates if two genes from a match are located at</span>
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634
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654
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<pre style="margin: 0;"> <span id="LC654" class="line" lang="html">  the same strands (1) or not (-1). The second one is an internal score</span>
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655
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<pre style="margin: 0;"> <span id="LC655" class="line" lang="html">  which can be interpreted as a normalized weight ranging from 0 to 1 based</span>
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656
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<pre style="margin: 0;"> <span id="LC656" class="line" lang="html">  on the respective e-values. Moreover, a second comment line is followed</span>
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<pre style="margin: 0;">-<span id="LC637" class="line" lang="html">  after the species lines, e.g.<span class="nt" style="color: #000080;"><span class="idiff left right"></p></span></span></span>
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="html">  after the species lines, e.g.</span>
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<pre style="margin: 0;"> <span id="LC658" class="line" lang="html"></span>
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639
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<td class="new_line diff-line-num old" data-linenumber="659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC639" class="line" lang="html"><span class="nt" style="color: #000080;"><pre><code></span># M.faa L.faa</span>
</pre>
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640
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<td class="new_line diff-line-num old" data-linenumber="659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC640" class="line" lang="html"># Scores: 4   39    34.000000     39.000000</span>
</pre>
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641
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<td class="new_line diff-line-num old" data-linenumber="659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC641" class="line" lang="html"><span class="nt" style="color: #000080;"></code></pre></span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="642" 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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<td class="new_line diff-line-num new" data-linenumber="659" 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">
659
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="html">    # M.faa L.faa</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="642" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="660" 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">
660
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="html">    # Scores: 4   39    34.000000     39.000000</span>
</pre>
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642
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661
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<pre style="margin: 0;"> <span id="LC661" class="line" lang="html"></span>
</pre>
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643
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<td class="new_line diff-line-num old" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC643" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left right"><p></span><details></span></span>
</pre>
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644
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<td class="new_line diff-line-num old" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC644" class="line" lang="html">  <span class="nt" style="color: #000080;"><summary></span>myproject.ffadj-graph (Click to expand)<span class="nt" style="color: #000080;"></summary><span class="idiff left right"></p></span></span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="645" 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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662
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="html"><span class="idiff left right">  </span><span class="nt" style="color: #000080;"><details></span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="645" 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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663
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="html">  <span class="nt" style="color: #000080;"><summary></span>myproject.ffadj-graph (Click to expand)<span class="nt" style="color: #000080;"></summary></span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="645" 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">
645
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664
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC664" class="line" lang="html"></span>
</pre>
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646
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<td class="new_line diff-line-num old" data-linenumber="665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC646" class="line" lang="html"><span class="nt" style="color: #000080;"><pre><code></span>filtered blast data based on adaptive reciprocal best blast matches</span>
</pre>
</td>
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647
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<td class="new_line diff-line-num old" data-linenumber="665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC647" class="line" lang="html">and synteny (only if -synteny is set)</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
648
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<td class="new_line diff-line-num old" data-linenumber="665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
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<pre style="margin: 0;">-<span id="LC648" class="line" lang="html"><span class="nt" style="color: #000080;"></code></pre></span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="649" 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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<td class="new_line diff-line-num new" data-linenumber="665" 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="LC665" class="line" lang="html">    filtered blast data based on adaptive reciprocal best blast matches</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="649" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="666" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC666" class="line" lang="html">    and synteny (only if -synteny is set)</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="649" 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">
649
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<td class="new_line diff-line-num" data-linenumber="667" 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">
667
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC667" class="line" lang="html"></span>
</pre>
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650
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</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC650" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left right"><p></span></details></span></span>
</pre>
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651
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<td class="new_line diff-line-num old" data-linenumber="668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC651" class="line" lang="html"> <span class="nt" style="color: #000080;"><br><span class="idiff left right"></p></span></span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="652" 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="LC668" class="line" lang="html"><span class="idiff left right"> </span><span class="nt" style="color: #000080;"></details></span></span>
</pre>
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669
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="html"> <span class="nt" style="color: #000080;"><br></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC653" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left right"><p></span><details></span></span>
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<pre style="margin: 0;">-<span id="LC654" class="line" lang="html">  <span class="nt" style="color: #000080;"><summary></span>myproject.poff.tsv (tab separated file)-graph (Click to expand)<span class="nt" style="color: #000080;"></summary><span class="idiff left right"></p></span></span></span>
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="html"><span class="idiff left right">  </span><span class="nt" style="color: #000080;"><details></span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC672" class="line" lang="html">  <span class="nt" style="color: #000080;"><summary></span>myproject.poff.tsv (tab separated file)-graph (Click to expand)<span class="nt" style="color: #000080;"></summary></span></span>
</pre>
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655
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673
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<pre style="margin: 0;"> <span id="LC673" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC656" class="line" lang="html"><span class="nt" style="color: #000080;"><pre><code></span>clustered ffadj graph. Its connected components are represented in</span>
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<pre style="margin: 0;">-<span id="LC657" class="line" lang="html">myproject.poff.tsv (tab separated file) (only if -synteny is set)</span>
</pre>
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<pre style="margin: 0;">-<span id="LC658" class="line" lang="html"><span class="nt" style="color: #000080;"></code></pre></span></span>
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="html">    clustered ffadj graph. Its connected components are represented in</span>
</pre>
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="html">    myproject.poff.tsv (tab separated file) (only if -synteny is set)</span>
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<pre style="margin: 0;"> <span id="LC676" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC660" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left right"><p></span></details></span></span>
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<pre style="margin: 0;">-<span id="LC661" class="line" lang="html"> <span class="nt" style="color: #000080;"><br><span class="idiff left right"></p></span></span></span>
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="html"><span class="idiff left right"> </span><span class="nt" style="color: #000080;"></details></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="html"> <span class="nt" style="color: #000080;"><br></span></span>
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<pre style="margin: 0;"> <span id="LC679" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC663" class="line" lang="html"><span class="nt" style="color: #000080;"><h1</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"examples"</span><span class="nt" style="color: #000080;">></span>EXAMPLES<span class="nt" style="color: #000080;"></h1></span></span>
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680
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<pre style="margin: 0;"> <span id="LC680" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC665" class="line" lang="html"><span class="nt" style="color: #000080;"><p><strong></span>Calling proteinortho<span class="nt" style="color: #000080;"></strong></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="html"># EXAMPLES</span>
</pre>
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682
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="html"> <span class="nt" style="color: #000080;"><strong></span>Calling proteinortho<span class="nt" style="color: #000080;"></strong></span></span>
</pre>
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666
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683
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<pre style="margin: 0;"> <span id="LC683" class="line" lang="html">  Sequences are typically given in plain fasta format like the files in</span>
</pre>
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667
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<pre style="margin: 0;">-<span id="LC667" class="line" lang="html">  test/<span class="nt" style="color: #000080;"><span class="idiff left right"></p></span></span></span>
</pre>
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684
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC684" class="line" lang="html">  test/</span>
</pre>
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668
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685
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<pre style="margin: 0;"> <span id="LC685" class="line" lang="html"></span>
</pre>
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669
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<td class="new_line diff-line-num old" data-linenumber="686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC669" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left"><p></span></span>test/C.faa:<span class="nt" style="color: #000080;"><span class="idiff right"></p></span></span></span>
</pre>
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686
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="html"><span class="idiff left right">  </span>test/C.faa:</span>
</pre>
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670
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687
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<pre style="margin: 0;"> <span id="LC687" class="line" lang="html"></span>
</pre>
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671
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<td class="new_line diff-line-num old" data-linenumber="688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC671" class="line" lang="html"><span class="nt" style="color: #000080;"><pre><code></span><span class="ni" style="color: #800080;">&gt;</span>C_10</span>
</pre>
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672
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<pre style="margin: 0;">-<span id="LC672" class="line" lang="html">VVLCRYEIGGLAQVLDTQFDMYTNCHKMCSADSQVTYKEAANLTARVTTDRQKEPLTGGY</span>
</pre>
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673
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<pre style="margin: 0;">-<span id="LC673" class="line" lang="html">HGAKLGFLGCSLLRSRDYGYPEQNFHAKTDLFALPMGDHYCGDEGSGNAYLCDFDNQYGR</span>
</pre>
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674
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<pre style="margin: 0;">-<span id="LC674" class="line" lang="html">...</span>
</pre>
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675
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<pre style="margin: 0;">-<span id="LC675" class="line" lang="html"><span class="nt" style="color: #000080;"></code></pre></span></span>
</pre>
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688
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="html">    <span class="ni" style="color: #800080;">&gt;</span>C_10</span>
</pre>
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689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="html">    VVLCRYEIGGLAQVLDTQFDMYTNCHKMCSADSQVTYKEAANLTARVTTDRQKEPLTGGY</span>
</pre>
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690
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="html">    HGAKLGFLGCSLLRSRDYGYPEQNFHAKTDLFALPMGDHYCGDEGSGNAYLCDFDNQYGR</span>
</pre>
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691
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="html">    ...</span>
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676
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692
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<pre style="margin: 0;"> <span id="LC692" class="line" lang="html"></span>
</pre>
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677
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<pre style="margin: 0;">-<span id="LC677" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left"><p></span></span>test/E.faa:<span class="nt" style="color: #000080;"><span class="idiff right"></p></span></span></span>
</pre>
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693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="html"><span class="idiff left right">   </span>test/E.faa:</span>
</pre>
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678
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694
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<pre style="margin: 0;"> <span id="LC694" class="line" lang="html"></span>
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679
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<pre style="margin: 0;">-<span id="LC679" class="line" lang="html"><span class="nt" style="color: #000080;"><pre><code></span><span class="ni" style="color: #800080;">&gt;</span>E_10</span>
</pre>
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680
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<pre style="margin: 0;">-<span id="LC680" class="line" lang="html">CVLDNYQIALLRNVLPKLFMTKNFIEGMCGGGGEENYKAMTRATAKSTTDNQNAPLSGGF</span>
</pre>
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681
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<td class="new_line diff-line-num old" data-linenumber="695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC681" class="line" lang="html">NDGKMGTGCLPSAAKNYKYPENAVSGASNLYALIVGESYCGDENDDKAYLCDVNQYAPNV</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
682
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<td class="new_line diff-line-num old" data-linenumber="695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC682" class="line" lang="html">...</span>
</pre>
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683
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<td class="new_line diff-line-num old" data-linenumber="695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC683" class="line" lang="html"><span class="nt" style="color: #000080;"></code></pre></span></span>
</pre>
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695
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC695" class="line" lang="html">    <span class="ni" style="color: #800080;">&gt;</span>E_10</span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="684" 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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696
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="html">    CVLDNYQIALLRNVLPKLFMTKNFIEGMCGGGGEENYKAMTRATAKSTTDNQNAPLSGGF</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="697" 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">
697
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="html">    NDGKMGTGCLPSAAKNYKYPENAVSGASNLYALIVGESYCGDENDDKAYLCDVNQYAPNV</span>
</pre>
</td>
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698
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC698" class="line" lang="html">    ...</span>
</pre>
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684
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<td class="new_line diff-line-num" data-linenumber="699" 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">
699
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC699" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
685
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<td class="new_line diff-line-num old" data-linenumber="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC685" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left"><p></span></span>To run proteinortho for these sequences, simply call<span class="nt" style="color: #000080;"><span class="idiff right"></p></span></span></span>
</pre>
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700
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="html"><span class="idiff left right">  </span>To run proteinortho for these sequences, simply call</span>
</pre>
</td>
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686
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701
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC701" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
687
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<td class="new_line diff-line-num old" data-linenumber="702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC687" class="line" lang="html"><span class="nt" style="color: #000080;"><pre><code></span>perl proteinortho6.pl test/C.faa test/E.faa test/L.faa test/M.faa</span>
</pre>
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688
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<td class="new_line diff-line-num old" data-linenumber="702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC688" class="line" lang="html"><span class="nt" style="color: #000080;"></code></pre></span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="689" 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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<td class="new_line diff-line-num new" data-linenumber="702" 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">
702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="html">    perl proteinortho6.pl test/C.faa test/E.faa test/L.faa test/M.faa</span>
</pre>
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689
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<td class="new_line diff-line-num" data-linenumber="703" 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">
703
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC703" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
690
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<td class="new_line diff-line-num old" data-linenumber="704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC690" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left"><p></span></span>To give the outputs the name <span class="idiff">'test'</span>, call<span class="nt" style="color: #000080;"><span class="idiff right"></p></span></span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="691" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="704" 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">
704
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC704" class="line" lang="html"><span class="idiff left">  </span>To give the outputs the name <span class="ni" style="color: #800080;"><span class="idiff">&#39;</span></span><span class="idiff">test</span><span class="ni" style="color: #800080;"><span class="idiff right">&#39;</span></span>, call</span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="691" 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">
691
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<td class="new_line diff-line-num" data-linenumber="705" 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">
705
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC705" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
692
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<td class="new_line diff-line-num old" data-linenumber="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC692" class="line" lang="html"><span class="nt" style="color: #000080;"><pre><code></span>perl proteinortho6.pl -project=test test/*faa</span>
</pre>
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693
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<td class="new_line diff-line-num old" data-linenumber="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC693" class="line" lang="html"><span class="nt" style="color: #000080;"></code></pre></span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="694" 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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<td class="new_line diff-line-num new" data-linenumber="706" 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">
706
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC706" class="line" lang="html">    perl proteinortho6.pl -project=test test/<span class="nt" style="color: #000080;"></em></span>faa</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="694" 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">
694
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<td class="new_line diff-line-num" data-linenumber="707" 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">
707
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC707" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
695
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<td class="new_line diff-line-num old" data-linenumber="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC695" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left"><p></span></span>To use blast instead of the default diamond, call<span class="nt" style="color: #000080;"><span class="idiff right"></p></span></span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="696" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="708" 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">
708
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC708" class="line" lang="html"><span class="idiff left right">  </span>To use blast instead of the default diamond, call</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="696" 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">
696
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<td class="new_line diff-line-num" data-linenumber="709" 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">
709
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC709" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
697
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<td class="new_line diff-line-num old" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC697" class="line" lang="html"><span class="nt" style="color: #000080;"><pre><code></span>perl proteinortho6.pl -project=test -p=blastp+ test/*faa</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
698
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<td class="new_line diff-line-num old" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC698" class="line" lang="html"><span class="nt" style="color: #000080;"></code></pre></span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="699" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="710" 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">
710
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="html">    perl proteinortho6.pl -project=test -p=blastp+ test/<span class="nt" style="color: #000080;"><em></span>faa</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="699" 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">
699
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<td class="new_line diff-line-num" data-linenumber="711" 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">
711
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC711" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
700
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<td class="new_line diff-line-num old" data-linenumber="712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC700" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left"><p></span></span>If installed with make install, you can also call<span class="nt" style="color: #000080;"><span class="idiff right"></p></span></span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="701" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="712" 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">
712
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC712" class="line" lang="html"><span class="idiff left right">  </span>If installed with make install, you can also call</span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="701" 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">
701
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<td class="new_line diff-line-num" data-linenumber="713" 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">
713
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC713" class="line" lang="html"></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
702
</td>
<td class="new_line diff-line-num old" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC702" class="line" lang="html"><span class="nt" style="color: #000080;"><pre><code></span>proteinortho -project=test -p=blastp+ test/*faa</span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
703
</td>
<td class="new_line diff-line-num old" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC703" class="line" lang="html"><span class="nt" style="color: #000080;"></code></pre></span></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="704" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="714" 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">
714
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC714" class="line" lang="html">    proteinortho -project=test -p=blastp+ test/<span class="nt" style="color: #000080;"></em></span>faa</span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="704" 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">
704
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<td class="new_line diff-line-num" data-linenumber="715" 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">
715
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC715" class="line" lang="html"></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
705
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<td class="new_line diff-line-num old" data-linenumber="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC705" class="line" lang="html"><span class="nt" style="color: #000080;"><h1</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"hints"</span><span class="nt" style="color: #000080;">></span>Hints<span class="nt" style="color: #000080;"></h1></span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="706" 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">
706
</td>
<td class="new_line diff-line-num" data-linenumber="716" 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">
716
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC716" class="line" lang="html"></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num old" data-linenumber="707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
707
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<td class="new_line diff-line-num old" data-linenumber="717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC707" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Using .faa to indicate that your file contains amino acids and .fna to</span>
</pre>
</td>
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708
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<td class="new_line diff-line-num old" data-linenumber="717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC708" class="line" lang="html">  show it contains nucleotides makes life much easier.<span class="nt" style="color: #000080;"></p></span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="709" 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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<td class="new_line diff-line-num new" data-linenumber="717" 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">
717
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="html"># Hints</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="709" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="718" 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">
718
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC718" class="line" lang="html">  Using .faa to indicate that your file contains amino acids and .fna to</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="709" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="719" 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">
719
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC719" class="line" lang="html">  show it contains nucleotides makes life much easier.</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="709" 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">
709
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<td class="new_line diff-line-num" data-linenumber="720" 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">
720
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC720" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
710
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<td class="new_line diff-line-num old" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC710" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left right"><p></span></span>Sequence IDs must be unique within a single FASTA file. Consider renaming</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="711" 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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<td class="new_line diff-line-num new" data-linenumber="721" 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">
721
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC721" class="line" lang="html"><span class="idiff left right">  </span>Sequence IDs must be unique within a single FASTA file. Consider renaming</span>
</pre>
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711
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<td class="new_line diff-line-num" data-linenumber="722" 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">
722
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<pre style="margin: 0;"> <span id="LC722" class="line" lang="html">  otherwise. Note: Till version 5.15 sequences IDs had to be unique among</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="712" 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">
712
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<td class="new_line diff-line-num" data-linenumber="723" 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">
723
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<pre style="margin: 0;"> <span id="LC723" class="line" lang="html">  the whole dataset. Proteinortho now keeps track of name and species to</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
713
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<td class="new_line diff-line-num old" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC713" class="line" lang="html">  avoid the necessissity of renaming.<span class="nt" style="color: #000080;"><span class="idiff left right"></p></span></span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="714" 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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<td class="new_line diff-line-num new" data-linenumber="724" 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">
724
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="html">  avoid the necessissity of renaming.</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="714" 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">
714
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<td class="new_line diff-line-num" data-linenumber="725" 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">
725
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC725" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
715
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<td class="new_line diff-line-num old" data-linenumber="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC715" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left right"><p></span></span>You need write permissions in the directory of your FASTA files as</span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="716" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="726" 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">
726
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC726" class="line" lang="html"><span class="idiff left right">  </span>You need write permissions in the directory of your FASTA files as</span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="716" 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">
716
</td>
<td class="new_line diff-line-num" data-linenumber="727" 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">
727
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC727" class="line" lang="html">  Proteinortho will create blast databases. If this is not the case,</span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
717
</td>
<td class="new_line diff-line-num old" data-linenumber="728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC717" class="line" lang="html">  consider using symbolic links to the FASTA files.<span class="nt" style="color: #000080;"><span class="idiff left right"></p></span></span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="718" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="728" 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">
728
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC728" class="line" lang="html">  consider using symbolic links to the FASTA files.</span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="718" 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">
718
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<td class="new_line diff-line-num" data-linenumber="729" 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">
729
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC729" class="line" lang="html"></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
719
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<td class="new_line diff-line-num old" data-linenumber="730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC719" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left"><p></span></span>The directory src contains useful tools, e.g. proteinortho<span class="nt" style="color: #000080;"><span class="idiff"><em></span></span><span class="idiff">grab</span><span class="nt" style="color: #000080;"><span class="idiff right"></em></span></span>proteins.pl which</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="720" 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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<td class="new_line diff-line-num new" data-linenumber="730" 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">
730
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC730" class="line" lang="html"><span class="idiff left">  </span>The directory src contains useful tools, e.g. proteinortho<span class="idiff right">_grab_</span>proteins.pl which</span>
</pre>
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720
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731
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<pre style="margin: 0;"> <span id="LC731" class="line" lang="html">  fetches protein sequences of orthologous groups from Proteinortho output</span>
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<pre style="margin: 0;">-<span id="LC721" class="line" lang="html">  table. (These files are installed during <span class="idiff left">'</span>make install<span class="idiff">')</span><span class="nt" style="color: #000080;"><span class="idiff right"></p></span></span></span>
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="html">  table. (These files are installed during <span class="ni" style="color: #800080;"><span class="idiff left">&#39;</span></span>make install<span class="ni" style="color: #800080;"><span class="idiff">&#39;</span></span><span class="idiff right">)</span></span>
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733
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<pre style="margin: 0;"> <span id="LC733" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC723" class="line" lang="html"><span class="nt" style="color: #000080;"><h1</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"kmereheuristic"</span><span class="nt" style="color: #000080;">></span>Kmere Heuristic<span class="nt" style="color: #000080;"></h1></span></span>
</pre>
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734
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<pre style="margin: 0;"> <span id="LC734" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC725" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left"><h2</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">id=</span></span><span class="s" style="color: #d14;"><span class="idiff">"example1"</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff">Example 1</span><span class="nt" style="color: #000080;"><span class="idiff right"></h2></span></span></span>
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="html"><span class="idiff left right"># Kmere Heuristic</span></span>
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<pre style="margin: 0;"> <span id="LC736" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC727" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>In the following example a huge blast graph is used for step 3 (clustering). </span>
</pre>
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728
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<pre style="margin: 0;">-<span id="LC728" class="line" lang="html">The first connected component contains 7410694 nodes, hence the kmere heuristic is activated.</span>
</pre>
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<pre style="margin: 0;">-<span id="LC729" class="line" lang="html">Since the fiedler vector would result in a good split, the kmere heuristic is then deactivated immediatly.<span class="nt" style="color: #000080;"></p></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC730" class="line" lang="html"></span>
</pre>
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<pre style="margin: 0;">-<span id="LC731" class="line" lang="html"><span class="nt" style="color: #000080;"><p><details></span></span>
</pre>
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732
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<pre style="margin: 0;">-<span id="LC732" class="line" lang="html">  <span class="nt" style="color: #000080;"><summary></span>as fallback (Click to expand)<span class="nt" style="color: #000080;"></summary></p></span></span>
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737
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<pre style="margin: 0;"> <span id="LC737" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC734" class="line" lang="html"><span class="nt" style="color: #000080;"><pre><code></span>...</span>
</pre>
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<pre style="margin: 0;">-<span id="LC735" class="line" lang="html">[CRITICAL WARNING]   Failed to partition subgraph with 6929 nodes into (6929,0,0) sized groups, now using kmere heuristic as fall-back.</span>
</pre>
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736
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<pre style="margin: 0;">-<span id="LC736" class="line" lang="html">...</span>
</pre>
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737
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<pre style="margin: 0;">-<span id="LC737" class="line" lang="html"><span class="nt" style="color: #000080;"></code></pre></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="html">## Example 1</span>
</pre>
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<pre style="margin: 0;"> <span id="LC739" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC739" class="line" lang="html"><span class="nt" style="color: #000080;"><p></details></p></span></span>
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="html">In the following example a huge blast graph is used for step 3 (clustering).</span>
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="html">The first connected component contains 7410694 nodes, hence the kmere heuristic is activated.</span>
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="html">Since the fiedler vector would result in a good split, the kmere heuristic is then deactivated immediatly.</span>
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<pre style="margin: 0;"> <span id="LC743" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC741" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left right"><p></span><details></span></span>
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<pre style="margin: 0;">-<span id="LC742" class="line" lang="html"><span class="nt" style="color: #000080;"><summary></span><span class="idiff left">working example for large graphs</span> (Click to expand)<span class="nt" style="color: #000080;"></summary><span class="idiff right"></p></span></span></span>
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="html"><span class="nt" style="color: #000080;"><details></span></span>
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="html"><span class="idiff left">  </span><span class="nt" style="color: #000080;"><summary></span><span class="idiff right">as fallback</span> (Click to expand)<span class="nt" style="color: #000080;"></summary></span></span>
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<pre style="margin: 0;"> <span id="LC746" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC744" class="line" lang="html"><span class="nt" style="color: #000080;"><pre><code></span>...</span>
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<pre style="margin: 0;">-<span id="LC745" class="line" lang="html">17:32:15 [DEBUG] (kmere-heuristic) The current connected component is so large that the k-mere heuristic can be used. First: Testing if a normal split would result in a good partition (|.|<span class="ni" style="color: #800080;">&gt;</span>20%) of the CC.</span>
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<pre style="margin: 0;">-<span id="LC746" class="line" lang="html"> [WARNING] (kmere-heuristic) A normal split would NOT result in a good partition (|.|<span class="ni" style="color: #800080;">&gt;</span>20%) of the CC, therefore  the k-mere heuristic is now used. The current connected component will be split in 3.85373 (= number of proteins <span class="ni" style="color: #800080;">&lt;</span>6929<span class="ni" style="color: #800080;">&gt;</span> / ( n</span>
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<pre style="margin: 0;">-<span id="LC747" class="line" lang="html">odes per species <span class="ni" style="color: #800080;">&lt;</span>1<span class="ni" style="color: #800080;">&gt;</span> * number of species <span class="ni" style="color: #800080;">&lt;</span>1798<span class="ni" style="color: #800080;">&gt;</span>)) groups greedily accordingly to the fiedler vector.</span>
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<pre style="margin: 0;">-<span id="LC748" class="line" lang="html">...</span>
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<pre style="margin: 0;">-<span id="LC749" class="line" lang="html"><span class="nt" style="color: #000080;"></code></pre></span></span>
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="html">    ...</span>
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="html">    [CRITICAL WARNING]   Failed to partition subgraph with 6929 nodes into (6929,0,0) sized groups, now using kmere heuristic as fall-back.</span>
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="html">    ...</span>
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<pre style="margin: 0;">-<span id="LC751" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left"><p></span></details><span class="idiff right"></p></span></span></span>
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<pre style="margin: 0;">-<span id="LC753" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left right"><p></span><details></span></span>
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<pre style="margin: 0;">-<span id="LC754" class="line" lang="html"><span class="nt" style="color: #000080;"><summary></span>example for large graphs<span class="idiff left">, where kmere is tested but not needed</span> (Click to expand)<span class="nt" style="color: #000080;"></summary><span class="idiff right"></p></span></span></span>
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="html"><span class="nt" style="color: #000080;"><details></span></span>
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="html"><span class="nt" style="color: #000080;"><summary></span><span class="idiff left right">working </span>example for large graphs (Click to expand)<span class="nt" style="color: #000080;"></summary></span></span>
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<pre style="margin: 0;">-<span id="LC756" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left right"><pre><code></span></span>...</span>
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<pre style="margin: 0;">-<span id="LC757" class="line" lang="html"><span class="idiff left right">20:27:07</span> [DEBUG] (kmere-heuristic) The current connected component is so large that the k-mere heuristic can be used. First: Testing if a normal split would result in a good partition (|.|<span class="ni" style="color: #800080;">&gt;</span>20%) of the CC.</span>
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<pre style="margin: 0;">-<span id="LC758" class="line" lang="html"><span class="idiff left">20:27:09 [DEBU</span>G] (kmere-heuristic) A normal split would result in a good partition (|.|<span class="ni" style="color: #800080;">&gt;</span>20%) of the CC, therefore <span class="idiff right">returning now to the normal algorithm (no k-mere heuristic).</span></span>
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<pre style="margin: 0;">-<span id="LC759" class="line" lang="html"><span class="idiff left right">..</span>.</span>
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<pre style="margin: 0;">-<span id="LC760" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left right"></code></pre></span></span></span>
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="html"><span class="idiff left right">    </span>...</span>
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="html"><span class="idiff left right">    17:32:15</span> [DEBUG] (kmere-heuristic) The current connected component is so large that the k-mere heuristic can be used. First: Testing if a normal split would result in a good partition (|.|<span class="ni" style="color: #800080;">&gt;</span>20%) of the CC.</span>
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="html"><span class="idiff left">     [WARNIN</span>G] (kmere-heuristic) A normal split would <span class="idiff">NOT </span>result in a good partition (|.|<span class="ni" style="color: #800080;">&gt;</span>20%) of the CC, therefore <span class="idiff"> the k-mere heuristic is now used. The current connected component will be split in 3.85373 (= number of proteins </span><span class="nt" style="color: #000080;"><span class="idiff"><</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">6929</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff right"> / ( n</span></span>
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="html"><span class="idiff left">    odes per species </span><span class="nt" style="color: #000080;"><span class="idiff"><</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">1</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff"> * number of species </span><span class="nt" style="color: #000080;"><span class="idiff"><</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">1798</span></span><span class="nt" style="color: #000080;"><span class="idiff">></span></span><span class="idiff right">)) groups greedily accordingly to the fiedler vector</span>.</span>
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="html"><span class="idiff left right">    ...</span></span>
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<pre style="margin: 0;"> <span id="LC761" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC762" class="line" lang="html"><span class="nt" style="color: #000080;"><span class="idiff left"><p></span></details><span class="idiff right"></p></span></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="html"><span class="nt" style="color: #000080;"></details></span></span>
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<pre style="margin: 0;"> <span id="LC763" class="line" lang="html"></span>
</pre>
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764
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<pre style="margin: 0;">-<span id="LC764" class="line" lang="html"><span class="nt" style="color: #000080;"><h1</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"creditwherecreditisdue"</span><span class="nt" style="color: #000080;">></span>Credit where credit is due<span class="nt" style="color: #000080;"></h1></span></span>
</pre>
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764
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="html"><span class="nt" style="color: #000080;"><details></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="html"><span class="nt" style="color: #000080;"><summary></span>example for large graphs, where kmere is tested but not needed (Click to expand)<span class="nt" style="color: #000080;"></summary></span></span>
</pre>
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766
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<pre style="margin: 0;"> <span id="LC766" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC766" class="line" lang="html"><span class="nt" style="color: #000080;"><ul></span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC767" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>The all-versus-all BLAST-analysis (-step=2) is only possible with (one of) the following underlying algorithms:</span>
</pre>
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="html">    ...</span>
</pre>
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="html">    20:27:07 [DEBUG] (kmere-heuristic) The current connected component is so large that the k-mere heuristic can be used. First: Testing if a normal split would result in a good partition (|.|<span class="ni" style="color: #800080;">&gt;</span>20%) of the CC.</span>
</pre>
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="html">    20:27:09 [DEBUG] (kmere-heuristic) A normal split would result in a good partition (|.|<span class="ni" style="color: #800080;">&gt;</span>20%) of the CC, therefore returning now to the normal algorithm (no k-mere heuristic).</span>
</pre>
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="html">    ...</span>
</pre>
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771
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<pre style="margin: 0;"> <span id="LC771" class="line" lang="html"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="html"><span class="nt" style="color: #000080;"></details></span></span>
</pre>
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773
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<pre style="margin: 0;"> <span id="LC773" class="line" lang="html"></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="774" 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">
774
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="html"><span class="nt" style="color: #000080;"><h1</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"credit-where-credit-is-due"</span><span class="nt" style="color: #000080;">></span>Credit where credit is due<span class="nt" style="color: #000080;"></h1></span></span>
</pre>
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775
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<pre style="margin: 0;"> <span id="LC775" class="line" lang="html"><span class="nt" style="color: #000080;"><ul></span></span>
</pre>
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771
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<td class="new_line diff-line-num old" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC771" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>NCBI BLAST+ or NCBI BLAST legacy (https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE<span class="nt" style="color: #000080;"><em></span>TYPE=BlastDocs<span class="ni" style="color: #800080;">&amp;</span>DOC<span class="nt" style="color: #000080;"></em></span>TYPE=Download)<span class="nt" style="color: #000080;"></li></span></span>
</pre>
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772
</td>
<td class="new_line diff-line-num old" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC772" class="line" lang="html"></span>
</pre>
</td>
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773
</td>
<td class="new_line diff-line-num old" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC773" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>Diamond (doi:10.1038/nmeth.3176, https://github.com/bbuchfink/diamond)<span class="nt" style="color: #000080;"></li></span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="774" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
774
</td>
<td class="new_line diff-line-num old" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC774" class="line" lang="html"></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num old" data-linenumber="775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
775
</td>
<td class="new_line diff-line-num old" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC775" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>Last (doi:10.1101/gr.113985.110, http://last.cbrc.jp/)<span class="nt" style="color: #000080;"></li></span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
776
</td>
<td class="new_line diff-line-num old" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC776" class="line" lang="html"></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num old" data-linenumber="777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
777
</td>
<td class="new_line diff-line-num old" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC777" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>Rapsearch2 (doi:10.1093/bioinformatics/btr595, https://github.com/zhaoyanswill/RAPSearch2)<span class="nt" style="color: #000080;"></li></span></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num old" data-linenumber="778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
778
</td>
<td class="new_line diff-line-num old" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC778" class="line" lang="html"></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num old" data-linenumber="779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
779
</td>
<td class="new_line diff-line-num old" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC779" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>Topaz (doi:10.1186/s12859-018-2290-3, https://github.com/ajm/topaz)<span class="nt" style="color: #000080;"></li></span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
780
</td>
<td class="new_line diff-line-num old" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC780" class="line" lang="html"></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num old" data-linenumber="781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
781
</td>
<td class="new_line diff-line-num old" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC781" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>usearch,ublast (doi:10.1093/bioinformatics/btq461, https://www.drive5.com/usearch/download.html)<span class="nt" style="color: #000080;"></li></span></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num old" data-linenumber="782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
782
</td>
<td class="new_line diff-line-num old" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC782" class="line" lang="html"></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num old" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
783
</td>
<td class="new_line diff-line-num old" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC783" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>blat (http://hgdownload.soe.ucsc.edu/admin/)<span class="nt" style="color: #000080;"></li></span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
784
</td>
<td class="new_line diff-line-num old" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC784" class="line" lang="html"></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num old" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
785
</td>
<td class="new_line diff-line-num old" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC785" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>mmseqs2 (doi:10.1038/nbt.3988 (2017). https://github.com/soedinglab/MMseqs2)<span class="nt" style="color: #000080;"></li></ul></span></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="786" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="776" 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">
776
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC776" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>The all-versus-all BLAST-analysis (-step=2) is only possible with (one of) the following underlying algorithms:<span class="nt" style="color: #000080;"><ul></span></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="786" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="777" 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">
777
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC777" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>NCBI BLAST+ or NCBI BLAST legacy (<span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&amp;DOC_TYPE=Download"</span><span class="nt" style="color: #000080;">></span>https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs<span class="ni" style="color: #800080;">&amp;</span>DOC_TYPE=Download<span class="nt" style="color: #000080;"></a></span>)<span class="nt" style="color: #000080;"></li></span></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="786" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="778" 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">
778
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC778" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>Diamond (doi:10.1038/nmeth.3176, <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://github.com/bbuchfink/diamond"</span><span class="nt" style="color: #000080;">></span>https://github.com/bbuchfink/diamond<span class="nt" style="color: #000080;"></a></span>)<span class="nt" style="color: #000080;"></li></span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="786" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="779" 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">
779
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC779" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>Last (doi:10.1101/gr.113985.110, <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"http://last.cbrc.jp/"</span><span class="nt" style="color: #000080;">></span>http://last.cbrc.jp/<span class="nt" style="color: #000080;"></a></span>)<span class="nt" style="color: #000080;"></li></span></span>
</pre>
</td>
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</td>
<td class="new_line diff-line-num new" data-linenumber="780" 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">
780
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC780" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>Rapsearch2 (doi:10.1093/bioinformatics/btr595, <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://github.com/zhaoyanswill/RAPSearch2"</span><span class="nt" style="color: #000080;">></span>https://github.com/zhaoyanswill/RAPSearch2<span class="nt" style="color: #000080;"></a></span>)<span class="nt" style="color: #000080;"></li></span></span>
</pre>
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</td>
<td class="new_line diff-line-num new" data-linenumber="781" 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">
781
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC781" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>Topaz (doi:10.1186/s12859-018-2290-3, <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://github.com/ajm/topaz"</span><span class="nt" style="color: #000080;">></span>https://github.com/ajm/topaz<span class="nt" style="color: #000080;"></a></span>)<span class="nt" style="color: #000080;"></li></span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="786" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="782" 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">
782
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC782" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>usearch,ublast (doi:10.1093/bioinformatics/btq461, <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://www.drive5.com/usearch/download.html"</span><span class="nt" style="color: #000080;">></span>https://www.drive5.com/usearch/download.html<span class="nt" style="color: #000080;"></a></span>)<span class="nt" style="color: #000080;"></li></span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="786" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="783" 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">
783
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC783" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>blat (<span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"http://hgdownload.soe.ucsc.edu/admin/"</span><span class="nt" style="color: #000080;">></span>http://hgdownload.soe.ucsc.edu/admin/<span class="nt" style="color: #000080;"></a></span>)<span class="nt" style="color: #000080;"></li></span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="786" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="784" 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">
784
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC784" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>mmseqs2 (doi:10.1038/nbt.3988 (2017). <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://github.com/soedinglab/MMseqs2"</span><span class="nt" style="color: #000080;">></span>https://github.com/soedinglab/MMseqs2<span class="nt" style="color: #000080;"></a></span>)<span class="nt" style="color: #000080;"></li></span></span>
</pre>
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</td>
<td class="new_line diff-line-num new" data-linenumber="785" 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">
785
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC785" class="line" lang="html"><span class="nt" style="color: #000080;"></ul></span></span>
</pre>
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786
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<td class="new_line diff-line-num" data-linenumber="786" 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">
786
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC786" class="line" lang="html"><span class="nt" style="color: #000080;"></li></span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
787
</td>
<td class="new_line diff-line-num old" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC787" class="line" lang="html"></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
788
</td>
<td class="new_line diff-line-num old" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC788" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>The clustering step (-step=3) got a huge speedup with the integration of LAPACK (Univ. of Tennessee; Univ. of California, Berkeley; Univ. of Colorado Denver; and NAG Ltd., http://www.netlib.org/lapack/)<span class="nt" style="color: #000080;"></li></span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
789
</td>
<td class="new_line diff-line-num old" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC789" class="line" lang="html"></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
790
</td>
<td class="new_line diff-line-num old" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC790" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>The html output of the *proteinortho.tsv (orthology groups) is enhanced by clusterize (https://github.com/NeXTs/Clusterize.js), reducing the scroll lag.<span class="nt" style="color: #000080;"></li></span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="791" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="787" 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">
787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>The clustering step (-step=3) got a huge speedup with the integration of LAPACK (Univ. of Tennessee; Univ. of California, Berkeley; Univ. of Colorado Denver; and NAG Ltd., <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"http://www.netlib.org/lapack/"</span><span class="nt" style="color: #000080;">></span>http://www.netlib.org/lapack/<span class="nt" style="color: #000080;"></a></span>)<span class="nt" style="color: #000080;"></li></span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="791" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="788" 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">
788
</td>
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>The html output of the *proteinortho.tsv (orthology groups) is enhanced by clusterize (<span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://github.com/NeXTs/Clusterize.js"</span><span class="nt" style="color: #000080;">></span>https://github.com/NeXTs/Clusterize.js<span class="nt" style="color: #000080;"></a></span>), reducing the scroll lag.<span class="nt" style="color: #000080;"></li></span></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num" data-linenumber="791" 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">
791
</td>
<td class="new_line diff-line-num" data-linenumber="789" 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">
789
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC789" class="line" lang="html"><span class="nt" style="color: #000080;"></ul></span></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num old" data-linenumber="792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
792
</td>
<td class="new_line diff-line-num old" data-linenumber="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC792" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
793
</td>
<td class="new_line diff-line-num old" data-linenumber="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC793" class="line" lang="html"><span class="nt" style="color: #000080;"><h1</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"onlineinformation"</span><span class="nt" style="color: #000080;">></span>ONLINE INFORMATION<span class="nt" style="color: #000080;"></h1></span></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num old" data-linenumber="794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
794
</td>
<td class="new_line diff-line-num old" data-linenumber="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC794" class="line" lang="html"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
795
</td>
<td class="new_line diff-line-num old" data-linenumber="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC795" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>For download and online information, see</span>
</pre>
</td>
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</td>
<td class="new_line diff-line-num new" data-linenumber="790" 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">
790
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="html"><span class="nt" style="color: #000080;"><h1</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"online-information"</span><span class="nt" style="color: #000080;">></span>ONLINE INFORMATION<span class="nt" style="color: #000080;"></h1></span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="796" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="791" 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">
791
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<pre style="margin: 0;">+<span id="LC791" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>  For download and online information, see</span>
</pre>
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796
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<td class="new_line diff-line-num" data-linenumber="792" 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">
792
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<pre style="margin: 0;"> <span id="LC792" class="line" lang="html">  <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://www.bioinf.uni-leipzig.de/Software/proteinortho/"</span><span class="nt" style="color: #000080;">></span>https://www.bioinf.uni-leipzig.de/Software/proteinortho/<span class="nt" style="color: #000080;"></a></span></span>
</pre>
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797
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<td class="new_line diff-line-num" data-linenumber="793" 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">
793
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC793" class="line" lang="html">  or</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="798" 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">
798
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<td class="new_line diff-line-num" data-linenumber="794" 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">
794
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<pre style="margin: 0;"> <span id="LC794" class="line" lang="html">  <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://gitlab.com/paulklemm_PHD/proteinortho"</span><span class="nt" style="color: #000080;">></span>https://gitlab.com/paulklemm_PHD/proteinortho<span class="nt" style="color: #000080;"></a></p></span></span>
</pre>
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799
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<pre style="margin: 0;">-<span id="LC799" class="line" lang="html"></span>
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795
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<pre style="margin: 0;"> <span id="LC795" class="line" lang="html"><span class="nt" style="color: #000080;"><h1</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"references"</span><span class="nt" style="color: #000080;">></span>REFERENCES<span class="nt" style="color: #000080;"></h1></span></span>
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<pre style="margin: 0;">-<span id="LC801" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC802" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Lechner, M., Findeisz, S., Steiner, L., Marz, M., Stadler, P. F., <span class="ni" style="color: #800080;">&amp;</span></span>
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>  Lechner, M., Findeisz, S., Steiner, L., Marz, M., Stadler, P. F., <span class="ni" style="color: #800080;">&amp;</span></span>
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803
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<pre style="margin: 0;"> <span id="LC797" class="line" lang="html">  Prohaska, S. J. (2011). Proteinortho: detection of (co-) orthologs in</span>
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<td class="new_line diff-line-num old" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC804" class="line" lang="html">  large-scale analysis. BMC bioinformatics, 12(1), 124.<span class="nt" style="color: #000080;"></p></span></span></pre>
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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">\ No newline at end of file</td>
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="html">  large-scale analysis. BMC bioinformatics, 12(1), 124.<span class="nt" style="color: #000080;"></p></span></span></pre>
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<a href="https://salsa.debian.org/med-team/proteinortho/-/commit/3746e15da8bc7609707daf904845cd274344cd8f#c9e37a96ac72f9ef076d7a41a57470524d63b36e"><strong>proteinortho6.pl</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="118" 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">@@ -118,6 +118,11 @@ ncbi -> if the word 'isoform' is found</td>
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">uniprot -> 'Isoform of XYZ' (You need to add the *_additional.fasta files to the analysis)</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">trinity -> using '_iX' suffix</span></span>
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<td class="old_line diff-line-num" data-linenumber="120" 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="LC120" class="line" lang="perl"></span>
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<td class="old_line diff-line-num new" data-linenumber="121" 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="LC121" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">All isoforms are united to a single entity and treated as one. </span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">Extracting a group with an isoform will result in all isoforms.</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">For more information have a look at: </span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">https://gitlab.com/paulklemm_PHD/proteinortho/-/wikis/FAQ#how-does-the-isoform-work</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=back</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=head2 Search options (step 1-2)</span></span>
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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">@@ -158,7 +163,11 @@ apply selfblast, detects paralogs without orthologs</td>
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=item B<--sim>=float (default: 0.95)</span></span>
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">min. similarity for additional hits</span></span>
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">The -sim relaxes the one best reciprocal hit to all adaptive reciprocal best hits. </span></span>
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">E.g. for -sim=0.9 all reciprocal hits within 90% of the highest bitscore are returned. </span></span>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">This can reduces false negative on the cost of maybe increasing the false positives too.</span></span>
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">-sim=1 will result in only the best reciprocal hits. In the most case this correspond to obe-to-one orthologs.</span></span>
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">-sim=0 will result in all reciprocal hits within the evalue threshold.</span></span>
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=item B<--identity>=number (default: 25)</span></span>
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="perl"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="461" 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">@@ -452,11 +461,11 @@ Lechner, M., Findeisz, S., Steiner, L., Marz, M., Stadler, P. F., & Prohaska, S.</td>
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>
</pre>
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<td class="new_line diff-line-num" data-linenumber="462" 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="LC462" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>
</pre>
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<td class="new_line diff-line-num" data-linenumber="463" 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="LC463" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">warnings</span> <span class="p">"</span><span class="s2" style="color: #d14;">all</span><span class="p">";</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="455" 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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<td class="new_line diff-line-num new" data-linenumber="464" 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="LC464" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">threads</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="455" 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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<td class="new_line diff-line-num new" data-linenumber="465" 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="LC465" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">threads::</span><span class="nv" style="color: #008080;">shared</span><span class="p">;</span></span>
</pre>
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<td class="new_line diff-line-num" data-linenumber="466" 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="LC466" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">File::</span><span class="nv" style="color: #008080;">Basename</span><span class="p">;</span></span>
</pre>
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<td class="new_line diff-line-num" data-linenumber="467" 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="LC467" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">Cwd</span><span class="p">;</span></span>
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<td class="new_line diff-line-num" data-linenumber="468" 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="LC468" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">Cwd</span> <span class="p">'</span><span class="s1" style="color: #d14;">abs_path</span><span class="p">';</span></span>
</pre>
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<td class="new_line diff-line-num old" data-linenumber="469" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC458" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">threads</span><span class="p">;</span></span>
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<td class="new_line diff-line-num old" data-linenumber="469" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC459" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">threads::</span><span class="nv" style="color: #008080;">shared</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC469" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Thread::</span><span class="nv" style="color: #008080;">Queue</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC470" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Pod::</span><span class="nv" style="color: #008080;">Usage</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># --man</span></span>
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<pre style="margin: 0;"> <span id="LC471" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">POSIX</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="464" 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="473" 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">@@ -464,7 +473,7 @@ use POSIX;</td>
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<td class="new_line diff-line-num" data-linenumber="473" 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="LC473" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>
</pre>
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<td class="new_line diff-line-num" data-linenumber="474" 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="LC474" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Variables</span></span>
</pre>
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<td class="new_line diff-line-num" data-linenumber="475" 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="LC475" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>
</pre>
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<td class="new_line diff-line-num old" data-linenumber="476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC467" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$version</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">6.0.<span class="idiff left right">28</span></span><span class="p">";</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="468" 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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<td class="new_line diff-line-num new" data-linenumber="476" 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="LC476" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$version</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">6.0.<span class="idiff left right">30</span></span><span class="p">";</span></span>
</pre>
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468
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477
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<pre style="margin: 0;"> <span id="LC477" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$step</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span>    <span class="c1" style="color: #998; font-style: italic;"># 0/1/2/3 -> do all / only apply step 1 / only apply step 2 / only apply step 3</span></span>
</pre>
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469
</td>
<td class="new_line diff-line-num" data-linenumber="478" 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">
478
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># 0/1   -> don't / be verbose</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
470
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<td class="new_line diff-line-num" data-linenumber="479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
479
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<pre style="margin: 0;"> <span id="LC479" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$debug</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span>   <span class="c1" style="color: #998; font-style: italic;"># 0/1   -> don't / show debug data</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="516" 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="525" 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">@@ -516,6 +525,8 @@ our $syn_lock :shared;</td>
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<td class="old_line diff-line-num" data-linenumber="516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
516
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<td class="new_line diff-line-num" data-linenumber="525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
525
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<pre style="margin: 0;"> <span id="LC525" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$all_jobs_submitted</span> <span class="p">:</span><span class="nv" style="color: #008080;">shared</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="517" 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">
517
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<td class="new_line diff-line-num" data-linenumber="526" 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">
526
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC526" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$po_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"";</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
518
</td>
<td class="new_line diff-line-num" data-linenumber="527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
527
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<pre style="margin: 0;"> <span id="LC527" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$run_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"";</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="519" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="528" 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">
528
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC528" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$hmm_search_evalue</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">1e-100</span><span class="p">";</span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="519" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="529" 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">
529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$hmm_minprots</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">15</span><span class="p">;</span> </span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="519" 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">
519
</td>
<td class="new_line diff-line-num" data-linenumber="530" 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">
530
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<pre style="margin: 0;"> <span id="LC530" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">%gene_counter</span><span class="p">;</span>    <span class="c1" style="color: #998; font-style: italic;"># Holds the number of genes for each data file (for sorting)</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="520" 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">
520
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<td class="new_line diff-line-num" data-linenumber="531" 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">
531
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC531" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">%max_gene_length_diamond</span><span class="p">;</span>    <span class="c1" style="color: #998; font-style: italic;"># Holds the maximum length of genes for each data file (for diamond -> -sensitive option)</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="521" 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">
521
</td>
<td class="new_line diff-line-num" data-linenumber="532" 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">
532
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC532" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$threads_per_process</span> <span class="p">:</span><span class="nv" style="color: #008080;">shared</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># Number of subthreads for blast</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="539" 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="550" 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">@@ -539,6 +550,7 @@ our $BLUE="\033[1;36m";</td>
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<td class="old_line diff-line-num" data-linenumber="539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
539
</td>
<td class="new_line diff-line-num" data-linenumber="550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
550
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<pre style="margin: 0;"> <span id="LC550" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$ORANGE</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="se" style="color: #d14;">\033</span><span class="s2" style="color: #d14;">[1;33m</span><span class="p">";</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="540" 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">
540
</td>
<td class="new_line diff-line-num" data-linenumber="551" 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">
551
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC551" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$NC</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="se" style="color: #d14;">\033</span><span class="s2" style="color: #d14;">[0m</span><span class="p">";</span> <span class="c1" style="color: #998; font-style: italic;"># No Color</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="541" 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">
541
</td>
<td class="new_line diff-line-num" data-linenumber="552" 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">
552
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<pre style="margin: 0;"> <span id="LC552" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">%isoform_mapping</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="542" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="553" 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">
553
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC553" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">%isoform_mapping_best</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="542" 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">
542
</td>
<td class="new_line diff-line-num" data-linenumber="554" 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">
554
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<pre style="margin: 0;"> <span id="LC554" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="543" 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">
543
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555
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<pre style="margin: 0;"> <span id="LC555" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$tput</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">tput color 2>/dev/null</span><span class="p">`;</span> <span class="c1" style="color: #998; font-style: italic;"># test if the shell supports colors</span></span>
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544
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556
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<pre style="margin: 0;"> <span id="LC556" class="line" lang="perl"><span class="nv" style="color: #008080;">$tput</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/[\r\n]+$//</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="556" 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="568" 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">@@ -556,7 +568,7 @@ our @files = ();</td>
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556
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568
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<pre style="margin: 0;"> <span id="LC568" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">@files_cleanup</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">();</span></span>
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557
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<td class="new_line diff-line-num" data-linenumber="569" 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">
569
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<pre style="margin: 0;"> <span id="LC569" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">%files_map</span><span class="p">;</span></span>
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558
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<td class="new_line diff-line-num" data-linenumber="570" 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">
570
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<pre style="margin: 0;"> <span id="LC570" class="line" lang="perl"><span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$option</span> <span class="p">(</span><span class="nv" style="color: #008080;">@ARGV</span><span class="p">)</span> <span class="p">{</span></span>
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559
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<td class="new_line diff-line-num old" data-linenumber="571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC559" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?step=(0|1|2|3)$/</span><span class="p">)</span>      <span class="p">{</span> <span class="nv" style="color: #008080;">$step</span> <span class="o" style="font-weight: 600;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">;</span>   <span class="p">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="560" 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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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?step=(0|1|2|3<span class="idiff left right">|4</span>)$/</span><span class="p">)</span>      <span class="p">{</span> <span class="nv" style="color: #008080;">$step</span> <span class="o" style="font-weight: 600;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">;</span>   <span class="p">}</span></span>
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560
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<td class="new_line diff-line-num" data-linenumber="572" 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">
572
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<pre style="margin: 0;"> <span id="LC572" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?verbose$/</span><span class="p">)</span>      <span class="p">{</span> <span class="nv" style="color: #008080;">$verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span>  <span class="p">}</span></span>
</pre>
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561
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<td class="new_line diff-line-num" data-linenumber="573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC573" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?verbose=([012])$/</span><span class="p">)</span>      <span class="p">{</span> <span class="nv" style="color: #008080;">$verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">;</span>  <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC574" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?silent$/</span><span class="p">)</span>      <span class="p">{</span> <span class="nv" style="color: #008080;">$verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span>  <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="587" 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="599" 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">@@ -587,6 +599,9 @@ foreach my $option (@ARGV) {</td>
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<pre style="margin: 0;"> <span id="LC599" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?cpus=(\d*)$/</span><span class="p">)</span>       <span class="p">{</span> <span class="nv" style="color: #008080;">$cpus</span> <span class="o" style="font-weight: 600;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span></span>
</pre>
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<td class="new_line diff-line-num" data-linenumber="600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC600" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?cpus=auto$/</span><span class="p">)</span>          <span class="p">{</span> <span class="nv" style="color: #008080;">$cpus</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="p">}</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC601" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?alpha=([0-9\.]+)$/</span><span class="p">)</span>     <span class="p">{</span> <span class="nv" style="color: #008080;">$alpha</span> <span class="o" style="font-weight: 600;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="590" 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="LC602" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?hmm_?evalue=([0-9\.eE+-]+)$/</span><span class="p">)</span>     <span class="p">{</span> <span class="nv" style="color: #008080;">$hmm_search_evalue</span> <span class="o" style="font-weight: 600;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="590" 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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<td class="new_line diff-line-num new" data-linenumber="603" 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">
603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?hmm_?e=([0-9\.eE+-]+)$/</span><span class="p">)</span>     <span class="p">{</span> <span class="nv" style="color: #008080;">$hmm_search_evalue</span> <span class="o" style="font-weight: 600;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="590" 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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<td class="new_line diff-line-num new" data-linenumber="604" 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">
604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?hmm_?minprots?=([0-9]+)$/</span><span class="p">)</span>     <span class="p">{</span> <span class="nv" style="color: #008080;">$hmm_minprots</span> <span class="o" style="font-weight: 600;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span></span>
</pre>
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590
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<td class="new_line diff-line-num" data-linenumber="605" 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">
605
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<pre style="margin: 0;"> <span id="LC605" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?purity=([0-9\.]+)$/</span><span class="p">)</span>      <span class="p">{</span> <span class="nv" style="color: #008080;">$purity</span> <span class="o" style="font-weight: 600;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span></span>
</pre>
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591
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<td class="new_line diff-line-num" data-linenumber="606" 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">
606
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<pre style="margin: 0;"> <span id="LC606" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?report=([0-9]+)$/</span><span class="p">)</span>      <span class="p">{</span> <span class="nv" style="color: #008080;">$report</span> <span class="o" style="font-weight: 600;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span></span>
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592
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<td class="new_line diff-line-num" data-linenumber="607" 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">
607
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<pre style="margin: 0;"> <span id="LC607" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?minspecies=([0-9.]+)$/</span><span class="p">)</span>       <span class="p">{</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">>=</span><span class="mi" style="color: #099;">0</span><span class="p">){</span><span class="nv" style="color: #008080;">$minspecies</span> <span class="o" style="font-weight: 600;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span><span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">the argument -minspecies=$1 is invalid.</span><span class="si" style="color: #d14;">$RED</span><span class="s2" style="color: #d14;"> minspecies needs to be >=0!</span><span class="si" style="color: #d14;">$NC</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">minspecies: the min. number of genes per species. If a group is found with up to (minspecies) genes/species, it wont be split again (regardless of the connectivity).</span><span class="p">");}</span> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="637" 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="652" 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">@@ -637,6 +652,7 @@ foreach my $option (@ARGV) {</td>
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637
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<td class="new_line diff-line-num" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
652
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<pre style="margin: 0;"> <span id="LC652" class="line" lang="perl">  <span class="k" style="font-weight: 600;">else</span>  <span class="p">{</span><span class="nv" style="color: #008080;">&print_usage</span><span class="p">();</span> <span class="nv" style="color: #008080;">&reset_locale</span><span class="p">();</span><span class="nb" style="color: #0086b3;">die</span> <span class="p">"</span><span class="si" style="color: #d14;">$RED</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">[Error]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> Invalid command line option: </span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">'</span><span class="si" style="color: #d14;">$option</span><span class="se" style="color: #d14;">\</span><span class="s2" style="color: #d14;">'! </span><span class="si" style="color: #d14;">$NC</span><span class="se" style="color: #d14;">\n\n</span><span class="p">";</span> <span class="p">}</span></span>
</pre>
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638
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653
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<pre style="margin: 0;"> <span id="LC653" class="line" lang="perl"><span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="639" 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">
639
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<td class="new_line diff-line-num" data-linenumber="654" 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">
654
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<pre style="margin: 0;"> <span id="LC654" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="640" 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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<td class="new_line diff-line-num new" data-linenumber="655" 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">
655
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="640" 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">
640
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<td class="new_line diff-line-num" data-linenumber="656" 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">
656
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<pre style="margin: 0;"> <span id="LC656" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$jobnumber</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$tmp_path</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">""</span> <span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Please consider to use the -tmp option in combination with -jobs if you use proteinortho on a computing cluster system. Usually these clusters have dedicated local scratch directories.</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
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641
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<td class="new_line diff-line-num" data-linenumber="657" 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">
657
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<pre style="margin: 0;"> <span id="LC657" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$selfblast</span><span class="p">){</span><span class="nv" style="color: #008080;">$checkblast</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="642" 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">
642
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<td class="new_line diff-line-num" data-linenumber="658" 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">
658
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<pre style="margin: 0;"> <span id="LC658" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="709" 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="725" 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">@@ -709,7 +725,6 @@ if($gccversion_main eq "" || $gccversion_main < 5){</td>
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709
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<pre style="margin: 0;"> <span id="LC725" class="line" lang="perl">  <span class="nv" style="color: #008080;">$ompprocbind</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;">true</span><span class="p">";</span></span>
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710
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<td class="new_line diff-line-num" data-linenumber="726" 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="LC726" class="line" lang="perl"><span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="711" 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">
711
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<td class="new_line diff-line-num" data-linenumber="727" 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">
727
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<pre style="margin: 0;"> <span id="LC727" class="line" lang="perl"></span>
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<td class="old_line diff-line-num old" data-linenumber="712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
712
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<td class="new_line diff-line-num old" data-linenumber="728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC712" class="line" lang="perl"></span>
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713
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<td class="new_line diff-line-num" data-linenumber="728" 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">
728
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<pre style="margin: 0;"> <span id="LC728" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$simgraph</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="si" style="color: #d14;">$project</span><span class="s2" style="color: #d14;">.blast-graph</span><span class="si" style="color: #d14;">$run_id</span><span class="p">";</span>    <span class="c1" style="color: #998; font-style: italic;"># Output file graph</span></span>
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<td class="old_line diff-line-num" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
714
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<td class="new_line diff-line-num" data-linenumber="729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC729" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$syngraph</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="si" style="color: #d14;">$project</span><span class="s2" style="color: #d14;">.ffadj-graph</span><span class="si" style="color: #d14;">$run_id</span><span class="p">";</span>    <span class="c1" style="color: #998; font-style: italic;"># Output file synteny</span></span>
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<td class="old_line diff-line-num" data-linenumber="715" 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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730
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<pre style="margin: 0;"> <span id="LC730" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$csimgraph</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="si" style="color: #d14;">$project</span><span class="s2" style="color: #d14;">.proteinortho-graph</span><span class="p">";</span>   <span class="c1" style="color: #998; font-style: italic;"># Output file graph</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="736" 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="751" 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">@@ -736,7 +751,7 @@ sub get_parameter{</td>
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<pre style="margin: 0;"> <span id="LC751" class="line" lang="perl">  <span class="k" style="font-weight: 600;">return</span> <span class="p">"</span><span class="s2" style="color: #d14;">Parameter-vector : (</span><span class="p">",'</span><span class="s1" style="color: #d14;">version</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$version</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">step</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$step</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">verbose</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$verbose</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">debug</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$debug</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">exactstep3</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$exactstep3</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">synteny</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$synteny</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">duplication</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$duplication</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">cs</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$cs</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">alpha</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$alpha</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">connectivity</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$connectivity</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">cpus</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$cpus</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">evalue</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$evalue</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">purity</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$purity</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">coverage</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$coverage</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">identity</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$identity</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">blastmode</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$blastmode</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">sim</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$sim</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">report</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$report</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">keep</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$keep</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">force</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$force</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">selfblast</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$selfblast</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">twilight</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$twilight</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">singles</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$singles</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">clean</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$clean</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">blastOptions</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$blastOptions</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">nograph</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$nograph</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">xml</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$doxml</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">desc</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$desc</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">tmp_path</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">blastversion</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$blastversion</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">binpath</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$binpath</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">makedb</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$makedb</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">blast</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$blast</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">jobs_todo</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$jobs_todo</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">project</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$project</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">po_path</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$po_path</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">run_id</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$run_id</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">",'</span><span class="s1" style="color: #d14;">threads_per_process</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$threads_per_process</span><span class="p">","</span><span class="s2" style="color: #d14;">,</span><span class="p">","</span><span class="s2" style="color: #d14;">useMcl</span><span class="p">","</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$useMcl</span><span class="p">",'</span><span class="s1" style="color: #d14;">,freemem</span><span class="p">',"</span><span class="s2" style="color: #d14;">=</span><span class="si" style="color: #d14;">$freemem_inMB</span><span class="p">","</span><span class="s2" style="color: #d14;">)</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="737" 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">
737
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<td class="new_line diff-line-num" data-linenumber="752" 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">
752
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC752" class="line" lang="perl"><span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="738" 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">
738
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<td class="new_line diff-line-num" data-linenumber="753" 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">
753
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC753" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
739
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<td class="new_line diff-line-num old" data-linenumber="754" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC739" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">e</span> <span class="p">"</span><span class="si" style="color: #d14;">$project</span><span class="s2" style="color: #d14;">.proteinortho.tsv</span><span class="p">"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span> <span class="p">(</span> <span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: #008080;">@files</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">3</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">3</span> <span class="p">)</span> <span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="740" 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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<td class="new_line diff-line-num new" data-linenumber="754" 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">
754
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">e</span> <span class="p">"</span><span class="si" style="color: #d14;">$project</span><span class="s2" style="color: #d14;">.proteinortho.tsv</span><span class="p">"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;"><span class="idiff left">$step</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="mi" style="color: #099;"><span class="idiff">4</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff right"> </span><span class="p">(</span> <span class="p">(</span> <span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: #008080;">@files</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">3</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">3</span> <span class="p">)</span> <span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
740
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<td class="new_line diff-line-num" data-linenumber="755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
755
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<pre style="margin: 0;"> <span id="LC755" class="line" lang="perl">  <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">!!!</span><span class="si" style="color: #d14;">$ORANGE</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[Warning]:</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> Data files for project '</span><span class="si" style="color: #d14;">$project</span><span class="s2" style="color: #d14;">' already exists. Previous output files might be overwritten.</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$NC</span><span class="p">";</span></span>
</pre>
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741
</td>
<td class="new_line diff-line-num" data-linenumber="756" 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">
756
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<pre style="margin: 0;"> <span id="LC756" class="line" lang="perl">  <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Press 'strg+c' to prevent me from proceeding or wait 10 seconds to continue...</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">!!!</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="742" 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">
742
</td>
<td class="new_line diff-line-num" data-linenumber="757" 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">
757
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<pre style="margin: 0;"> <span id="LC757" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">sleep</span> <span class="mi" style="color: #099;">10</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="744" 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="759" 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">@@ -744,7 +759,7 @@ if (-e "$project.proteinortho.tsv" && $step!=1 && ( ( scalar(@files) > 2 && $ste</td>
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<td class="old_line diff-line-num" data-linenumber="744" 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">
744
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<td class="new_line diff-line-num" data-linenumber="759" 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">
759
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<pre style="margin: 0;"> <span id="LC759" class="line" lang="perl"><span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="745" 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">
745
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<td class="new_line diff-line-num" data-linenumber="760" 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">
760
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC760" class="line" lang="perl"></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="746" 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">
746
</td>
<td class="new_line diff-line-num" data-linenumber="761" 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">
761
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC761" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># if step=1 -> generate blast db, no need for unlinking results</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
747
</td>
<td class="new_line diff-line-num old" data-linenumber="762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC747" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">1</span><span class="p">){</span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="748" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="762" 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">
762
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC762" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">1</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$step</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="mi" style="color: #099;"><span class="idiff right">4</span></span><span class="p">){</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="748" 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">
748
</td>
<td class="new_line diff-line-num" data-linenumber="763" 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">
763
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC763" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">3</span><span class="p">){</span> <span class="c1" style="color: #998; font-style: italic;"># if step 3 then dont destroy the blast results ...</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
749
</td>
<td class="new_line diff-line-num" data-linenumber="764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
764
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC764" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">unlink</span><span class="p">(</span><span class="nv" style="color: #008080;">$simgraph</span><span class="p">);</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="750" 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">
750
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<td class="new_line diff-line-num" data-linenumber="765" 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">
765
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC765" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">unlink</span><span class="p">(</span><span class="nv" style="color: #008080;">$syngraph</span><span class="p">);</span></span>
</pre>
</td>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -837,7 +852,7 @@ if($isoform eq "uniprot"){</td>
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<td class="old_line diff-line-num" data-linenumber="837" 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">
837
</td>
<td class="new_line diff-line-num" data-linenumber="852" 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">
852
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<pre style="margin: 0;"> <span id="LC852" class="line" lang="perl"><span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="838" 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">
838
</td>
<td class="new_line diff-line-num" data-linenumber="853" 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">
853
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC853" class="line" lang="perl"></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="839" 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">
839
</td>
<td class="new_line diff-line-num" data-linenumber="854" 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">
854
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC854" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Always do</span></span>
</pre>
</td>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
840
</td>
<td class="new_line diff-line-num old" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC840" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">3</span><span class="p">){</span> <span class="c1" style="color: #998; font-style: italic;"># don't check for step=3=clustering (not necessary) and if step=2, then files are allready checked with step=1</span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="841" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="855" 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">
855
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC855" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">3</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$step</span></span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="mi" style="color: #099;"><span class="idiff right">4</span></span><span class="p">){</span> <span class="c1" style="color: #998; font-style: italic;"># don't check for step=3=clustering (not necessary) and if step=2, then files are allready checked with step=1</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="841" 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">
841
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856
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<pre style="margin: 0;"> <span id="LC856" class="line" lang="perl">  <span class="nv" style="color: #008080;">&check_files</span><span class="p">;</span>   <span class="c1" style="color: #998; font-style: italic;"># Check files, count sequences</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="842" 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">
842
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857
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<pre style="margin: 0;"> <span id="LC857" class="line" lang="perl"><span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="843" 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">
843
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<td class="new_line diff-line-num" data-linenumber="858" 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">
858
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<pre style="margin: 0;"> <span id="LC858" class="line" lang="perl"><span class="nv" style="color: #008080;">@files</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">();</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="882" 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="897" 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">@@ -882,7 +897,7 @@ if ($step == 0 || $step == 2) {</td>
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882
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<td class="new_line diff-line-num" data-linenumber="897" 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">
897
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<pre style="margin: 0;"> <span id="LC897" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="883" 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">
883
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<td class="new_line diff-line-num" data-linenumber="898" 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="LC898" class="line" lang="perl">  <span class="c1" style="color: #998; font-style: italic;"># check if database exists for inputs:</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="884" 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">
884
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<td class="new_line diff-line-num" data-linenumber="899" 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="LC899" class="line" lang="perl">  <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">keys</span> <span class="nv" style="color: #008080;">%gene_counter</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
885
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<td class="new_line diff-line-num old" data-linenumber="900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC885" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="o" style="font-weight: 600;">!~</span> <span class="sr" style="color: #009926;">m/blat/</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">`</span><span class="sb" style="color: #d14;">ls '</span><span class="si" style="color: #d14;">${file}</span><span class="sb" style="color: #d14;">'.</span><span class="si" style="color: #d14;">${blastmode}</span><span class="sb" style="color: #d14;">* <span class="idiff left">1</span>>/dev/null<span class="idiff right"> 2>&1</span></span><span class="p">`</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span> <span class="c1" style="color: #998; font-style: italic;"># test here</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="886" 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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<td class="new_line diff-line-num new" data-linenumber="900" 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="LC900" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="o" style="font-weight: 600;">!~</span> <span class="sr" style="color: #009926;">m/blat/</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">`</span><span class="sb" style="color: #d14;">ls '</span><span class="si" style="color: #d14;">${file}</span><span class="sb" style="color: #d14;">'.</span><span class="si" style="color: #d14;">${blastmode}</span><span class="sb" style="color: #d14;">* <span class="idiff left right">2</span>>/dev/null</span><span class="p">`</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span> <span class="c1" style="color: #998; font-style: italic;"># test here</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="886" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
886
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<td class="new_line diff-line-num" data-linenumber="901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
901
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<pre style="margin: 0;"> <span id="LC901" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$a</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/DB/</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">basename</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">);</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="887" 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">
887
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<td class="new_line diff-line-num" data-linenumber="902" 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">
902
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<pre style="margin: 0;"> <span id="LC902" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(`</span><span class="sb" style="color: #d14;">ls '</span><span class="si" style="color: #d14;">${a}</span><span class="sb" style="color: #d14;">'.</span><span class="si" style="color: #d14;">${blastmode}</span><span class="sb" style="color: #d14;">* 1>/dev/null 2>&1</span><span class="p">`</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span>                           <span class="c1" style="color: #998; font-style: italic;"># or here</span></span>
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<td class="old_line diff-line-num" data-linenumber="888" 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">
888
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<td class="new_line diff-line-num" data-linenumber="903" 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">
903
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<pre style="margin: 0;"> <span id="LC903" class="line" lang="perl">        <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">I did not find the database for </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="vg" style="color: #008080;">$_</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> (</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$a</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">). Did you run --step=1 and maybe removed the databases? Please rerun 'proteinortho --step=1 --force /path/to/fastas' such that the databases can be recreated and then proceed with -step=2 and -step=3.</span><span class="p">");</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="900" 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="915" 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">@@ -900,6 +915,9 @@ if ($step == 0 || $step == 2) {</td>
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<td class="old_line diff-line-num" data-linenumber="900" 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">
900
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<td class="new_line diff-line-num" data-linenumber="915" 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">
915
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<pre style="margin: 0;"> <span id="LC915" class="line" lang="perl">  <span class="nv" style="color: #008080;">&run_blast</span><span class="p">;</span>   <span class="c1" style="color: #998; font-style: italic;"># Run blasts</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="901" 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">
901
</td>
<td class="new_line diff-line-num" data-linenumber="916" 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">
916
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<pre style="margin: 0;"> <span id="LC916" class="line" lang="perl"><span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="902" 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">
902
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<td class="new_line diff-line-num" data-linenumber="917" 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">
917
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<pre style="margin: 0;"> <span id="LC917" class="line" lang="perl"></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="903" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="918" 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">
918
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<pre style="margin: 0;">+<span id="LC918" class="line" lang="perl"><span class="nb" style="color: #0086b3;">undef</span> <span class="nv" style="color: #008080;">%max_gene_length_diamond</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="903" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="919" 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">
919
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<pre style="margin: 0;">+<span id="LC919" class="line" lang="perl"><span class="nv" style="color: #008080;">%max_gene_length_diamond</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="903" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="920" 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">
920
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC920" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="903" 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">
903
</td>
<td class="new_line diff-line-num" data-linenumber="921" 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">
921
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC921" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Check for duplicated edges if --unique or --checkblast</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="904" 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">
904
</td>
<td class="new_line diff-line-num" data-linenumber="922" 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">
922
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC922" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$checkblast</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">){</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
905
</td>
<td class="new_line diff-line-num" data-linenumber="923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
923
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC923" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="960" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -942,8 +960,22 @@ if($checkblast == 1){</td>
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<td class="old_line diff-line-num" data-linenumber="942" 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">
942
</td>
<td class="new_line diff-line-num" data-linenumber="960" 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">
960
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<pre style="margin: 0;"> <span id="LC960" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$step</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="943" 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">
943
</td>
<td class="new_line diff-line-num" data-linenumber="961" 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">
961
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<pre style="margin: 0;"> <span id="LC961" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$GREEN</span><span class="s2" style="color: #d14;">**Step 3**</span><span class="si" style="color: #d14;">$NC</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="944" 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">
944
</td>
<td class="new_line diff-line-num" data-linenumber="962" 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">
962
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<pre style="margin: 0;"> <span id="LC962" class="line" lang="perl">  <span class="nv" style="color: #008080;">&cluster</span><span class="p">;</span>             <span class="c1" style="color: #998; font-style: italic;"># form clusters and write outputs</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
945
</td>
<td class="new_line diff-line-num old" data-linenumber="963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC945" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$GREEN</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">All finished.</span><span class="si" style="color: #d14;">$NC</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="946" 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">
946
</td>
<td class="new_line diff-line-num" data-linenumber="963" 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">
963
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC963" class="line" lang="perl"><span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="947" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="964" 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">
964
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC964" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="947" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="965" 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">
965
</td>
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<pre style="margin: 0;">+<span id="LC965" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Step 4</span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="947" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="966" 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">
966
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<pre style="margin: 0;">+<span id="LC966" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$hmm_QUEUE</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Thread::</span><span class="nv" style="color: #008080;">Queue</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">();</span>    <span class="c1" style="color: #998; font-style: italic;"># A new empty queue</span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="947" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="967" 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">
967
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC967" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$hmm_QUEUE_maxNumEl</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="947" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="968" 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">
968
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC968" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$hmm_proteinorthofile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$synteny</span> <span class="p">?</span> <span class="nv" style="color: #008080;">$syntable</span> <span class="p">:</span> <span class="nv" style="color: #008080;">$simtable</span><span class="p">;</span></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="947" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="969" 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">
969
</td>
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<pre style="margin: 0;">+<span id="LC969" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$hmm_header</span><span class="o" style="font-weight: 600;">=</span><span class="p">"";</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="947" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="970" 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">
970
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC970" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">@hmm_filenames</span><span class="p">;</span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="947" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="971" 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">
971
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC971" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">%hmm_filenames2colid</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="947" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="972" 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">
972
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC972" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$hmm_num_cols</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="947" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="973" 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">
973
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC973" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="947" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="974" 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">
974
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC974" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="p">{</span>  </span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="947" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="975" 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">
975
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC975" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$GREEN</span><span class="s2" style="color: #d14;">**Step 4**</span><span class="si" style="color: #d14;">$NC</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="947" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="976" 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">
976
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC976" class="line" lang="perl">  <span class="nv" style="color: #008080;">&hmmenriched</span><span class="p">;</span>             </span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="947" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="977" 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">
977
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC977" class="line" lang="perl"><span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="947" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="978" 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">
978
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC978" class="line" lang="perl"></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="947" 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">
947
</td>
<td class="new_line diff-line-num" data-linenumber="979" 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">
979
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC979" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$clean</span><span class="p">)</span> <span class="p">{</span><span class="nv" style="color: #008080;">&clean</span><span class="p">;}</span>           <span class="c1" style="color: #998; font-style: italic;"># remove blast indices</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="948" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
948
</td>
<td class="new_line diff-line-num" data-linenumber="980" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
980
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC980" class="line" lang="perl"></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="949" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
949
</td>
<td class="new_line diff-line-num" data-linenumber="981" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
981
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC981" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$nograph</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="956" 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="988" 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">@@ -956,18 +988,178 @@ if (!$keep && $tmp_path =~ m/\/proteinortho_cache_[^\/]+\d*\/$/ && $step!=1){sys</td>
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<td class="old_line diff-line-num" data-linenumber="956" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
956
</td>
<td class="new_line diff-line-num" data-linenumber="988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
988
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC988" class="line" lang="perl"></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num" data-linenumber="957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
957
</td>
<td class="new_line diff-line-num" data-linenumber="989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
989
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC989" class="line" lang="perl"><span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file</span> <span class="p">(</span><span class="nv" style="color: #008080;">@files_cleanup</span><span class="p">){</span><span class="nb" style="color: #0086b3;">unlink</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">);}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="958" 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">
958
</td>
<td class="new_line diff-line-num" data-linenumber="990" 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">
990
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC990" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="959" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="991" 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">
991
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC991" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$GREEN</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">All finished.</span><span class="si" style="color: #d14;">$NC</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="959" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="992" 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">
992
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC992" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="959" 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">
959
</td>
<td class="new_line diff-line-num" data-linenumber="993" 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">
993
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC993" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="960" 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">
960
</td>
<td class="new_line diff-line-num" data-linenumber="994" 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">
994
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC994" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Functions</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="961" 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">
961
</td>
<td class="new_line diff-line-num" data-linenumber="995" 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">
995
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC995" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="962" 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">
962
</td>
<td class="new_line diff-line-num" data-linenumber="996" 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">
996
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC996" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="963" 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">
963
</td>
<td class="new_line diff-line-num" data-linenumber="997" 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">
997
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC997" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">clean</span> <span class="p">{</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
964
</td>
<td class="new_line diff-line-num old" data-linenumber="998" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC964" class="line" lang="perl">  <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Removing temporary files...</span><span class="se" style="color: #d14;">\n</span><span class="p">"<span class="idiff left right">;</span></span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="965" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="998" 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">
998
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC998" class="line" lang="perl">  <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$verbose</span></span><span class="p"><span class="idiff">){</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Removing temporary files...</span><span class="se" style="color: #d14;">\n</span><span class="p">"</span><span class="idiff"> </span><span class="p"><span class="idiff right">}</span></span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
965
</td>
<td class="new_line diff-line-num" data-linenumber="999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
999
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC999" class="line" lang="perl">  <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file</span> <span class="p">(</span><span class="nv" style="color: #008080;">@files</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="966" 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">
966
</td>
<td class="new_line diff-line-num" data-linenumber="1000" 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">
1000
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1000" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">rm </span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">*</span><span class="p">");</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="967" 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">
967
</td>
<td class="new_line diff-line-num" data-linenumber="1001" 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">
1001
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1001" class="line" lang="perl">  <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1002" 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">
1002
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1002" class="line" lang="perl"><span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1003" 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">
1003
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1003" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1004" 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">
1004
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1004" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">workertest</span> <span class="p">{</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1005" 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">
1005
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1005" class="line" lang="perl">  <span class="nb" style="color: #0086b3;">local</span> <span class="nv" style="color: #008080;">$SIG</span><span class="p">{</span><span class="nv" style="color: #008080;">KILL</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">sub </span><span class="p">{</span> <span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nb" style="color: #0086b3;">exit</span> <span class="p">};</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1006" 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">
1006
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1006" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$tid</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">tid</span><span class="p">();</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1007" 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">
1007
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1007" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1008" 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">
1008
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1008" class="line" lang="perl">  <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$job</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$hmm_QUEUE</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">dequeue</span><span class="p">()){</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1009" 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">
1009
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1009" class="line" lang="perl">    <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$tid</span><span class="s2" style="color: #d14;"> - -> start</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1010" 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">
1010
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1010" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">sleep 2</span><span class="p">");</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1011" 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">
1011
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1011" class="line" lang="perl">    <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$tid</span><span class="s2" style="color: #d14;"> -> end</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1012" 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">
1012
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1012" class="line" lang="perl">  <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1013" 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">
1013
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1013" class="line" lang="perl"><span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1014" 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">
1014
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1014" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1015" 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">
1015
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1015" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">hmmenriched</span> <span class="p">{</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1016" 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">
1016
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1016" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1017" 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">
1017
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1017" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!-</span><span class="nv" style="color: #008080;">e</span> <span class="p">"</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/proteinortho_grab_proteins.</span><span class="si" style="color: #d14;">$hmm_proteinorthofile</span><span class="s2" style="color: #d14;">.done</span><span class="p">"){</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1018" 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">
1018
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1018" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">proteinortho_grab_proteins.pl -cpus=</span><span class="si" style="color: #d14;">$cpus</span><span class="s2" style="color: #d14;"> -minprots=</span><span class="si" style="color: #d14;">$hmm_minprots</span><span class="s2" style="color: #d14;"> -ignoreWarning -tofiles='</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/' </span><span class="si" style="color: #d14;">$hmm_proteinorthofile</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">join</span><span class="p">("</span><span class="s2" style="color: #d14;"> </span><span class="p">",</span><span class="nv" style="color: #008080;">@files</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">; touch </span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/proteinortho_grab_proteins.</span><span class="si" style="color: #d14;">$hmm_proteinorthofile</span><span class="s2" style="color: #d14;">.done</span><span class="p">");</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1019" 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">
1019
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1019" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">'proteinortho_grab_proteins.pl' failed with code $?.</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code).</span><span class="p">")</span> <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1020" 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">
1020
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1020" class="line" lang="perl">  <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1021" 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">
1021
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1021" class="line" lang="perl"> </span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1022" 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">
1022
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1022" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">%orthogroupfiles</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1023" 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">
1023
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1023" class="line" lang="perl">  <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$fp</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">glob</span><span class="p">("</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/*OrthoGroup*.fasta</span><span class="p">"))</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$fp</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">m/OrthoGroup([0-9]+)\.fasta/</span><span class="p">){</span> <span class="nv" style="color: #008080;">$orthogroupfiles</span><span class="p">{</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">}</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$fp</span> <span class="p">}}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1024" 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">
1024
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1024" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1025" 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">
1025
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1025" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1026" 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">
1026
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1026" class="line" lang="perl">  <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$FH</span><span class="p">,"</span><span class="s2" style="color: #d14;"><</span><span class="si" style="color: #d14;">$hmm_proteinorthofile</span><span class="p">");</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1027" 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">
1027
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1027" class="line" lang="perl">  <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="o" style="font-weight: 600;"><</span><span class="nv" style="color: #008080;">$FH</span><span class="o" style="font-weight: 600;">></span><span class="p">){</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1028" 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">
1028
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1028" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">chomp</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1029" 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">
1029
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1029" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$line</span><span class="o" style="font-weight: 600;">=</span><span class="vg" style="color: #008080;">$_</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1030" 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">
1030
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1030" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="sr" style="color: #009926;">/^#/</span><span class="p">){</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1031" 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">
1031
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1031" class="line" lang="perl">      <span class="c1" style="color: #998; font-style: italic;">#print RESULTFH "$line\n";</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1032" 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">
1032
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1032" class="line" lang="perl">      <span class="nv" style="color: #008080;">$hmm_header</span> <span class="o" style="font-weight: 600;">.=</span> <span class="nv" style="color: #008080;">$line</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1033" 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">
1033
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1033" class="line" lang="perl">      <span class="nv" style="color: #008080;">@hmm_filenames</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\t</span><span class="p">",</span><span class="nv" style="color: #008080;">$line</span><span class="p">);</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1034" 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">
1034
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1034" class="line" lang="perl">      <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@hmm_filenames</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span> </span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1035" 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">
1035
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1035" class="line" lang="perl">        <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$base_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$hmm_filenames</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">];</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1036" 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">
1036
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1036" class="line" lang="perl">        <span class="nv" style="color: #008080;">$base_file</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/\.fasta|\.faa|\.fna//g</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1037" 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">
1037
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1037" class="line" lang="perl">        <span class="nv" style="color: #008080;">$hmm_filenames2colid</span><span class="p">{</span><span class="nv" style="color: #008080;">$base_file</span><span class="p">}</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$i</span> </span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1038" 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">
1038
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1038" class="line" lang="perl">      <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1039" 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">
1039
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1039" class="line" lang="perl">      <span class="k" style="font-weight: 600;">next</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="968" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1040" 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">
1040
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1040" class="line" lang="perl">    <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="968" 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">
968
</td>
<td class="new_line diff-line-num" data-linenumber="1041" 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">
1041
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1041" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1042" 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">
1042
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1042" class="line" lang="perl">    <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1043" 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">
1043
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1043" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@a</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\t</span><span class="p">",</span><span class="nv" style="color: #008080;">$line</span><span class="p">);</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1044" 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">
1044
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1044" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1045" 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">
1045
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1045" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$hmm_num_cols</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">){</span> <span class="nv" style="color: #008080;">$hmm_num_cols</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@a</span> <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1046" 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">
1046
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1046" class="line" lang="perl">    </span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1047" 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">
1047
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1047" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$groupfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"";</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1048" 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">
1048
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1048" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="nb" style="color: #0086b3;">exists</span> <span class="nv" style="color: #008080;">$orthogroupfiles</span><span class="p">{</span><span class="nv" style="color: #008080;">$i</span><span class="p">}</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$a</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">>=</span> <span class="nv" style="color: #008080;">$hmm_minprots</span> <span class="p">){</span> <span class="nv" style="color: #008080;">$groupfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">basename</span><span class="p">(</span><span class="nv" style="color: #008080;">$orthogroupfiles</span><span class="p">{</span><span class="nv" style="color: #008080;">$i</span><span class="p">});</span> <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1049" 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">
1049
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1049" class="line" lang="perl">    <span class="nv" style="color: #008080;">$hmm_QUEUE</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">enqueue</span><span class="p">(</span><span class="nv" style="color: #008080;">$groupfile</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">$;</span><span class="si" style="color: #d14;">$line</span><span class="s2" style="color: #d14;">$;</span><span class="si" style="color: #d14;">$i</span><span class="p">");</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1050" 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">
1050
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1050" class="line" lang="perl">  <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1051" 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">
1051
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1051" class="line" lang="perl">  <span class="nb" style="color: #0086b3;">close</span><span class="p">(</span><span class="nv" style="color: #008080;">$FH</span><span class="p">);</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1052" 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">
1052
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1052" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1053" 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">
1053
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1053" class="line" lang="perl">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: #008080;">$cpus</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: #008080;">$hmm_QUEUE</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">enqueue</span><span class="p">(</span><span class="nb" style="color: #0086b3;">undef</span><span class="p">)</span> <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1054" 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">
1054
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1054" class="line" lang="perl">  <span class="nv" style="color: #008080;">$hmm_QUEUE_maxNumEl</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$hmm_QUEUE</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">pending</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1055" 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">
1055
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1055" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1056" 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">
1056
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1056" class="line" lang="perl">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: #008080;">$cpus</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">create</span><span class="p">('</span><span class="s1" style="color: #d14;">hmmWorker</span><span class="p">')</span> <span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;"># spawn a thread for each core</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1057" 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">
1057
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1057" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1058" 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">
1058
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1058" class="line" lang="perl">  <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">head -n1 </span><span class="si" style="color: #d14;">$hmm_proteinorthofile</span><span class="s2" style="color: #d14;"> ></span><span class="si" style="color: #d14;">$hmm_proteinorthofile</span><span class="s2" style="color: #d14;">.enriched</span><span class="p">");</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1059" 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">
1059
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1059" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1060" 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">
1060
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1060" class="line" lang="perl">  <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$FH_RESULT</span><span class="p">,"</span><span class="s2" style="color: #d14;">>></span><span class="si" style="color: #d14;">$hmm_proteinorthofile</span><span class="s2" style="color: #d14;">.enriched</span><span class="p">");</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1061" 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">
1061
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1061" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">%hmm_has_protein</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1062" 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">
1062
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1062" class="line" lang="perl">  <span class="k" style="font-weight: 600;">foreach</span> <span class="p">(</span><span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">list</span><span class="p">())</span> <span class="p">{</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1063" 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">
1063
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1063" class="line" lang="perl">    <span class="vg" style="color: #008080;">$_</span><span class="o" style="font-weight: 600;">-></span><span class="nb" style="color: #0086b3;">join</span><span class="p">();</span> <span class="c1" style="color: #998; font-style: italic;"># await all threads</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1064" 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">
1064
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1064" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$tid</span><span class="o" style="font-weight: 600;">=</span><span class="vg" style="color: #008080;">$_</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">tid</span><span class="p">();</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1065" 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">
1065
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1065" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$FH</span><span class="p">,"</span><span class="s2" style="color: #d14;"><</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/tid.</span><span class="si" style="color: #d14;">$tid</span><span class="s2" style="color: #d14;">.out</span><span class="p">");</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1066" 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">
1066
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1066" class="line" lang="perl">    <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="o" style="font-weight: 600;"><</span><span class="nv" style="color: #008080;">$FH</span><span class="o" style="font-weight: 600;">></span><span class="p">){</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1067" 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">
1067
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1067" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">chomp</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1068" 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">
1068
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1068" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$line</span><span class="o" style="font-weight: 600;">=</span><span class="vg" style="color: #008080;">$_</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1069" 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">
1069
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1069" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@a</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\t</span><span class="p">",</span><span class="nv" style="color: #008080;">$line</span><span class="p">);</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1070" 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">
1070
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1070" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$species</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1071" 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">
1071
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1071" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$prots</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1072" 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">
1072
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1072" class="line" lang="perl">      <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span> <span class="nv" style="color: #008080;">$j</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@a</span><span class="p">;</span> <span class="nv" style="color: #008080;">$j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1073" 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">
1073
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1073" class="line" lang="perl">        <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@newel</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1074" 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">
1074
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1074" class="line" lang="perl">        <span class="k" style="font-weight: 600;">foreach</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="s2" style="color: #d14;">,</span><span class="p">",</span><span class="nv" style="color: #008080;">$a</span><span class="p">[</span><span class="nv" style="color: #008080;">$j</span><span class="p">])){</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1075" 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">
1075
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1075" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nb" style="color: #0086b3;">exists</span> <span class="nv" style="color: #008080;">$hmm_has_protein</span><span class="p">{</span><span class="vg" style="color: #008080;">$_</span><span class="p">}){</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1076" 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">
1076
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1076" class="line" lang="perl">            <span class="nv" style="color: #008080;">$hmm_has_protein</span><span class="p">{</span><span class="vg" style="color: #008080;">$_</span><span class="p">}</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1077" 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">
1077
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1077" class="line" lang="perl">            <span class="nb" style="color: #0086b3;">push</span><span class="p">(</span><span class="nv" style="color: #008080;">@newel</span><span class="p">,</span><span class="vg" style="color: #008080;">$_</span><span class="p">);</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1078" 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">
1078
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1078" class="line" lang="perl">          <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1079" 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">
1079
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1079" class="line" lang="perl">        <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1080" 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">
1080
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1080" class="line" lang="perl">        <span class="nv" style="color: #008080;">$a</span><span class="p">[</span><span class="nv" style="color: #008080;">$j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">join</span><span class="p">("</span><span class="s2" style="color: #d14;">,</span><span class="p">",</span><span class="nv" style="color: #008080;">@newel</span><span class="p">);</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1081" 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">
1081
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1081" class="line" lang="perl">        <span class="nv" style="color: #008080;">$prots</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@newel</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1082" 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">
1082
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1082" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$a</span><span class="p">[</span><span class="nv" style="color: #008080;">$j</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">""){</span><span class="nv" style="color: #008080;">$a</span><span class="p">[</span><span class="nv" style="color: #008080;">$j</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;">*</span><span class="p">"}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span><span class="nv" style="color: #008080;">$species</span><span class="o" style="font-weight: 600;">++</span><span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1083" 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">
1083
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1083" class="line" lang="perl">      <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1084" 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">
1084
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1084" class="line" lang="perl">      <span class="nv" style="color: #008080;">$a</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$species</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1085" 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">
1085
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1085" class="line" lang="perl">      <span class="nv" style="color: #008080;">$a</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$prots</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1086" 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">
1086
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1086" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$species</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: #008080;">$FH_RESULT</span> <span class="nb" style="color: #0086b3;">join</span><span class="p">("</span><span class="se" style="color: #d14;">\t</span><span class="p">",</span><span class="nv" style="color: #008080;">@a</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span>      </span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1087" 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">
1087
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1087" class="line" lang="perl">    <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1088" 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">
1088
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1088" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">close</span><span class="p">(</span><span class="nv" style="color: #008080;">$FH</span><span class="p">);</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1089" 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">
1089
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1089" class="line" lang="perl">  <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1090" 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">
1090
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1090" class="line" lang="perl">  <span class="nb" style="color: #0086b3;">close</span><span class="p">(</span><span class="nv" style="color: #008080;">$FH_RESULT</span><span class="p">);</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1091" 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">
1091
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1091" class="line" lang="perl"><span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1092" 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">
1092
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1092" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1093" 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">
1093
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1093" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">hmmWorker</span> <span class="p">{</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1094" 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">
1094
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1094" class="line" lang="perl">  <span class="nb" style="color: #0086b3;">local</span> <span class="nv" style="color: #008080;">$SIG</span><span class="p">{</span><span class="nv" style="color: #008080;">KILL</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">sub </span><span class="p">{</span> <span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nb" style="color: #0086b3;">exit</span> <span class="p">};</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1095" 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">
1095
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1095" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1096" 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">
1096
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1096" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$tid</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">tid</span><span class="p">();</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1097" 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">
1097
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1097" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">%has_protein</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1098" 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">
1098
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1098" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1099" 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">
1099
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1099" class="line" lang="perl">  <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$FHret</span><span class="p">,"</span><span class="s2" style="color: #d14;">></span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/tid.</span><span class="si" style="color: #d14;">$tid</span><span class="s2" style="color: #d14;">.out</span><span class="p">");</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1100" 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">
1100
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1100" class="line" lang="perl">  <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$job</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$hmm_QUEUE</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">dequeue</span><span class="p">())){</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1101" 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">
1101
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1101" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1102" 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">
1102
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1102" class="line" lang="perl">    <span class="nv" style="color: #008080;">$job</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;">/</span><span class="si" style="color: #d14;">$job</span><span class="p">";</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1103" 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">
1103
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1103" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\r</span><span class="s2" style="color: #d14;">[tid=</span><span class="si" style="color: #d14;">$tid</span><span class="s2" style="color: #d14;">] -step=4 in progress : </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="mi" style="color: #099;">10000</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">$hmm_QUEUE</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">pending</span><span class="sr" style="color: #009926;">/$hmm_QUEUE_maxNumEl))/</span><span class="mi" style="color: #099;">100</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">%</span><span class="p">"</span> <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1104" 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">
1104
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1104" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1105" 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">
1105
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1105" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: #008080;">$groupfile</span><span class="p">,</span><span class="nv" style="color: #008080;">$line</span><span class="p">,</span><span class="nv" style="color: #008080;">$i</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="s2" style="color: #d14;">$;</span><span class="p">",</span><span class="nv" style="color: #008080;">$job</span><span class="p">);</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1106" 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">
1106
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1106" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@tmp_hmm_cols</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\t</span><span class="p">",</span><span class="nv" style="color: #008080;">$line</span><span class="p">);</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1107" 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">
1107
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1107" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$tmp_hmm_cols</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: #008080;">$hmm_minprots</span><span class="p">){</span> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: #008080;">$FHret</span> <span class="nb" style="color: #0086b3;">join</span><span class="p">("</span><span class="se" style="color: #d14;">\t</span><span class="p">",</span><span class="nv" style="color: #008080;">@tmp_hmm_cols</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span> <span class="k" style="font-weight: 600;">next</span> <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1108" 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">
1108
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1108" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1109" 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">
1109
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1109" class="line" lang="perl">    <span class="nv" style="color: #008080;">@has_protein</span><span class="p">{</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="s2" style="color: #d14;">,</span><span class="p">",</span><span class="nb" style="color: #0086b3;">join</span><span class="p">("</span><span class="s2" style="color: #d14;">,</span><span class="p">",</span> <span class="nv" style="color: #008080;">@tmp_hmm_cols</span><span class="p">[</span><span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">..</span> <span class="nv" style="color: #008080;">$#tmp_hmm_cols</span> <span class="p">]))</span> <span class="p">}</span><span class="o" style="font-weight: 600;">=</span><span class="p">();</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1110" 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">
1110
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1110" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1111" 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">
1111
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1111" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">aligning grouped sequences</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1112" 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">
1112
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1112" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1113" 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">
1113
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1113" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!-</span><span class="nv" style="color: #008080;">e</span> <span class="p">"</span><span class="si" style="color: #d14;">$groupfile</span><span class="s2" style="color: #d14;">.aln</span><span class="p">"){</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1114" 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">
1114
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1114" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">mafft --anysymbol --auto --thread 1 </span><span class="si" style="color: #d14;">$groupfile</span><span class="s2" style="color: #d14;"> 2>/dev/null | MSAtrimmer.pl -fasta -HminPairId=5% -norealn - > </span><span class="si" style="color: #d14;">$groupfile</span><span class="s2" style="color: #d14;">.aln 2>/dev/null</span><span class="p">");</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1115" 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">
1115
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1115" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">'mafft' (</span><span class="si" style="color: #d14;">$groupfile</span><span class="s2" style="color: #d14;">) failed with code $?.</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code).</span><span class="p">")</span> <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1116" 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">
1116
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1116" class="line" lang="perl">    <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1117" 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">
1117
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1117" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1118" 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">
1118
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1118" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">build hmm database</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1119" 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">
1119
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1119" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1120" 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">
1120
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1120" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!-</span><span class="nv" style="color: #008080;">e</span> <span class="p">"</span><span class="si" style="color: #d14;">$groupfile</span><span class="s2" style="color: #d14;">.aln.hmm</span><span class="p">"){</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1121" 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">
1121
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1121" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">hmmbuild </span><span class="si" style="color: #d14;">$groupfile</span><span class="s2" style="color: #d14;">.aln.hmm </span><span class="si" style="color: #d14;">$groupfile</span><span class="s2" style="color: #d14;">.aln >/dev/null 2>/dev/null</span><span class="p">");</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1122" 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">
1122
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1122" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">'hmmbuild' (</span><span class="si" style="color: #d14;">$groupfile</span><span class="s2" style="color: #d14;">) failed with code $?.</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code).</span><span class="p">")</span> <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1123" 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">
1123
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1123" class="line" lang="perl">    <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1124" 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">
1124
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1124" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1125" 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">
1125
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1125" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">search hmm database against input sequences</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1126" 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">
1126
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1126" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1127" 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">
1127
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1127" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$newprots</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1128" 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">
1128
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1128" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$newspecies</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1129" 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">
1129
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1129" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1130" 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">
1130
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1130" class="line" lang="perl">    <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file</span> <span class="p">(</span><span class="nv" style="color: #008080;">@files</span><span class="p">){</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1131" 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">
1131
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1131" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$base_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">basename</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">);</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1132" 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">
1132
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1132" class="line" lang="perl">      <span class="nv" style="color: #008080;">$base_file</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/\.fasta|\.faa|\.fna//g</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1133" 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">
1133
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1133" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nb" style="color: #0086b3;">exists</span> <span class="nv" style="color: #008080;">$hmm_filenames2colid</span><span class="p">{</span><span class="nv" style="color: #008080;">$base_file</span><span class="p">}){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$base_file</span><span class="s2" style="color: #d14;"> invalid</span><span class="p">";</span> <span class="nb" style="color: #0086b3;">die</span><span class="p">;}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1134" 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">
1134
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1134" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$coli</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$hmm_filenames2colid</span><span class="p">{</span><span class="nv" style="color: #008080;">$base_file</span><span class="p">};</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1135" 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">
1135
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1135" class="line" lang="perl">      </span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1136" 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">
1136
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1136" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$hmm_ret</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">hmmsearch --cpu 1 -E </span><span class="si" style="color: #d14;">$hmm_search_evalue</span><span class="sb" style="color: #d14;"> </span><span class="si" style="color: #d14;">$groupfile</span><span class="sb" style="color: #d14;">.aln.hmm </span><span class="si" style="color: #d14;">$file</span><span class="sb" style="color: #d14;"> 2>/dev/null | grep '</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="sb" style="color: #d14;">></span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="sb" style="color: #d14;">>'</span><span class="p">`;</span><span class="c1" style="color: #998; font-style: italic;"># |  2>/dev/null</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1137" 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">
1137
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1137" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1138" 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">
1138
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1138" class="line" lang="perl">      <span class="k" style="font-weight: 600;">foreach</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="p">",</span><span class="nv" style="color: #008080;">$hmm_ret</span><span class="p">))</span> <span class="p">{</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1139" 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">
1139
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1139" class="line" lang="perl">        <span class="vg" style="color: #008080;">$_</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/^>> ?//</span><span class="p">;</span><span class="vg" style="color: #008080;">$_</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/[ \t].*$//</span><span class="p">;</span> <span class="nb" style="color: #0086b3;">chomp</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1140" 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">
1140
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1140" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nb" style="color: #0086b3;">exists</span> <span class="nv" style="color: #008080;">$has_protein</span><span class="p">{</span><span class="vg" style="color: #008080;">$_</span><span class="p">}){</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1141" 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">
1141
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1141" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="nv" style="color: #008080;">$tmp_hmm_cols</span><span class="p">[</span><span class="nv" style="color: #008080;">$coli</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">""</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$tmp_hmm_cols</span><span class="p">[</span><span class="nv" style="color: #008080;">$coli</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">*</span><span class="p">"</span> <span class="p">){</span> <span class="nv" style="color: #008080;">$newspecies</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span><span class="nv" style="color: #008080;">$tmp_hmm_cols</span><span class="p">[</span><span class="nv" style="color: #008080;">$coli</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="p">""</span> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span> <span class="vg" style="color: #008080;">$_</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;">,</span><span class="si" style="color: #d14;">$_</span><span class="p">"</span> <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1142" 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">
1142
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1142" class="line" lang="perl">          <span class="nv" style="color: #008080;">$tmp_hmm_cols</span><span class="p">[</span><span class="nv" style="color: #008080;">$coli</span><span class="p">]</span> <span class="o" style="font-weight: 600;">.=</span> <span class="vg" style="color: #008080;">$_</span><span class="p">;</span> </span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1143" 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">
1143
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1143" class="line" lang="perl">          <span class="nv" style="color: #008080;">$newprots</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1144" 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">
1144
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1144" class="line" lang="perl">        <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1145" 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">
1145
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1145" class="line" lang="perl">      <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1146" 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">
1146
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1146" class="line" lang="perl">    <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1147" 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">
1147
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1147" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1148" 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">
1148
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1148" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$tid</span><span class="s2" style="color: #d14;"> evaluating results</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1149" 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">
1149
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1149" class="line" lang="perl">    </span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1150" 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">
1150
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1150" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$newprots</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1151" 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">
1151
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1151" class="line" lang="perl">      <span class="nv" style="color: #008080;">$tmp_hmm_cols</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nv" style="color: #008080;">$newspecies</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1152" 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">
1152
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1152" class="line" lang="perl">      <span class="nv" style="color: #008080;">$tmp_hmm_cols</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nv" style="color: #008080;">$newprots</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1153" 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">
1153
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1153" class="line" lang="perl">      <span class="nv" style="color: #008080;">$tmp_hmm_cols</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span>  <span class="p">"</span><span class="s2" style="color: #d14;">NA</span><span class="p">";</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1154" 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">
1154
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1154" class="line" lang="perl">    <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1155" 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">
1155
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1155" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$tmp_hmm_cols</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">>=</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="nv" style="color: #008080;">$singles</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$tmp_hmm_cols</span><span class="p">[</span><span class="mi" style="color: #099;">1</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>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1156" 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">
1156
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1156" class="line" lang="perl">      <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: #008080;">$FHret</span> <span class="nb" style="color: #0086b3;">join</span><span class="p">("</span><span class="se" style="color: #d14;">\t</span><span class="p">",</span><span class="nv" style="color: #008080;">@tmp_hmm_cols</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1157" 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">
1157
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1157" class="line" lang="perl">    <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1158" 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">
1158
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1158" class="line" lang="perl">  <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="969" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1159" 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">
1159
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1159" class="line" lang="perl">  <span class="nb" style="color: #0086b3;">close</span><span class="p">(</span><span class="nv" style="color: #008080;">$FHret</span><span class="p">);</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="969" 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">
969
</td>
<td class="new_line diff-line-num" data-linenumber="1160" 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">
1160
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1160" class="line" lang="perl"><span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="970" 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">
970
</td>
<td class="new_line diff-line-num" data-linenumber="1161" 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">
1161
</td>
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<pre style="margin: 0;"> <span id="LC1161" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="971" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1162" 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">
1162
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1162" class="line" lang="perl"></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="971" 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">
971
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<td class="new_line diff-line-num" data-linenumber="1163" 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">
1163
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<pre style="margin: 0;"> <span id="LC1163" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">cluster</span> <span class="p">{</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="972" 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">
972
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<td class="new_line diff-line-num" data-linenumber="1164" 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">
1164
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<pre style="margin: 0;"> <span id="LC1164" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="973" 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">
973
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<td class="new_line diff-line-num" data-linenumber="1165" 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">
1165
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<pre style="margin: 0;"> <span id="LC1165" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$useMcl</span><span class="p">){</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1012" 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="1204" 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">@@ -1012,10 +1204,14 @@ sub cluster {</td>
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<td class="old_line diff-line-num" data-linenumber="1012" 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">
1012
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<td class="new_line diff-line-num" data-linenumber="1204" 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">
1204
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<pre style="margin: 0;"> <span id="LC1204" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="1013" 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">
1013
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<td class="new_line diff-line-num" data-linenumber="1205" 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">
1205
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<pre style="margin: 0;"> <span id="LC1205" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">system</span> <span class="p">("</span><span class="s2" style="color: #d14;">OMP_PROC_BIND=</span><span class="si" style="color: #d14;">$ompprocbind</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$po_path</span><span class="s2" style="color: #d14;">/proteinortho_clustering </span><span class="si" style="color: #d14;">$cluster_verbose_level</span><span class="s2" style="color: #d14;"> -minspecies </span><span class="si" style="color: #d14;">$minspecies</span><span class="s2" style="color: #d14;"> -ram </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$freemem_inMB</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -kmere </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">$exactstep3</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -debug </span><span class="si" style="color: #d14;">$debug</span><span class="s2" style="color: #d14;"> -cpus </span><span class="si" style="color: #d14;">$cpus</span><span class="s2" style="color: #d14;"> -weighted 1 -conn </span><span class="si" style="color: #d14;">$connectivity</span><span class="s2" style="color: #d14;"> -purity </span><span class="si" style="color: #d14;">$purity</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nv" style="color: #008080;">$clusterOptions</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""</span> <span class="p">?</span> <span class="p">"</span><span class="si" style="color: #d14;">$clusterOptions</span><span class="p">"</span> <span class="p">:</span> <span class="p">""</span> <span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -rmgraph '</span><span class="si" style="color: #d14;">$rm_simgraph</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$simgraph</span><span class="s2" style="color: #d14;">'* >'</span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;">' </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span> <span class="p">?</span> <span class="p">""</span> <span class="p">:</span> <span class="p">"</span><span class="s2" style="color: #d14;">2>/dev/null</span><span class="p">"));</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="1014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1014
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<td class="new_line diff-line-num" data-linenumber="1206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1206
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1206" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="1015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1015
</td>
<td class="new_line diff-line-num old" data-linenumber="1207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC1015" class="line" lang="perl">          <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">'proteinortho_clustering' failed with code $?.</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Maybe your operating system does not support the statically compiled version, please try recompiling proteinortho with 'make clean' and 'make' (and 'make install PREFIX=...').</span><span class="p">");</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1016
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<td class="new_line diff-line-num old" data-linenumber="1207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1016" class="line" lang="perl">        <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1017" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1017
</td>
<td class="new_line diff-line-num old" data-linenumber="1207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1017" class="line" lang="perl">    <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1018
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<td class="new_line diff-line-num old" data-linenumber="1207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1018" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$stderrout</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">`</span><span class="si" style="color: #d14;">$po_path</span><span class="sb" style="color: #d14;">/proteinortho_do_mcl.pl </span><span class="si" style="color: #d14;">$cpus</span><span class="sb" style="color: #d14;"> </span><span class="si" style="color: #d14;">$simgraph</span><span class="sb" style="color: #d14;">*</span><span class="p">`;</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="1019" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1207" 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">
1207
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<pre style="margin: 0;">+<span id="LC1207" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> proteinortho_clustering failed. I will now retry without the OMP_PROC_BIND flag.</span><span class="si" style="color: #d14;">$NC</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span> <span class="c1" style="color: #998; font-style: italic;"># minimum 5 MB</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="1019" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1208" 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">
1208
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<pre style="margin: 0;">+<span id="LC1208" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">system</span> <span class="p">("</span><span class="si" style="color: #d14;">$po_path</span><span class="s2" style="color: #d14;">/proteinortho_clustering </span><span class="si" style="color: #d14;">$cluster_verbose_level</span><span class="s2" style="color: #d14;"> -minspecies </span><span class="si" style="color: #d14;">$minspecies</span><span class="s2" style="color: #d14;"> -ram </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$freemem_inMB</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -kmere </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">$exactstep3</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -debug </span><span class="si" style="color: #d14;">$debug</span><span class="s2" style="color: #d14;"> -cpus </span><span class="si" style="color: #d14;">$cpus</span><span class="s2" style="color: #d14;"> -weighted 1 -conn </span><span class="si" style="color: #d14;">$connectivity</span><span class="s2" style="color: #d14;"> -purity </span><span class="si" style="color: #d14;">$purity</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nv" style="color: #008080;">$clusterOptions</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""</span> <span class="p">?</span> <span class="p">"</span><span class="si" style="color: #d14;">$clusterOptions</span><span class="p">"</span> <span class="p">:</span> <span class="p">""</span> <span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -rmgraph '</span><span class="si" style="color: #d14;">$rm_simgraph</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$simgraph</span><span class="s2" style="color: #d14;">'* >'</span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;">' </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span> <span class="p">?</span> <span class="p">""</span> <span class="p">:</span> <span class="p">"</span><span class="s2" style="color: #d14;">2>/dev/null</span><span class="p">"));</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="1019" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1209" 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">
1209
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<pre style="margin: 0;">+<span id="LC1209" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="1019" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1210" 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">
1210
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<pre style="margin: 0;">+<span id="LC1210" class="line" lang="perl">        <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">'proteinortho_clustering' failed with code $?.</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Maybe your operating system does not support the statically compiled version, please try recompiling proteinortho with 'make clean' and 'make' (and 'make install PREFIX=...').</span><span class="p">");</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="1019" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1211" 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">
1211
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<pre style="margin: 0;">+<span id="LC1211" class="line" lang="perl">      <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="1019" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1212" 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">
1212
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<pre style="margin: 0;">+<span id="LC1212" class="line" lang="perl">    <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="1019" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1213" 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">
1213
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<pre style="margin: 0;">+<span id="LC1213" class="line" lang="perl">  <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="1019" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1214" 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">
1214
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<pre style="margin: 0;">+<span id="LC1214" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$stderrout</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">`</span><span class="si" style="color: #d14;">$po_path</span><span class="sb" style="color: #d14;">/proteinortho_do_mcl.pl </span><span class="si" style="color: #d14;">$cpus</span><span class="sb" style="color: #d14;"> </span><span class="si" style="color: #d14;">$simgraph</span><span class="sb" style="color: #d14;">*</span><span class="p">`;</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="1019" 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">
1019
</td>
<td class="new_line diff-line-num" data-linenumber="1215" 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">
1215
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<pre style="margin: 0;"> <span id="LC1215" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="1020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1020
</td>
<td class="new_line diff-line-num" data-linenumber="1216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1216
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<pre style="margin: 0;"> <span id="LC1216" class="line" lang="perl">      <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="nv" style="color: #008080;">$stderrout</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="1021" 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">
1021
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<td class="new_line diff-line-num" data-linenumber="1217" 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">
1217
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<pre style="margin: 0;"> <span id="LC1217" class="line" lang="perl">      <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">proteinortho_do_mcl.pl failed with code $?.</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Do you have a woring mcl version installed? (Try 'mcl' in the terminal) If not please install with e.g. 'apt-get install mcl'.</span><span class="p">");</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1076" 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="1272" 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">@@ -1076,8 +1272,14 @@ sub cluster {</td>
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1076
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<td class="new_line diff-line-num" data-linenumber="1272" 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">
1272
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<pre style="margin: 0;"> <span id="LC1272" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">){</span> <span class="nv" style="color: #008080;">$cluster_verbose_level</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">-debug 1 </span><span class="p">";</span> <span class="p">}</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="1077" 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">
1077
</td>
<td class="new_line diff-line-num" data-linenumber="1273" 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">
1273
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1273" class="line" lang="perl"></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="1078" 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">
1078
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<td class="new_line diff-line-num" data-linenumber="1274" 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">
1274
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<pre style="margin: 0;"> <span id="LC1274" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">system</span> <span class="p">("</span><span class="s2" style="color: #d14;">OMP_PROC_BIND=</span><span class="si" style="color: #d14;">$ompprocbind</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$po_path</span><span class="s2" style="color: #d14;">/proteinortho_clustering </span><span class="si" style="color: #d14;">$cluster_verbose_level</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nv" style="color: #008080;">$clusterOptions</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""</span> <span class="p">?</span> <span class="p">"</span><span class="si" style="color: #d14;">$clusterOptions</span><span class="p">"</span> <span class="p">:</span> <span class="p">""</span> <span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -minspecies </span><span class="si" style="color: #d14;">$minspecies</span><span class="s2" style="color: #d14;"> -ram </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$freemem_inMB</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -kmere </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">$exactstep3</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -debug </span><span class="si" style="color: #d14;">$debug</span><span class="s2" style="color: #d14;"> -cpus </span><span class="si" style="color: #d14;">$cpus</span><span class="s2" style="color: #d14;"> -weighted 1 -conn </span><span class="si" style="color: #d14;">$connectivity</span><span class="s2" style="color: #d14;"> -purity </span><span class="si" style="color: #d14;">$purity</span><span class="s2" style="color: #d14;"> -rmgraph '</span><span class="si" style="color: #d14;">$rm_syngraph</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$syngraph</span><span class="s2" style="color: #d14;">'* >'</span><span class="si" style="color: #d14;">$syntable</span><span class="s2" style="color: #d14;">' </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span> <span class="p">?</span> <span class="p">""</span> <span class="p">:</span> <span class="p">"</span><span class="s2" style="color: #d14;">2>/dev/null</span><span class="p">"));</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="1079" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1275" 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">
1275
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1275" class="line" lang="perl">      </span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="1079" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1276" 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">
1276
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<pre style="margin: 0;">+<span id="LC1276" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> proteinortho_clustering failed. I will now retry without the OMP_PROC_BIND flag.</span><span class="si" style="color: #d14;">$NC</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span> <span class="c1" style="color: #998; font-style: italic;"># minimum 5 MB</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="1079" 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">
1079
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<td class="new_line diff-line-num" data-linenumber="1277" 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">
1277
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1277" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1080
</td>
<td class="new_line diff-line-num old" data-linenumber="1278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1080" class="line" lang="perl">        <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">proteinortho_clustering failed with code $?.</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Did you use a static version? Maybe your operating system does not support the static compiled version, please recompile 'make clean' and 'make' or 'make USEPRECOMPILEDLAPACK=FALSE'.</span><span class="p">");</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="1081" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1278" 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">
1278
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1278" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> proteinortho_clustering failed. I will now retry without the OMP_PROC_BIND flag.</span><span class="si" style="color: #d14;">$NC</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span> <span class="c1" style="color: #998; font-style: italic;"># minimum 5 MB</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="1081" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1279" 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">
1279
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<pre style="margin: 0;">+<span id="LC1279" class="line" lang="perl">        <span class="nb" style="color: #0086b3;">system</span> <span class="p">("</span><span class="si" style="color: #d14;">$po_path</span><span class="s2" style="color: #d14;">/proteinortho_clustering </span><span class="si" style="color: #d14;">$cluster_verbose_level</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nv" style="color: #008080;">$clusterOptions</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""</span> <span class="p">?</span> <span class="p">"</span><span class="si" style="color: #d14;">$clusterOptions</span><span class="p">"</span> <span class="p">:</span> <span class="p">""</span> <span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -minspecies </span><span class="si" style="color: #d14;">$minspecies</span><span class="s2" style="color: #d14;"> -ram </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$freemem_inMB</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -kmere </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">$exactstep3</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -debug </span><span class="si" style="color: #d14;">$debug</span><span class="s2" style="color: #d14;"> -cpus </span><span class="si" style="color: #d14;">$cpus</span><span class="s2" style="color: #d14;"> -weighted 1 -conn </span><span class="si" style="color: #d14;">$connectivity</span><span class="s2" style="color: #d14;"> -purity </span><span class="si" style="color: #d14;">$purity</span><span class="s2" style="color: #d14;"> -rmgraph '</span><span class="si" style="color: #d14;">$rm_syngraph</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$syngraph</span><span class="s2" style="color: #d14;">'* >'</span><span class="si" style="color: #d14;">$syntable</span><span class="s2" style="color: #d14;">' </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span> <span class="p">?</span> <span class="p">""</span> <span class="p">:</span> <span class="p">"</span><span class="s2" style="color: #d14;">2>/dev/null</span><span class="p">"));</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1081" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1280" 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">
1280
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1280" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1081" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1281" 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">
1281
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1281" class="line" lang="perl">          <span class="nv" style="color: #008080;">&Error</span><span class="p">("</span><span class="s2" style="color: #d14;">proteinortho_clustering failed with code $?.</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> (Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Code)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Did you use a static version? Maybe your operating system does not support the static compiled version, please recompile 'make clean' and 'make' or 'make USEPRECOMPILEDLAPACK=FALSE'.</span><span class="p">");</span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1081" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1282" 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">
1282
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1282" class="line" lang="perl">        <span class="p">}</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="1081" 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">
1081
</td>
<td class="new_line diff-line-num" data-linenumber="1283" 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">
1283
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1283" class="line" lang="perl">      <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="1082" 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">
1082
</td>
<td class="new_line diff-line-num" data-linenumber="1284" 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">
1284
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1284" class="line" lang="perl">    <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC1285" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">system</span><span class="p">(</span><span class="nv" style="color: #008080;">$po_path</span><span class="o" style="font-weight: 600;">.</span><span class="p">'</span><span class="s1" style="color: #d14;">/proteinortho_do_mcl.pl </span><span class="p">'</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$cpus</span><span class="o" style="font-weight: 600;">.</span><span class="p">'</span><span class="s1" style="color: #d14;"> </span><span class="p">'</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$syngraph</span><span class="o" style="font-weight: 600;">.</span><span class="p">'</span><span class="s1" style="color: #d14;">*</span><span class="p">');</span></span>
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<pre style="margin: 0;"> <span id="LC1351" class="line" lang="perl"><span class="s2" style="color: #d14;">                      2 -> run blast (and ff-adj, if -synteny is set)</span></span>
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<pre style="margin: 0;"> <span id="LC1352" class="line" lang="perl"><span class="s2" style="color: #d14;">                      3 -> clustering</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC1353" class="line" lang="perl"><span class="s2" style="color: #d14;">                      0 -> all (default)</span></span>
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<pre style="margin: 0;">-<span id="LC1152" class="line" lang="perl"><span class="s2" style="color: #d14;">         -isoform=    Enables the isoform <span class="idiff left right">process</span>ing:</span></span>
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<pre style="margin: 0;">+<span id="LC1354" class="line" lang="perl"><span class="s2" style="color: #d14;">         -isoform=    Enables the isoform <span class="idiff left right">merg</span>ing:</span></span>
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<pre style="margin: 0;"> <span id="LC1355" class="line" lang="perl"><span class="s2" style="color: #d14;">                      ncbi -> if the word 'isoform' is found </span></span>
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<pre style="margin: 0;"> <span id="LC1356" class="line" lang="perl"><span class="s2" style="color: #d14;">                      uniprot -> 'Isoform of XYZ' (You need to add the *_additional.fasta files to the analysis)</span></span>
</pre>
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<td class="new_line diff-line-num" data-linenumber="1357" 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="LC1357" class="line" lang="perl"><span class="s2" style="color: #d14;">                      trinity -> using '_iX' suffix</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1161" 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="1363" 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">@@ -1161,7 +1363,10 @@ Options:</td>
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<pre style="margin: 0;"> <span id="LC1363" class="line" lang="perl"><span class="s2" style="color: #d14;">                      The suffix '_legacy' indicates legacy blastall (otherwise blast+ is used).</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC1364" class="line" lang="perl"><span class="s2" style="color: #d14;">         -checkfasta  Checks if the given fasta files are compatible with the algorithm of -p</span></span>
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<pre style="margin: 0;"> <span id="LC1365" class="line" lang="perl"><span class="s2" style="color: #d14;">         -e=          E-value for blast [default: 1e-05]</span></span>
</pre>
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<td class="new_line diff-line-num old" data-linenumber="1366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC1164" class="line" lang="perl"></span>
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<td class="new_line diff-line-num new" data-linenumber="1366" 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="LC1366" class="line" lang="perl"><span class="s2" style="color: #d14;">         -sim=        min. reciprocal similarity for additional hits (0..1) [default: 0.95]</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="1367" 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="LC1367" class="line" lang="perl"><span class="s2" style="color: #d14;">                      1 : only the best reciprocal hits are reported</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="1368" 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="LC1368" class="line" lang="perl"><span class="s2" style="color: #d14;">                      0 : all possible reciprocal blast matches (within the -evalue) are reported</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="1369" 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="LC1369" class="line" lang="perl"><span class="s2" style="color: #d14;">                      </span></span>
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<pre style="margin: 0;"> <span id="LC1370" class="line" lang="perl"><span class="s2" style="color: #d14;">         [Synteny options]</span></span>
</pre>
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1166
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1371
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<pre style="margin: 0;"> <span id="LC1371" class="line" lang="perl"><span class="s2" style="color: #d14;">         -synteny     activate PoFF extension to separate similar sequences print</span></span>
</pre>
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1167
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1372
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<pre style="margin: 0;"> <span id="LC1372" class="line" lang="perl"><span class="s2" style="color: #d14;">                      by contextual adjacencies (requires .gff for each .fasta)</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1171" 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="1376" 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">@@ -1171,7 +1376,7 @@ Options:</td>
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1171
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1376
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<pre style="margin: 0;"> <span id="LC1376" class="line" lang="perl"><span class="s2" style="color: #d14;">         [Clustering options]</span></span>
</pre>
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1172
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<td class="new_line diff-line-num" data-linenumber="1377" 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">
1377
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<pre style="margin: 0;"> <span id="LC1377" class="line" lang="perl"><span class="s2" style="color: #d14;">         -singles     report singleton genes without any hit</span></span>
</pre>
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1173
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<td class="new_line diff-line-num" data-linenumber="1378" 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="LC1378" class="line" lang="perl"><span class="s2" style="color: #d14;">         -conn=       min. algebraic connectivity [default: 0.1]</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1174
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<td class="new_line diff-line-num old" data-linenumber="1379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC1174" class="line" lang="perl"><span class="s2" style="color: #d14;">         -xml        produces an OrthoXML formatted file of the *.proteinortho.</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="1175" 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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<td class="new_line diff-line-num new" data-linenumber="1379" 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">
1379
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<pre style="margin: 0;">+<span id="LC1379" class="line" lang="perl"><span class="s2" style="color: #d14;">         -xml        <span class="idiff left right"> </span>produces an OrthoXML formatted file of the *.proteinortho.</span></span>
</pre>
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1175
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1380
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<pre style="margin: 0;"> <span id="LC1380" class="line" lang="perl"></span>
</pre>
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1176
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<pre style="margin: 0;"> <span id="LC1381" class="line" lang="perl"><span class="s2" style="color: #d14;">         (...) show more with --help</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="1177" 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">
1177
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<td class="new_line diff-line-num" data-linenumber="1382" 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">
1382
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<pre style="margin: 0;"> <span id="LC1382" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1204" 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="1409" 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">@@ -1204,10 +1409,12 @@ Options:</td>
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1204
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<pre style="margin: 0;"> <span id="LC1409" class="line" lang="perl"><span class="s2" style="color: #d14;">                      2 -> run blast (and ff-adj, if -synteny is set)</span></span>
</pre>
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1205
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<td class="new_line diff-line-num" data-linenumber="1410" 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">
1410
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<pre style="margin: 0;"> <span id="LC1410" class="line" lang="perl"><span class="s2" style="color: #d14;">                      3 -> clustering</span></span>
</pre>
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<td class="new_line diff-line-num" data-linenumber="1411" 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">
1411
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<pre style="margin: 0;"> <span id="LC1411" class="line" lang="perl"><span class="s2" style="color: #d14;">                      0 -> all (default)</span></span>
</pre>
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1207
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<td class="new_line diff-line-num old" data-linenumber="1412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC1207" class="line" lang="perl"><span class="s2" style="color: #d14;">         -isoform<span class="idiff left"> </span>    Enables the isoform <span class="idiff right">processing:</span></span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="1208" 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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<td class="new_line diff-line-num new" data-linenumber="1412" 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">
1412
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<pre style="margin: 0;">+<span id="LC1412" class="line" lang="perl"><span class="s2" style="color: #d14;">         -isoform<span class="idiff left">=</span>    Enables the isoform <span class="idiff right">merging. All isoforms are united to a single entity and treated as one. Extracting a group with an isoform will result in all isoforms.</span></span></span>
</pre>
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1208
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<td class="new_line diff-line-num" data-linenumber="1413" 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">
1413
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<pre style="margin: 0;"> <span id="LC1413" class="line" lang="perl"><span class="s2" style="color: #d14;">                      ncbi -> if the word 'isoform' is found </span></span>
</pre>
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1209
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<td class="new_line diff-line-num" data-linenumber="1414" 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">
1414
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<pre style="margin: 0;"> <span id="LC1414" class="line" lang="perl"><span class="s2" style="color: #d14;">                      uniprot -> 'Isoform of XYZ' (You need to add the *_additional.fasta files to the analysis)</span></span>
</pre>
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1210
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<td class="new_line diff-line-num" data-linenumber="1415" 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">
1415
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<pre style="margin: 0;"> <span id="LC1415" class="line" lang="perl"><span class="s2" style="color: #d14;">                      trinity -> using '_iX' suffix</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="1211" 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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<td class="new_line diff-line-num new" data-linenumber="1416" 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">
1416
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<pre style="margin: 0;">+<span id="LC1416" class="line" lang="perl"><span class="s2" style="color: #d14;">                      For more information have a look at: </span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="1211" 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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<td class="new_line diff-line-num new" data-linenumber="1417" 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">
1417
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<pre style="margin: 0;">+<span id="LC1417" class="line" lang="perl"><span class="s2" style="color: #d14;">                        https://gitlab.com/paulklemm_PHD/proteinortho/-/wikis/FAQ#how-does-the-isoform-work</span></span>
</pre>
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1211
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<td class="new_line diff-line-num" data-linenumber="1418" 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">
1418
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<pre style="margin: 0;"> <span id="LC1418" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="1212" 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">
1212
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<td class="new_line diff-line-num" data-linenumber="1419" 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">
1419
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<pre style="margin: 0;"> <span id="LC1419" class="line" lang="perl"><span class="s2" style="color: #d14;">         [Search options]</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="1213" 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">
1213
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<td class="new_line diff-line-num" data-linenumber="1420" 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">
1420
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<pre style="margin: 0;"> <span id="LC1420" class="line" lang="perl"><span class="s2" style="color: #d14;">         -p=          blast program [default: diamond]</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1233" 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="1440" 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">@@ -1233,7 +1440,9 @@ Options:</td>
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1233
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<pre style="margin: 0;"> <span id="LC1440" class="line" lang="perl"><span class="s2" style="color: #d14;">         -checkfasta  Checks if the given fasta files are compatible with the algorithm of -p</span></span>
</pre>
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<td class="new_line diff-line-num" data-linenumber="1441" 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">
1441
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<pre style="margin: 0;"> <span id="LC1441" class="line" lang="perl"><span class="s2" style="color: #d14;">         -e=          E-value for blast [default: 1e-05]</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="1235" 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">
1235
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<td class="new_line diff-line-num" data-linenumber="1442" 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">
1442
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<pre style="margin: 0;"> <span id="LC1442" class="line" lang="perl"><span class="s2" style="color: #d14;">         -selfblast   apply selfblast, detects paralogs without orthologs</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="1443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC1236" class="line" lang="perl"><span class="s2" style="color: #d14;">         -sim=        min. similarity for additional hits (0..1) [default: 0.95]</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="1237" 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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<td class="new_line diff-line-num new" data-linenumber="1443" 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="LC1443" class="line" lang="perl"><span class="s2" style="color: #d14;">         -sim=        min. reciprocal similarity for additional hits (0..1) [default: 0.95]</span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="1237" 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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<td class="new_line diff-line-num new" data-linenumber="1444" 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="LC1444" class="line" lang="perl"><span class="s2" style="color: #d14;">                      1 : only the best reciprocal hits are reported</span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="1237" 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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<td class="new_line diff-line-num new" data-linenumber="1445" 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="LC1445" class="line" lang="perl"><span class="s2" style="color: #d14;">                      0 : all possible reciprocal blast matches (within the -evalue) are reported</span></span>
</pre>
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<td class="new_line diff-line-num" data-linenumber="1446" 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="LC1446" class="line" lang="perl"><span class="s2" style="color: #d14;">         -identity=   min. percent identity of best blast hits [default: 25]</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="1238" 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">
1238
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<td class="new_line diff-line-num" data-linenumber="1447" 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">
1447
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<pre style="margin: 0;"> <span id="LC1447" class="line" lang="perl"><span class="s2" style="color: #d14;">         -cov=        min. coverage of best blast alignments in % [default: 50]</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="1239" 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">
1239
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<td class="new_line diff-line-num" data-linenumber="1448" 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="LC1448" class="line" lang="perl"><span class="s2" style="color: #d14;">         -subparaBlast=    additional parameters for the search tool</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1440" 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="1649" 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">@@ -1440,7 +1649,7 @@ sub workerthread {</td>
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1440
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<td class="new_line diff-line-num" data-linenumber="1649" 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">
1649
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<pre style="margin: 0;"> <span id="LC1649" class="line" lang="perl">    <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="1441" 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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<td class="new_line diff-line-num" data-linenumber="1650" 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="LC1650" class="line" lang="perl">      <span class="nv" style="color: #008080;">%lengths</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">%</span><span class="p">{</span><span class="nv" style="color: #008080;">&get_gene_lengths</span><span class="p">(</span><span class="nv" style="color: #008080;">$file_i</span><span class="p">,</span><span class="nv" style="color: #008080;">$file_j</span><span class="p">)};</span></span>
</pre>
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<td class="new_line diff-line-num" data-linenumber="1651" 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="LC1651" class="line" lang="perl">    <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1443
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<td class="new_line diff-line-num old" data-linenumber="1652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1443" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">%reciprocal_matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">%</span><span class="p">{</span><span class="nv" style="color: #008080;">&match</span><span class="p">(</span><span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: #008080;">%lengths</span><span class="p">,</span><span class="nv" style="color: #008080;">$file_<span class="idiff left">i</span></span><span class="p">,</span><span class="nv" style="color: #008080;">$file_<span class="idiff right">j</span></span><span class="p">,</span><span class="nv" style="color: #008080;">$result_ij</span><span class="p">,</span><span class="nv" style="color: #008080;">$result_ji</span><span class="p">)};</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1444" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1652" 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">
1652
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1652" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">%reciprocal_matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">%</span><span class="p">{</span><span class="nv" style="color: #008080;">&match</span><span class="p">(</span><span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: #008080;">%lengths</span><span class="p">,</span><span class="nv" style="color: #008080;">$file_<span class="idiff left">j</span></span><span class="p">,</span><span class="nv" style="color: #008080;">$file_<span class="idiff right">i</span></span><span class="p">,</span><span class="nv" style="color: #008080;">$result_ij</span><span class="p">,</span><span class="nv" style="color: #008080;">$result_ji</span><span class="p">)};</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="1444" 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">
1444
</td>
<td class="new_line diff-line-num" data-linenumber="1653" 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">
1653
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1653" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="1445" 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">
1445
</td>
<td class="new_line diff-line-num" data-linenumber="1654" 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">
1654
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<pre style="margin: 0;"> <span id="LC1654" class="line" lang="perl">    <span class="c1" style="color: #998; font-style: italic;"># Remove secondary hits if better exist (test here instead of later)</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="1446" 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">
1446
</td>
<td class="new_line diff-line-num" data-linenumber="1655" 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">
1655
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1655" class="line" lang="perl">    <span class="nv" style="color: #008080;">%reciprocal_matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">%</span><span class="p">{</span><span class="nv" style="color: #008080;">&adaptive_best_blast_matches</span><span class="p">(</span><span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: #008080;">%reciprocal_matches</span><span class="p">)};</span></span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1509" 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="1718" 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">@@ -1509,9 +1718,15 @@ sub workerthread {</td>
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<td class="old_line diff-line-num" data-linenumber="1509" 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">
1509
</td>
<td class="new_line diff-line-num" data-linenumber="1718" 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">
1718
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1718" class="line" lang="perl"><span class="s1" style="color: #d14;">          }</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="1510" 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">
1510
</td>
<td class="new_line diff-line-num" data-linenumber="1719" 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">
1719
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1719" class="line" lang="perl"><span class="s1" style="color: #d14;">          # Remap to full ID</span></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num" data-linenumber="1511" 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">
1511
</td>
<td class="new_line diff-line-num" data-linenumber="1720" 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">
1720
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1720" class="line" lang="perl"><span class="s1" style="color: #d14;">          my $a = $track{$file_i.$i};</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="1512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1512
</td>
<td class="new_line diff-line-num old" data-linenumber="1721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1512" class="line" lang="perl"><span class="s1" style="color: #d14;">          if (defined($full_id_map_i{$a})) {$a = $full_id_map_i{$a};}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1513" 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">
1513
</td>
<td class="new_line diff-line-num" data-linenumber="1721" 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">
1721
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1721" class="line" lang="perl"><span class="s1" style="color: #d14;">          my $b = $track{$file_j.$j};</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1514" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1722" 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">
1722
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1722" class="line" lang="perl"><span class="s1" style="color: #d14;">          </span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1514" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1723" 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">
1723
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1723" class="line" lang="perl"><span class="s1" style="color: #d14;">          #if($isoform ne "" && exists $isoform_mapping_best{$file_j." ".$a." vs ".$file_i." ".$b}){</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1514" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1724" 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">
1724
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1724" class="line" lang="perl"><span class="s1" style="color: #d14;">          #  ($a,$b)=split(" ",$isoform_mapping_best{$file_j." ".$a." vs ".$file_i." ".$b});</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1514" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1725" 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">
1725
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1725" class="line" lang="perl"><span class="s1" style="color: #d14;">          #} </span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1514" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1726" 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">
1726
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1726" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1514" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1727" 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">
1727
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1727" class="line" lang="perl"><span class="s1" style="color: #d14;">          if (defined($full_id_map_i{$a})) {$a = $full_id_map_i{$a};}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1514" 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">
1514
</td>
<td class="new_line diff-line-num" data-linenumber="1728" 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">
1728
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1728" class="line" lang="perl"><span class="s1" style="color: #d14;">          if (defined($full_id_map_j{$b})) {$b = $full_id_map_j{$b};}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1515" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1729" 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">
1729
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1729" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1515" 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">
1515
</td>
<td class="new_line diff-line-num" data-linenumber="1730" 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">
1730
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1730" class="line" lang="perl"><span class="s1" style="color: #d14;">          # Store</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1516" 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">
1516
</td>
<td class="new_line diff-line-num" data-linenumber="1731" 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">
1731
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1731" class="line" lang="perl"><span class="s1" style="color: #d14;">          $synteny{"$b $a"} = $score;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1517" 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">
1517
</td>
<td class="new_line diff-line-num" data-linenumber="1732" 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">
1732
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1732" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1567" 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="1782" 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">@@ -1567,7 +1782,19 @@ sub workerthread {</td>
</tr>
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<td class="old_line diff-line-num" data-linenumber="1567" 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">
1567
</td>
<td class="new_line diff-line-num" data-linenumber="1782" 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">
1782
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1782" class="line" lang="perl"><span class="s1" style="color: #d14;">      open(GRAPH,">>$simgraph") || &Error("Could not open file </span><span class="p">'</span><span class="nv" style="color: #008080;">$simgraph</span><span class="p">'</span><span class="s1" style="color: #d14;">: $!");</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1568" 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">
1568
</td>
<td class="new_line diff-line-num" data-linenumber="1783" 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">
1783
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1783" class="line" lang="perl"><span class="s1" style="color: #d14;">      print GRAPH "# $short_file_j\t$short_file_i\n# ".median(@arr0)."\t".median(@arr1)."\t".median(@arr2)."\t".median(@arr3)."\n";</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1569" 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">
1569
</td>
<td class="new_line diff-line-num" data-linenumber="1784" 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">
1784
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1784" class="line" lang="perl"><span class="s1" style="color: #d14;">      foreach (sort keys %reciprocal_matches) {</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="1570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1570
</td>
<td class="new_line diff-line-num old" data-linenumber="1785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1570" class="line" lang="perl"><span class="s1" style="color: #d14;">        my $line = "$_ ".$reciprocal_matches{$_};</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1785" 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">
1785
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1785" class="line" lang="perl"><span class="s1" style="color: #d14;">        my ($a,$b) = split(" ",$_);</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1786" 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">
1786
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1786" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1787" 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">
1787
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1787" class="line" lang="perl"><span class="s1" style="color: #d14;">        #if($isoform ne "" && exists $isoform_mapping_best{$file_j." ".$a." vs ".$file_i." ".$b}){</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1788" 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">
1788
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1788" class="line" lang="perl"><span class="s1" style="color: #d14;">        #  ($a,$b)=split(" ",$isoform_mapping_best{$file_j." ".$a." vs ".$file_i." ".$b});</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1789" 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">
1789
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1789" class="line" lang="perl"><span class="s1" style="color: #d14;">        #} </span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1790" 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">
1790
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1790" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1791" 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">
1791
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1791" class="line" lang="perl"><span class="s1" style="color: #d14;"># if($a =~ /137_TRINITY_DN39932_c6_g1/){print STDERR "RECIPROCAL $_\n"}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1792" 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">
1792
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1792" class="line" lang="perl"><span class="s1" style="color: #d14;"># elsif($b =~ /137_TRINITY_DN39932_c6_g1/){print STDERR "RECIPROCAL $_\n"}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1793" 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">
1793
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1793" class="line" lang="perl"><span class="s1" style="color: #d14;"># elsif($a =~ /138_TRINITY_DN47563_c4_g1/){print STDERR "RECIPROCAL $_\n"}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1794" 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">
1794
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1794" class="line" lang="perl"><span class="s1" style="color: #d14;"># elsif($b =~ /138_TRINITY_DN47563_c4_g1/){print STDERR "RECIPROCAL $_\n"}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1795" 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">
1795
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1795" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1796" 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">
1796
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1796" class="line" lang="perl"><span class="s1" style="color: #d14;">        my $line = "$a $b ".$reciprocal_matches{$_};</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="1797" 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">
1797
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1797" class="line" lang="perl"></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="1571" 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">
1571
</td>
<td class="new_line diff-line-num" data-linenumber="1798" 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">
1798
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1798" class="line" lang="perl"><span class="s1" style="color: #d14;">        $line =~ s/ /\t/g;</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="1572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1572
</td>
<td class="new_line diff-line-num" data-linenumber="1799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1799
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1799" class="line" lang="perl"><span class="s1" style="color: #d14;">        print GRAPH "$line\n";</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="1573" 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">
1573
</td>
<td class="new_line diff-line-num" data-linenumber="1800" 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">
1800
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1800" class="line" lang="perl"><span class="s1" style="color: #d14;">      }</span></span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1819" 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="2046" 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">@@ -1819,7 +2046,7 @@ sub match {</td>
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<td class="old_line diff-line-num" data-linenumber="1819" 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">
1819
</td>
<td class="new_line diff-line-num" data-linenumber="2046" 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">
2046
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2046" class="line" lang="perl"><span class="s1" style="color: #d14;">  my @j = @{(shift)};</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="1820" 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">
1820
</td>
<td class="new_line diff-line-num" data-linenumber="2047" 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">
2047
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2047" class="line" lang="perl"></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num" data-linenumber="1821" 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">
1821
</td>
<td class="new_line diff-line-num" data-linenumber="2048" 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">
2048
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2048" class="line" lang="perl"><span class="s1" style="color: #d14;">  my %legal_i = &get_legal_matches(\%length,$file_i,$file_j,@i);</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="1822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1822
</td>
<td class="new_line diff-line-num old" data-linenumber="2049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1822" class="line" lang="perl"><span class="s1" style="color: #d14;">  my %legal_j = &get_legal_matches(\%length,$file_<span class="idiff left">i</span>,$file_<span class="idiff right">j</span>,@j);</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1823" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2049" 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">
2049
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2049" class="line" lang="perl"><span class="s1" style="color: #d14;">  my %legal_j = &get_legal_matches(\%length,$file_<span class="idiff left">j</span>,$file_<span class="idiff right">i</span>,@j);</span></span>
</pre>
</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1823" 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">
1823
</td>
<td class="new_line diff-line-num" data-linenumber="2050" 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">
2050
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2050" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1824" 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">
1824
</td>
<td class="new_line diff-line-num" data-linenumber="2051" 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">
2051
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2051" class="line" lang="perl"><span class="s1" style="color: #d14;">  return &get_reciprocal_matches(\%legal_i,\%legal_j);</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1825" 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">
1825
</td>
<td class="new_line diff-line-num" data-linenumber="2052" 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">
2052
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2052" class="line" lang="perl"><span class="s1" style="color: #d14;">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1861" 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="2088" 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">@@ -1861,7 +2088,7 @@ sub get_legal_matches {</td>
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<td class="old_line diff-line-num" data-linenumber="1861" 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">
1861
</td>
<td class="new_line diff-line-num" data-linenumber="2088" 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">
2088
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2088" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1862" 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">
1862
</td>
<td class="new_line diff-line-num" data-linenumber="2089" 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">
2089
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2089" class="line" lang="perl">    <span class="c1" style="color: #998; font-style: italic;">## Check for criteria</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1863" 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">
1863
</td>
<td class="new_line diff-line-num" data-linenumber="2090" 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">
2090
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2090" class="line" lang="perl">    <span class="c1" style="color: #998; font-style: italic;"># Well formatted</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="1864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1864
</td>
<td class="new_line diff-line-num old" data-linenumber="2091" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1864" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: #008080;">$local_bitscore</span><span class="p">))</span><span class="idiff left right">              </span><span class="p">{</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1865" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2091" 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">
2091
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2091" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: #008080;">$local_bitscore</span><span class="p">)){</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="1865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1865
</td>
<td class="new_line diff-line-num" data-linenumber="2092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2092
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2092" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$evalue</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: #008080;">$local_evalue</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span> <span class="c1" style="color: #998; font-style: italic;"># 5.17, post filter e-value</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="1866" 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">
1866
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<td class="new_line diff-line-num" data-linenumber="2093" 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">
2093
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<pre style="margin: 0;"> <span id="LC2093" class="line" lang="perl"></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="1867" 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">
1867
</td>
<td class="new_line diff-line-num" data-linenumber="2094" 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">
2094
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<pre style="margin: 0;"> <span id="LC2094" class="line" lang="perl">    <span class="c1" style="color: #998; font-style: italic;"># Percent identity</span></span>
</pre>
</td>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1870" 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="2097" 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">@@ -1870,35 +2097,66 @@ sub get_legal_matches {</td>
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<td class="old_line diff-line-num" data-linenumber="1870" 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">
1870
</td>
<td class="new_line diff-line-num" data-linenumber="2097" 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">
2097
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<pre style="margin: 0;"> <span id="LC2097" class="line" lang="perl">    <span class="c1" style="color: #998; font-style: italic;"># Min. length</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="1871" 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">
1871
</td>
<td class="new_line diff-line-num" data-linenumber="2098" 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">
2098
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<pre style="margin: 0;"> <span id="LC2098" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">tblastx+</span><span class="p">"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">tblastx</span><span class="p">")</span> <span class="p">{</span><span class="nv" style="color: #008080;">$alignment_length</span> <span class="o" style="font-weight: 600;">*=</span> <span class="mi" style="color: #099;">3</span><span class="p">;}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="1872" 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">
1872
</td>
<td class="new_line diff-line-num" data-linenumber="2099" 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">
2099
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2099" class="line" lang="perl"></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="1873" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1873
</td>
<td class="new_line diff-line-num old" data-linenumber="2100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
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<pre style="margin: 0;">-<span id="LC1873" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">autoblast</span><span class="p">"){</span></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="1874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1874
</td>
<td class="new_line diff-line-num old" data-linenumber="2100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1874" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$file_i</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">nucl</span><span class="p">"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$file_j</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">nucl</span><span class="p">"){</span></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="1875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1875
</td>
<td class="new_line diff-line-num old" data-linenumber="2100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1875" class="line" lang="perl">        <span class="nv" style="color: #008080;">$alignment_length</span> <span class="o" style="font-weight: 600;">/=</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="1876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1876
</td>
<td class="new_line diff-line-num old" data-linenumber="2100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1876" class="line" lang="perl">      <span class="p">}</span></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num old" data-linenumber="1877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1877
</td>
<td class="new_line diff-line-num old" data-linenumber="2100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1877" class="line" lang="perl">      <span class="c1" style="color: #998; font-style: italic;"># if i is nucl and j is prot -> then the alignment length is in aa length (all nucl lengths are allready /3) -> ok</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="1878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1878
</td>
<td class="new_line diff-line-num old" data-linenumber="2100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1878" class="line" lang="perl">    <span class="p">}</span></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="1879" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2100" 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">
2100
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2100" class="line" lang="perl">    <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>if($blastmode eq "autoblast"){</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1879" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2101" 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">
2101
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2101" class="line" lang="perl">    <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>  if($file_i eq "nucl" && $file_j eq "nucl"){</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1879" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2102" 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">
2102
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2102" class="line" lang="perl">    <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>    $alignment_length /= 3;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1879" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2103" 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">
2103
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2103" class="line" lang="perl">    <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>  }</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1879" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2104" 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">
2104
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2104" class="line" lang="perl">    <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>  # if i is nucl and j is prot -> then the alignment length is in aa length (all nucl lengths are allready /3) -> ok</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1879" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2105" 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">
2105
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2105" class="line" lang="perl">    <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1879" 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">
1879
</td>
<td class="new_line diff-line-num" data-linenumber="2106" 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">
2106
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2106" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="1880" 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">
1880
</td>
<td class="new_line diff-line-num" data-linenumber="2107" 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">
2107
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2107" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$alignment_length</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: #008080;">$length</span><span class="p">{</span><span class="nv" style="color: #008080;">$query_id</span><span class="p">}</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="nv" style="color: #008080;">$coverage</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">100</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mf" style="color: #099;">0.5</span><span class="p">)</span>     <span class="p">{</span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">!</span><span class="si" style="color: #d14;">$query_id</span><span class="s2" style="color: #d14;"> -> </span><span class="si" style="color: #d14;">$subject_id</span><span class="s2" style="color: #d14;"> is removed because of coverage threshold</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span> <span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="1881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1881
</td>
<td class="new_line diff-line-num" data-linenumber="2108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2108
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<pre style="margin: 0;"> <span id="LC2108" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$alignment_length</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: #008080;">$length</span><span class="p">{</span><span class="nv" style="color: #008080;">$subject_id</span><span class="p">}</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="nv" style="color: #008080;">$coverage</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">100</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mf" style="color: #099;">0.5</span><span class="p">)</span>     <span class="p">{</span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">!</span><span class="si" style="color: #d14;">$query_id</span><span class="s2" style="color: #d14;"> -> </span><span class="si" style="color: #d14;">$subject_id</span><span class="s2" style="color: #d14;"> is removed because of coverage threshold</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span> <span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="1882" 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">
1882
</td>
<td class="new_line diff-line-num" data-linenumber="2109" 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">
2109
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2109" class="line" lang="perl"></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num" data-linenumber="1883" 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">
1883
</td>
<td class="new_line diff-line-num" data-linenumber="2110" 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">
2110
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2110" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$isoform</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>
</pre>
</td>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="1884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1884
</td>
<td class="new_line diff-line-num old" data-linenumber="2111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1884" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">exists</span> <span class="nv" style="color: #008080;">$isoform_mapping</span><span class="p">{</span><span class="nv" style="color: #008080;">$query_id</span><span class="p">}</span> <span class="p">){</span> <span class="nv" style="color: #008080;">$query_id</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$isoform_mapping</span><span class="p">{</span><span class="nv" style="color: #008080;">$query_id</span><span class="p">};</span> <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="1885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1885
</td>
<td class="new_line diff-line-num old" data-linenumber="2111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1885" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">exists</span> <span class="nv" style="color: #008080;">$isoform_mapping</span><span class="p">{</span><span class="nv" style="color: #008080;">$subject_id</span><span class="p">}</span> <span class="p">){</span> <span class="nv" style="color: #008080;">$subject_id</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$isoform_mapping</span><span class="p">{</span><span class="nv" style="color: #008080;">$subject_id</span><span class="p">};</span> <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="1886" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1886
</td>
<td class="new_line diff-line-num old" data-linenumber="2111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1886" class="line" lang="perl">    <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="1887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1887
</td>
<td class="new_line diff-line-num old" data-linenumber="2111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1887" class="line" lang="perl">   </span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="1888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1888
</td>
<td class="new_line diff-line-num old" data-linenumber="2111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1888" class="line" lang="perl">    <span class="c1" style="color: #998; font-style: italic;"># It hit itself (only during selfblast)</span></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="1889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1889
</td>
<td class="new_line diff-line-num old" data-linenumber="2111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1889" class="line" lang="perl">    <span class="c1" style="color: #998; font-style: italic;"># if ($selfblast && $query_id eq $subject_id)           {next;} # 5.16 reuse IDs</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="1890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1890
</td>
<td class="new_line diff-line-num old" data-linenumber="2111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1890" class="line" lang="perl">    <span class="c1" style="color: #998; font-style: italic;">## Listing them in the graph is okay, clustering will ignore them</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="1891" 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">
1891
</td>
<td class="new_line diff-line-num" data-linenumber="2111" 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">
2111
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2111" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="1892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1892
</td>
<td class="new_line diff-line-num old" data-linenumber="2112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1892" class="line" lang="perl">    <span class="c1" style="color: #998; font-style: italic;"># Similar hits? Take the better one</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="1893" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1893
</td>
<td class="new_line diff-line-num old" data-linenumber="2112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1893" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: #008080;">$result</span><span class="p">{"</span><span class="si" style="color: #d14;">$query_id</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$subject_id</span><span class="p">"}))</span> <span class="p">{</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="1894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1894
</td>
<td class="new_line diff-line-num old" data-linenumber="2112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1894" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: #008080;">$remote_evalue</span><span class="p">,</span> <span class="nv" style="color: #008080;">$remote_bitscore</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="s2" style="color: #d14;"> </span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">{"</span><span class="si" style="color: #d14;">$query_id</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$subject_id</span><span class="p">"});</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="1895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1895
</td>
<td class="new_line diff-line-num old" data-linenumber="2112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1895" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$local_evalue</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$remote_evalue</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1896
</td>
<td class="new_line diff-line-num old" data-linenumber="2112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1896" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$local_bitscore</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: #008080;">$remote_bitscore</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="1897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1897
</td>
<td class="new_line diff-line-num old" data-linenumber="2112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1897" class="line" lang="perl">    <span class="p">}</span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="1898" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2112" 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">
2112
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2112" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$query_id_iso</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$query_id</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1898" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2113" 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">
2113
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2113" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$subject_id_iso</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$subject_id</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1898" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2114" 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">
2114
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2114" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">exists</span> <span class="nv" style="color: #008080;">$isoform_mapping</span><span class="p">{</span><span class="nv" style="color: #008080;">$file_i</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_id</span><span class="p">}</span> <span class="p">){</span>   <span class="nv" style="color: #008080;">$query_id_iso</span>   <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$isoform_mapping</span><span class="p">{</span><span class="nv" style="color: #008080;">$file_i</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$query_id</span><span class="p">}</span> <span class="p">}</span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1898" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2115" 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">
2115
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2115" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">exists</span> <span class="nv" style="color: #008080;">$isoform_mapping</span><span class="p">{</span><span class="nv" style="color: #008080;">$file_j</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$subject_id</span><span class="p">}</span> <span class="p">){</span> <span class="nv" style="color: #008080;">$subject_id_iso</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$isoform_mapping</span><span class="p">{</span><span class="nv" style="color: #008080;">$file_j</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$subject_id</span><span class="p">}</span> <span class="p">}</span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1898" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2116" 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">
2116
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2116" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1898" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2117" 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">
2117
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<pre style="margin: 0;">+<span id="LC2117" class="line" lang="perl">      <span class="c1" style="color: #998; font-style: italic;"># It hit itself (only during selfblast)</span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1898" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2118" 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">
2118
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2118" class="line" lang="perl">      <span class="c1" style="color: #998; font-style: italic;"># if ($selfblast && $query_id eq $subject_id)           {next;} # 5.16 reuse IDs</span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="1898" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2119" 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">
2119
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2119" class="line" lang="perl">      <span class="c1" style="color: #998; font-style: italic;">## Listing them in the graph is okay, clustering will ignore them</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1898" 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">
1898
</td>
<td class="new_line diff-line-num" data-linenumber="2120" 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">
2120
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2120" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="1899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1899
</td>
<td class="new_line diff-line-num old" data-linenumber="2121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1899" class="line" lang="perl">    <span class="c1" style="color: #998; font-style: italic;"># Store data</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="1900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1900
</td>
<td class="new_line diff-line-num old" data-linenumber="2121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1900" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">!</span><span class="si" style="color: #d14;">$query_id</span><span class="s2" style="color: #d14;"> -> </span><span class="si" style="color: #d14;">$subject_id</span><span class="s2" style="color: #d14;"> (</span><span class="si" style="color: #d14;">$local_evalue</span><span class="s2" style="color: #d14;">,</span><span class="si" style="color: #d14;">$local_bitscore</span><span class="s2" style="color: #d14;">)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="1901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1901
</td>
<td class="new_line diff-line-num old" data-linenumber="2121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1901" class="line" lang="perl">    <span class="nv" style="color: #008080;">$result</span><span class="p">{"</span><span class="si" style="color: #d14;">$query_id</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$subject_id</span><span class="p">"}</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="si" style="color: #d14;">$local_evalue</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$local_bitscore</span><span class="p">";</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1902" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2121" 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">
2121
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2121" class="line" lang="perl">      <span class="c1" style="color: #998; font-style: italic;"># Similar hits? Take the better one</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="2122" 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">
2122
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<pre style="margin: 0;">+<span id="LC2122" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: #008080;">$result</span><span class="p">{"</span><span class="si" style="color: #d14;">$query_id_iso</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$subject_id_iso</span><span class="p">"}))</span> <span class="p">{</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="2123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2123
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<pre style="margin: 0;">+<span id="LC2123" class="line" lang="perl">        <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: #008080;">$remote_evalue</span><span class="p">,</span> <span class="nv" style="color: #008080;">$remote_bitscore</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="s2" style="color: #d14;"> </span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">{"</span><span class="si" style="color: #d14;">$query_id_iso</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$subject_id_iso</span><span class="p">"});</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="2124" 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">
2124
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<pre style="margin: 0;">+<span id="LC2124" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$local_evalue</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$remote_evalue</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="2125" 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">
2125
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<pre style="margin: 0;">+<span id="LC2125" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$local_bitscore</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: #008080;">$remote_bitscore</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="2126" 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">
2126
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<pre style="margin: 0;">+<span id="LC2126" class="line" lang="perl">      <span class="p">}</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="2127" 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">
2127
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<pre style="margin: 0;">+<span id="LC2127" class="line" lang="perl"></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="2128" 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">
2128
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<pre style="margin: 0;">+<span id="LC2128" class="line" lang="perl">      <span class="c1" style="color: #998; font-style: italic;"># save the best isoform id (e.g. for trinity the query_id_iso contains the id without _iXX, this mapping resolves the missing suffix)</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="2129" 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">
2129
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<pre style="margin: 0;">+<span id="LC2129" class="line" lang="perl">      <span class="c1" style="color: #998; font-style: italic;">#$isoform_mapping_best{$file_i." ".$query_id_iso." vs ".$file_j." ".$subject_id_iso}   = $query_id." ". $subject_id;</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="2130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2130
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<pre style="margin: 0;">+<span id="LC2130" class="line" lang="perl"></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="2131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2131
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<pre style="margin: 0;">+<span id="LC2131" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># if($query_id =~ /137_TRINITY_DN39932_c6_g1/){print STDERR "$_\n"}</span></span>
</pre>
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</td>
<td class="new_line diff-line-num new" data-linenumber="2132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2132
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<pre style="margin: 0;">+<span id="LC2132" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># elsif($subject_id =~ /137_TRINITY_DN39932_c6_g1/){print STDERR "$_\n"}</span></span>
</pre>
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</td>
<td class="new_line diff-line-num new" data-linenumber="2133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2133
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<pre style="margin: 0;">+<span id="LC2133" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># elsif($query_id =~ /138_TRINITY_DN47563_c4_g1/){print STDERR "$_\n"}</span></span>
</pre>
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</td>
<td class="new_line diff-line-num new" data-linenumber="2134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2134
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<pre style="margin: 0;">+<span id="LC2134" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># elsif($subject_id =~ /138_TRINITY_DN47563_c4_g1/){print STDERR "$_\n"}</span></span>
</pre>
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</td>
<td class="new_line diff-line-num new" data-linenumber="2135" 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">
2135
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<pre style="margin: 0;">+<span id="LC2135" class="line" lang="perl"></span>
</pre>
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</td>
<td class="new_line diff-line-num new" data-linenumber="2136" 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">
2136
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<pre style="margin: 0;">+<span id="LC2136" class="line" lang="perl">      <span class="c1" style="color: #998; font-style: italic;">#print STDERR "DEBUG:: $query_id_iso --> $query_id\n";</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="1902" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2137" 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">
2137
</td>
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<pre style="margin: 0;">+<span id="LC2137" class="line" lang="perl"></span>
</pre>
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</td>
<td class="new_line diff-line-num new" data-linenumber="2138" 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">
2138
</td>
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<pre style="margin: 0;">+<span id="LC2138" class="line" lang="perl">      <span class="c1" style="color: #998; font-style: italic;"># Store data</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="1902" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2139" 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">
2139
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<pre style="margin: 0;">+<span id="LC2139" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">!</span><span class="si" style="color: #d14;">$query_id</span><span class="s2" style="color: #d14;"> -> </span><span class="si" style="color: #d14;">$subject_id</span><span class="s2" style="color: #d14;"> (</span><span class="si" style="color: #d14;">$local_evalue</span><span class="s2" style="color: #d14;">,</span><span class="si" style="color: #d14;">$local_bitscore</span><span class="s2" style="color: #d14;">)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="1902" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2140" 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">
2140
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<pre style="margin: 0;">+<span id="LC2140" class="line" lang="perl">      <span class="nv" style="color: #008080;">$result</span><span class="p">{"</span><span class="si" style="color: #d14;">$query_id_iso</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$subject_id_iso</span><span class="p">"}</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="si" style="color: #d14;">$local_evalue</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$local_bitscore</span><span class="p">";</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="1902" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2141" 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">
2141
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2141" class="line" lang="perl"></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="1902" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2142" 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">
2142
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<pre style="margin: 0;">+<span id="LC2142" class="line" lang="perl">    <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="1902" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2143" 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">
2143
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2143" class="line" lang="perl"></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="1902" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2144" 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">
2144
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<pre style="margin: 0;">+<span id="LC2144" class="line" lang="perl">      <span class="c1" style="color: #998; font-style: italic;"># It hit itself (only during selfblast)</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="1902" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2145" 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">
2145
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<pre style="margin: 0;">+<span id="LC2145" class="line" lang="perl">      <span class="c1" style="color: #998; font-style: italic;"># if ($selfblast && $query_id eq $subject_id)           {next;} # 5.16 reuse IDs</span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="1902" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2146" 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">
2146
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2146" class="line" lang="perl">      <span class="c1" style="color: #998; font-style: italic;">## Listing them in the graph is okay, clustering will ignore them</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="1902" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2147" 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">
2147
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2147" class="line" lang="perl"></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="1902" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2148" 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">
2148
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<pre style="margin: 0;">+<span id="LC2148" class="line" lang="perl">      <span class="c1" style="color: #998; font-style: italic;"># Similar hits? Take the better one</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="1902" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2149" 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">
2149
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<pre style="margin: 0;">+<span id="LC2149" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: #008080;">$result</span><span class="p">{"</span><span class="si" style="color: #d14;">$query_id</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$subject_id</span><span class="p">"}))</span> <span class="p">{</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="1902" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2150" 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">
2150
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2150" class="line" lang="perl">        <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: #008080;">$remote_evalue</span><span class="p">,</span> <span class="nv" style="color: #008080;">$remote_bitscore</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="s2" style="color: #d14;"> </span><span class="p">",</span><span class="nv" style="color: #008080;">$result</span><span class="p">{"</span><span class="si" style="color: #d14;">$query_id</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$subject_id</span><span class="p">"});</span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="1902" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2151" 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">
2151
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2151" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$local_evalue</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$remote_evalue</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="1902" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2152" 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">
2152
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2152" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$local_bitscore</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: #008080;">$remote_bitscore</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="1902" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2153" 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">
2153
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2153" class="line" lang="perl">      <span class="p">}</span></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="1902" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2154" 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">
2154
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2154" class="line" lang="perl"></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="1902" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2155" 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">
2155
</td>
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<pre style="margin: 0;">+<span id="LC2155" class="line" lang="perl">      <span class="c1" style="color: #998; font-style: italic;"># Store data</span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="1902" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2156" 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">
2156
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2156" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">!</span><span class="si" style="color: #d14;">$query_id</span><span class="s2" style="color: #d14;"> -> </span><span class="si" style="color: #d14;">$subject_id</span><span class="s2" style="color: #d14;"> (</span><span class="si" style="color: #d14;">$local_evalue</span><span class="s2" style="color: #d14;">,</span><span class="si" style="color: #d14;">$local_bitscore</span><span class="s2" style="color: #d14;">)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="1902" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2157" 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">
2157
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2157" class="line" lang="perl">      <span class="nv" style="color: #008080;">$result</span><span class="p">{"</span><span class="si" style="color: #d14;">$query_id</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$subject_id</span><span class="p">"}</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="si" style="color: #d14;">$local_evalue</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$local_bitscore</span><span class="p">";</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1902" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2158" 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">
2158
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2158" class="line" lang="perl">    <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1902" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2159" 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">
2159
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2159" class="line" lang="perl">   </span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="1902" 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">
1902
</td>
<td class="new_line diff-line-num" data-linenumber="2160" 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">
2160
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2160" class="line" lang="perl">  <span class="p">}</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="1903" 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">
1903
</td>
<td class="new_line diff-line-num" data-linenumber="2161" 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">
2161
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2161" class="line" lang="perl"></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="1904" 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">
1904
</td>
<td class="new_line diff-line-num" data-linenumber="2162" 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">
2162
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2162" class="line" lang="perl">  <span class="k" style="font-weight: 600;">return</span> <span class="nv" style="color: #008080;">%result</span><span class="p">;</span></span>
</pre>
</td>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1936" 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="2194" 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">@@ -1936,9 +2194,7 @@ sub generate_indices {</td>
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<td class="old_line diff-line-num" data-linenumber="1936" 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">
1936
</td>
<td class="new_line diff-line-num" data-linenumber="2194" 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">
2194
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2194" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Generating indices</span><span class="p">";</span><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$force</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;"> anyway (forced).</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">.</span><span class="se" style="color: #d14;">\n</span><span class="p">";}}</span></span>
</pre>
</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1937" 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">
1937
</td>
<td class="new_line diff-line-num" data-linenumber="2195" 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">
2195
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2195" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">rapsearch</span><span class="p">")</span> <span class="p">{</span></span>
</pre>
</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1938
</td>
<td class="new_line diff-line-num" data-linenumber="2196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2196
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2196" class="line" lang="perl">    <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file</span> <span class="p">(</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">@</span><span class="nv" style="color: #008080;">_</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="1939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1939
</td>
<td class="new_line diff-line-num old" data-linenumber="2197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1939" class="line" lang="perl">      <span class="c1" style="color: #998; font-style: italic;">#if ($file =~ /\s/) {print STDERR ("$ORANGE\n[WARNING]$NC : File name '$file' contains whitespaces. This might lead to undesired effects. If you encounter unusual behavior, please change the file name!$NC\n");}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="1940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1940
</td>
<td class="new_line diff-line-num old" data-linenumber="2197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1940" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="1941" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1941
</td>
<td class="new_line diff-line-num old" data-linenumber="2197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1941" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">`</span><span class="sb" style="color: #d14;">ls '</span><span class="si" style="color: #d14;">${file}</span><span class="sb" style="color: #d14;">'.</span><span class="si" style="color: #d14;">${blastmode}</span><span class="sb" style="color: #d14;">* 1>/dev/null 2>&1</span><span class="p">`</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1942" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2197" 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">
2197
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2197" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">`</span><span class="sb" style="color: #d14;">ls '</span><span class="si" style="color: #d14;">${file}</span><span class="sb" style="color: #d14;">'.</span><span class="si" style="color: #d14;">${blastmode}</span><span class="sb" style="color: #d14;">* 2>/dev/null</span><span class="p">`</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1942
</td>
<td class="new_line diff-line-num" data-linenumber="2198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2198
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2198" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">The database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' is present and will be used</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1943
</td>
<td class="new_line diff-line-num" data-linenumber="2199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2199
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2199" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1944
</td>
<td class="new_line diff-line-num" data-linenumber="2200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2200
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2200" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Building database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$gene_counter</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> sequences)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1957" 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="2213" 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">@@ -1957,9 +2213,7 @@ sub generate_indices {</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1957" 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">
1957
</td>
<td class="new_line diff-line-num" data-linenumber="2213" 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">
2213
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2213" class="line" lang="perl">  <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1958" 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">
1958
</td>
<td class="new_line diff-line-num" data-linenumber="2214" 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">
2214
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2214" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">diamond</span><span class="p">"</span> <span class="p">)</span> <span class="p">{</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1959" 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">
1959
</td>
<td class="new_line diff-line-num" data-linenumber="2215" 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">
2215
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2215" class="line" lang="perl">    <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file</span> <span class="p">(</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">@</span><span class="nv" style="color: #008080;">_</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="1960" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1960
</td>
<td class="new_line diff-line-num old" data-linenumber="2216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1960" class="line" lang="perl">      <span class="c1" style="color: #998; font-style: italic;">#if ($file =~ /\s/) {print STDERR ("$ORANGE\n[WARNING]$NC : File name '$file' contains whitespaces. This might lead to undesired effects. If you encounter unusual behavior, please change the file name!$NC\n");}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="1961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1961
</td>
<td class="new_line diff-line-num old" data-linenumber="2216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1961" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="1962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1962
</td>
<td class="new_line diff-line-num old" data-linenumber="2216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1962" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">`</span><span class="sb" style="color: #d14;">ls '</span><span class="si" style="color: #d14;">${file}</span><span class="sb" style="color: #d14;">'.</span><span class="si" style="color: #d14;">${blastmode}</span><span class="sb" style="color: #d14;">* 1>/dev/null 2>&1</span><span class="p">`</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1963" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2216" 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">
2216
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2216" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">`</span><span class="sb" style="color: #d14;">ls '</span><span class="si" style="color: #d14;">${file}</span><span class="sb" style="color: #d14;">'.</span><span class="si" style="color: #d14;">${blastmode}</span><span class="sb" style="color: #d14;">* 2>/dev/null</span><span class="p">`</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1963
</td>
<td class="new_line diff-line-num" data-linenumber="2217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2217
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2217" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">The database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' is present and will be used</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1964
</td>
<td class="new_line diff-line-num" data-linenumber="2218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2218
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2218" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1965
</td>
<td class="new_line diff-line-num" data-linenumber="2219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2219
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2219" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Building database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$gene_counter</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> sequences)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1981" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1981,7 +2235,7 @@ sub generate_indices {</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1981" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1981
</td>
<td class="new_line diff-line-num" data-linenumber="2235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2235
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2235" class="line" lang="perl">        <span class="c1" style="color: #998; font-style: italic;">#if ($file =~ /\s/) {print STDERR ("$ORANGE\n[WARNING]$NC : File name '$file' contains whitespaces. This might lead to undesired effects. If you encounter unusual behavior, please change the file name!$NC\n");}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1982" 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">
1982
</td>
<td class="new_line diff-line-num" data-linenumber="2236" 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">
2236
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2236" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1983" 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">
1983
</td>
<td class="new_line diff-line-num" data-linenumber="2237" 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">
2237
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2237" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="1984" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1984
</td>
<td class="new_line diff-line-num old" data-linenumber="2238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1984" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">`</span><span class="sb" style="color: #d14;">ls '</span><span class="si" style="color: #d14;">${file}</span><span class="sb" style="color: #d14;">'.</span><span class="si" style="color: #d14;">${blastmode}</span><span class="sb" style="color: #d14;">* <span class="idiff left">1</span>>/dev/null<span class="idiff right"> 2>&1</span></span><span class="p">`</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1985" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2238" 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">
2238
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2238" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">`</span><span class="sb" style="color: #d14;">ls '</span><span class="si" style="color: #d14;">${file}</span><span class="sb" style="color: #d14;">'.</span><span class="si" style="color: #d14;">${blastmode}</span><span class="sb" style="color: #d14;">* <span class="idiff left right">2</span>>/dev/null</span><span class="p">`</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1985" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1985
</td>
<td class="new_line diff-line-num" data-linenumber="2239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2239
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2239" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">The database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' is present and will be used</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1986
</td>
<td class="new_line diff-line-num" data-linenumber="2240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2240
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2240" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="1987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1987
</td>
<td class="new_line diff-line-num" data-linenumber="2241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2241
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2241" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Building database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$gene_counter</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> sequences)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2000" 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="2254" 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">@@ -2000,9 +2254,7 @@ sub generate_indices {</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="2000" 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">
2000
</td>
<td class="new_line diff-line-num" data-linenumber="2254" 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">
2254
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2254" class="line" lang="perl">  <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="2001" 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">
2001
</td>
<td class="new_line diff-line-num" data-linenumber="2255" 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">
2255
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2255" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">mmseqsp</span><span class="p">")</span> <span class="p">{</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="2002" 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">
2002
</td>
<td class="new_line diff-line-num" data-linenumber="2256" 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">
2256
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2256" class="line" lang="perl">    <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file</span> <span class="p">(</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">@</span><span class="nv" style="color: #008080;">_</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="2003" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2003
</td>
<td class="new_line diff-line-num old" data-linenumber="2257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2003" class="line" lang="perl">      <span class="c1" style="color: #998; font-style: italic;">#if ($file =~ /\s/) {print STDERR ("$ORANGE\n[WARNING]$NC : File name '$file' contains whitespaces. This might lead to undesired effects. If you encounter unusual behavior, please change the file name!$NC\n");}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="2004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2004
</td>
<td class="new_line diff-line-num old" data-linenumber="2257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2004" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="2005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2005
</td>
<td class="new_line diff-line-num old" data-linenumber="2257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2005" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">`</span><span class="sb" style="color: #d14;">ls '</span><span class="si" style="color: #d14;">${file}</span><span class="sb" style="color: #d14;">'.</span><span class="si" style="color: #d14;">${blastmode}</span><span class="sb" style="color: #d14;">* 1>/dev/null 2>&1</span><span class="p">`</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="2006" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2257" 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">
2257
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2257" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">`</span><span class="sb" style="color: #d14;">ls '</span><span class="si" style="color: #d14;">${file}</span><span class="sb" style="color: #d14;">'.</span><span class="si" style="color: #d14;">${blastmode}</span><span class="sb" style="color: #d14;">* 2>/dev/null</span><span class="p">`</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="2006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2006
</td>
<td class="new_line diff-line-num" data-linenumber="2258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2258
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2258" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">The database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' is present and will be used</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="2007" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2007
</td>
<td class="new_line diff-line-num" data-linenumber="2259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2259
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2259" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="2008" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2008
</td>
<td class="new_line diff-line-num" data-linenumber="2260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2260
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2260" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Building database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$gene_counter</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> sequences)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2021" 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="2273" 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">@@ -2021,10 +2273,7 @@ sub generate_indices {</td>
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<td class="old_line diff-line-num" data-linenumber="2021" 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">
2021
</td>
<td class="new_line diff-line-num" data-linenumber="2273" 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">
2273
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2273" class="line" lang="perl">  <span class="p">}</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="2022" 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">
2022
</td>
<td class="new_line diff-line-num" data-linenumber="2274" 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">
2274
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2274" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">mmseqsn</span><span class="p">")</span> <span class="p">{</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="2023" 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">
2023
</td>
<td class="new_line diff-line-num" data-linenumber="2275" 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">
2275
</td>
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<pre style="margin: 0;"> <span id="LC2275" class="line" lang="perl">    <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file</span> <span class="p">(</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">@</span><span class="nv" style="color: #008080;">_</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="2024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2024
</td>
<td class="new_line diff-line-num old" data-linenumber="2276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
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<pre style="margin: 0;">-<span id="LC2024" class="line" lang="perl">            <span class="c1" style="color: #998; font-style: italic;">#if ($file =~ /\s/) {print STDERR ("$ORANGE\n[WARNING]$NC : File name '$file' contains whitespaces. This might lead to undesired effects. If you encounter unusual behavior, please change the file name!$NC\n");}</span></span>
</pre>
</td>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="2025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2025
</td>
<td class="new_line diff-line-num old" data-linenumber="2276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2025" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="2026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2026
</td>
<td class="new_line diff-line-num old" data-linenumber="2276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2026" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="2027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2027
</td>
<td class="new_line diff-line-num old" data-linenumber="2276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2027" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">`</span><span class="sb" style="color: #d14;">ls '</span><span class="si" style="color: #d14;">${file}</span><span class="sb" style="color: #d14;">'.</span><span class="si" style="color: #d14;">${blastmode}</span><span class="sb" style="color: #d14;">* 1>/dev/null 2>&1</span><span class="p">`</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="2028" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2276" 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">
2276
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2276" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">`</span><span class="sb" style="color: #d14;">ls '</span><span class="si" style="color: #d14;">${file}</span><span class="sb" style="color: #d14;">'.</span><span class="si" style="color: #d14;">${blastmode}</span><span class="sb" style="color: #d14;">* 2>/dev/null</span><span class="p">`</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="2028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2028
</td>
<td class="new_line diff-line-num" data-linenumber="2277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2277
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2277" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">The database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' is present and will be used</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="2029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2029
</td>
<td class="new_line diff-line-num" data-linenumber="2278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2278
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2278" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="2030" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2030
</td>
<td class="new_line diff-line-num" data-linenumber="2279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2279
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2279" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Building database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$gene_counter</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> sequences)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2043" 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="2292" 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">@@ -2043,10 +2292,7 @@ sub generate_indices {</td>
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<td class="old_line diff-line-num" data-linenumber="2043" 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">
2043
</td>
<td class="new_line diff-line-num" data-linenumber="2292" 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">
2292
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2292" class="line" lang="perl">  <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="2044" 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">
2044
</td>
<td class="new_line diff-line-num" data-linenumber="2293" 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">
2293
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2293" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">usearch</span><span class="p">"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">ublast</span><span class="p">")</span> <span class="p">{</span></span>
</pre>
</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="2045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2045
</td>
<td class="new_line diff-line-num" data-linenumber="2294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2294
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2294" class="line" lang="perl">    <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file</span> <span class="p">(</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">@</span><span class="nv" style="color: #008080;">_</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="2046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2046
</td>
<td class="new_line diff-line-num old" data-linenumber="2295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2046" class="line" lang="perl">            <span class="c1" style="color: #998; font-style: italic;">#if ($file =~ /\s/) {print STDERR ("$ORANGE\n[WARNING]$NC : File name '$file' contains whitespaces. This might lead to undesired effects. If you encounter unusual behavior, please change the file name!$NC\n");}</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="2047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2047
</td>
<td class="new_line diff-line-num old" data-linenumber="2295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2047" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="2048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2048
</td>
<td class="new_line diff-line-num old" data-linenumber="2295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2048" class="line" lang="perl"></span>
</pre>
</td>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="2049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2049
</td>
<td class="new_line diff-line-num old" data-linenumber="2295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2049" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">`</span><span class="sb" style="color: #d14;">ls '</span><span class="si" style="color: #d14;">${file}</span><span class="sb" style="color: #d14;">'.</span><span class="si" style="color: #d14;">${blastmode}</span><span class="sb" style="color: #d14;">* 1>/dev/null 2>&1</span><span class="p">`</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="2050" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2295" 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">
2295
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2295" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">`</span><span class="sb" style="color: #d14;">ls '</span><span class="si" style="color: #d14;">${file}</span><span class="sb" style="color: #d14;">'.</span><span class="si" style="color: #d14;">${blastmode}</span><span class="sb" style="color: #d14;">* 2>/dev/null</span><span class="p">`</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="2050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2050
</td>
<td class="new_line diff-line-num" data-linenumber="2296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2296
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<pre style="margin: 0;"> <span id="LC2296" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">The database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' is present and will be used</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="2051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2051
</td>
<td class="new_line diff-line-num" data-linenumber="2297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2297
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2297" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="2052" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2052
</td>
<td class="new_line diff-line-num" data-linenumber="2298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2298
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2298" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Building database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$gene_counter</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> sequences)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
</td>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2065" 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="2311" 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">@@ -2065,9 +2311,7 @@ sub generate_indices {</td>
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<td class="old_line diff-line-num" data-linenumber="2065" 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">
2065
</td>
<td class="new_line diff-line-num" data-linenumber="2311" 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">
2311
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2311" class="line" lang="perl">  <span class="p">}</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="2066" 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">
2066
</td>
<td class="new_line diff-line-num" data-linenumber="2312" 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">
2312
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2312" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">lastp</span><span class="p">"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">lastn</span><span class="p">")</span> <span class="p">{</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="2067" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2067
</td>
<td class="new_line diff-line-num" data-linenumber="2313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2313
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2313" class="line" lang="perl">    <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file</span> <span class="p">(</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">@</span><span class="nv" style="color: #008080;">_</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="2068" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2068
</td>
<td class="new_line diff-line-num old" data-linenumber="2314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2068" class="line" lang="perl">            <span class="c1" style="color: #998; font-style: italic;">#if ($file =~ /\s/) {print STDERR ("$ORANGE\n[WARNING]$NC : File name '$file' contains whitespaces. This might lead to undesired effects. If you encounter unusual behavior, please change the file name!$NC\n");}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="2069" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2069
</td>
<td class="new_line diff-line-num old" data-linenumber="2314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2069" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="2070" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2070
</td>
<td class="new_line diff-line-num old" data-linenumber="2314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2070" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">`</span><span class="sb" style="color: #d14;">ls '</span><span class="si" style="color: #d14;">${file}</span><span class="sb" style="color: #d14;">'.</span><span class="si" style="color: #d14;">${blastmode}</span><span class="sb" style="color: #d14;">* 1>/dev/null 2>&1</span><span class="p">`</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="2071" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2314" 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">
2314
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2314" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">`</span><span class="sb" style="color: #d14;">ls '</span><span class="si" style="color: #d14;">${file}</span><span class="sb" style="color: #d14;">'.</span><span class="si" style="color: #d14;">${blastmode}</span><span class="sb" style="color: #d14;">* 2>/dev/null</span><span class="p">`</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="2071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2071
</td>
<td class="new_line diff-line-num" data-linenumber="2315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2315
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<pre style="margin: 0;"> <span id="LC2315" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">The database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' is present and will be used</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="2072" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2072
</td>
<td class="new_line diff-line-num" data-linenumber="2316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2316
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<pre style="margin: 0;"> <span id="LC2316" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="2073" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2073
</td>
<td class="new_line diff-line-num" data-linenumber="2317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2317
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2317" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Building database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$gene_counter</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> sequences)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
</td>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2102" 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="2346" 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">@@ -2102,9 +2346,7 @@ sub generate_indices {</td>
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<td class="old_line diff-line-num" data-linenumber="2102" 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">
2102
</td>
<td class="new_line diff-line-num" data-linenumber="2346" 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">
2346
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<pre style="margin: 0;"> <span id="LC2346" class="line" lang="perl">  <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="2103" 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">
2103
</td>
<td class="new_line diff-line-num" data-linenumber="2347" 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">
2347
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2347" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/blast.*\+$/</span><span class="p">)</span> <span class="p">{</span>  <span class="c1" style="color: #998; font-style: italic;"># new blast+</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="2104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2104
</td>
<td class="new_line diff-line-num" data-linenumber="2348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2348
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2348" class="line" lang="perl">    <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file</span> <span class="p">(</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">@</span><span class="nv" style="color: #008080;">_</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="2105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2105
</td>
<td class="new_line diff-line-num old" data-linenumber="2349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2105" class="line" lang="perl">            <span class="c1" style="color: #998; font-style: italic;">#if ($file =~ /\s/) {print STDERR ("$ORANGE\n[WARNING]$NC : File name '$file' contains whitespaces. This might lead to undesired effects. If you encounter unusual behavior, please change the file name!$NC\n");}</span></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="2106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2106
</td>
<td class="new_line diff-line-num old" data-linenumber="2349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2106" class="line" lang="perl"></span>
</pre>
</td>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="2107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2107
</td>
<td class="new_line diff-line-num old" data-linenumber="2349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2107" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">`</span><span class="sb" style="color: #d14;">ls '</span><span class="si" style="color: #d14;">${file}</span><span class="sb" style="color: #d14;">'.</span><span class="si" style="color: #d14;">${blastmode}</span><span class="sb" style="color: #d14;">* 1>/dev/null 2>&1</span><span class="p">`</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="2108" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2349" 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">
2349
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2349" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">`</span><span class="sb" style="color: #d14;">ls '</span><span class="si" style="color: #d14;">${file}</span><span class="sb" style="color: #d14;">'.</span><span class="si" style="color: #d14;">${blastmode}</span><span class="sb" style="color: #d14;">* 2>/dev/null</span><span class="p">`</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="2108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2108
</td>
<td class="new_line diff-line-num" data-linenumber="2350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2350
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2350" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">The database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' is present and will be used</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="2109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2109
</td>
<td class="new_line diff-line-num" data-linenumber="2351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2351
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2351" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="2110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2110
</td>
<td class="new_line diff-line-num" data-linenumber="2352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2352
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2352" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Building database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$gene_counter</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> sequences)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
</td>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2122" 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="2364" 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">@@ -2122,9 +2364,7 @@ sub generate_indices {</td>
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<td class="old_line diff-line-num" data-linenumber="2122" 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">
2122
</td>
<td class="new_line diff-line-num" data-linenumber="2364" 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">
2364
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2364" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">unlink</span><span class="p">('</span><span class="s1" style="color: #d14;">formatdb.log</span><span class="p">');</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="2123" 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">
2123
</td>
<td class="new_line diff-line-num" data-linenumber="2365" 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">
2365
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2365" class="line" lang="perl">  <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/autoblast/</span><span class="p">)</span> <span class="p">{</span>  <span class="c1" style="color: #998; font-style: italic;"># new blast+</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="2124" 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">
2124
</td>
<td class="new_line diff-line-num" data-linenumber="2366" 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">
2366
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2366" class="line" lang="perl">    <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file</span> <span class="p">(</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">@</span><span class="nv" style="color: #008080;">_</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="2125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2125
</td>
<td class="new_line diff-line-num old" data-linenumber="2367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2125" class="line" lang="perl">            <span class="c1" style="color: #998; font-style: italic;">#if ($file =~ /\s/) {print STDERR ("$ORANGE\n[WARNING]$NC : File name '$file' contains whitespaces. This might lead to undesired effects. If you encounter unusual behavior, please change the file name!$NC\n");}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="2126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2126
</td>
<td class="new_line diff-line-num old" data-linenumber="2367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2126" class="line" lang="perl"></span>
</pre>
</td>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="2127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2127
</td>
<td class="new_line diff-line-num old" data-linenumber="2367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2127" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">`</span><span class="sb" style="color: #d14;">ls '</span><span class="si" style="color: #d14;">${file}</span><span class="sb" style="color: #d14;">'.</span><span class="si" style="color: #d14;">${blastmode}</span><span class="sb" style="color: #d14;">* 1>/dev/null 2>&1</span><span class="p">`</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="2128" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2367" 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">
2367
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2367" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">`</span><span class="sb" style="color: #d14;">ls '</span><span class="si" style="color: #d14;">${file}</span><span class="sb" style="color: #d14;">'.</span><span class="si" style="color: #d14;">${blastmode}</span><span class="sb" style="color: #d14;">* 2>/dev/null</span><span class="p">`</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>
</pre>
</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="2128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2128
</td>
<td class="new_line diff-line-num" data-linenumber="2368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2368
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2368" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">The database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' is present and will be used</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="2129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2129
</td>
<td class="new_line diff-line-num" data-linenumber="2369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2369
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2369" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
</pre>
</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="2130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2130
</td>
<td class="new_line diff-line-num" data-linenumber="2370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2370
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2370" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Building database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$gene_counter</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> sequences)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2146" 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="2386" 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">@@ -2146,9 +2386,7 @@ sub generate_indices {</td>
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<td class="old_line diff-line-num" data-linenumber="2146" 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">
2146
</td>
<td class="new_line diff-line-num" data-linenumber="2386" 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">
2386
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2386" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">unlink</span><span class="p">('</span><span class="s1" style="color: #d14;">formatdb.log</span><span class="p">');</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="2147" 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">
2147
</td>
<td class="new_line diff-line-num" data-linenumber="2387" 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">
2387
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2387" class="line" lang="perl">  <span class="p">}</span><span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;"># old blastall</span></span>
</pre>
</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="2148" 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">
2148
</td>
<td class="new_line diff-line-num" data-linenumber="2388" 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">
2388
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2388" class="line" lang="perl">    <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file</span> <span class="p">(</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">@</span><span class="nv" style="color: #008080;">_</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="2149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2149
</td>
<td class="new_line diff-line-num old" data-linenumber="2389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2149" class="line" lang="perl">            <span class="c1" style="color: #998; font-style: italic;">#if ($file =~ /\s/) {print STDERR ("$ORANGE\n[WARNING]$NC : File name '$file' contains whitespaces. This might lead to undesired effects. If you encounter unusual behavior, please change the file name!$NC\n");}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="2150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2150
</td>
<td class="new_line diff-line-num old" data-linenumber="2389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2150" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="2151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2151
</td>
<td class="new_line diff-line-num old" data-linenumber="2389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
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<pre style="margin: 0;">-<span id="LC2151" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">`</span><span class="sb" style="color: #d14;">ls '</span><span class="si" style="color: #d14;">${file}</span><span class="sb" style="color: #d14;">'.</span><span class="si" style="color: #d14;">${blastmode}</span><span class="sb" style="color: #d14;">* 1>/dev/null 2>&1</span><span class="p">`</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="2152" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2389" 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">
2389
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<pre style="margin: 0;">+<span id="LC2389" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">`</span><span class="sb" style="color: #d14;">ls '</span><span class="si" style="color: #d14;">${file}</span><span class="sb" style="color: #d14;">'.</span><span class="si" style="color: #d14;">${blastmode}</span><span class="sb" style="color: #d14;">* 2>/dev/null</span><span class="p">`</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="2152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2152
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<td class="new_line diff-line-num" data-linenumber="2390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2390
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<pre style="margin: 0;"> <span id="LC2390" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">The database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' is present and will be used</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="2153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2153
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<td class="new_line diff-line-num" data-linenumber="2391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2391
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<pre style="margin: 0;"> <span id="LC2391" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="2154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2154
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<td class="new_line diff-line-num" data-linenumber="2392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2392
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<pre style="margin: 0;"> <span id="LC2392" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Building database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$gene_counter</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> sequences)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2653,19 +2891,19 @@ sub read_details {</td>
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<td class="old_line diff-line-num" data-linenumber="2653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2653
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<td class="new_line diff-line-num" data-linenumber="2891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC2891" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$curLine</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/>/</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">#head line -> gene name and description</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="2654" 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">
2654
</td>
<td class="new_line diff-line-num" data-linenumber="2892" 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">
2892
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<pre style="margin: 0;"> <span id="LC2892" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="2655" 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">
2655
</td>
<td class="new_line diff-line-num" data-linenumber="2893" 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">
2893
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<pre style="margin: 0;"> <span id="LC2893" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$isoform</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">uniprot</span><span class="p">"){</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="2656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2656
</td>
<td class="new_line diff-line-num old" data-linenumber="2894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2656" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$curLine</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/isoform of ([^ <span class="idiff left">,]+)/i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$curLine</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=~</span></span><span class="idiff"> </span><span class="sr" style="color: #009926;"><span class="idiff right">m/isoform ([^ </span>,]+)/i</span><span class="p">){</span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="2657" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2894" 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">
2894
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2894" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$curLine</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/isoform of ([^ ,]+)/i</span><span class="p">){</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="2657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2657
</td>
<td class="new_line diff-line-num" data-linenumber="2895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2895
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2895" class="line" lang="perl">          <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$iso</span> <span class="o" style="font-weight: 600;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="2658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2658
</td>
<td class="new_line diff-line-num" data-linenumber="2896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2896
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2896" class="line" lang="perl">          <span class="nv" style="color: #008080;">$curLine</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/[\r\n]+$//</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">#chomp only removes last \n newline, now also \r are removed and all occurences</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="2659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2659
</td>
<td class="new_line diff-line-num" data-linenumber="2897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2897
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2897" class="line" lang="perl">          <span class="nv" style="color: #008080;">$curLine</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/^>//</span><span class="p">;</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="2660" 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">
2660
</td>
<td class="new_line diff-line-num" data-linenumber="2898" 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">
2898
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2898" class="line" lang="perl">          <span class="nv" style="color: #008080;">$curLine</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/\s.*//</span><span class="p">;</span></span>
</pre>
</td>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="2661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2661
</td>
<td class="new_line diff-line-num old" data-linenumber="2899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2661" class="line" lang="perl">          <span class="nv" style="color: #008080;">$isoform_mapping</span><span class="p">{</span><span class="nv" style="color: #008080;">$curLine</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$iso</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="2662" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2899" 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">
2899
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2899" class="line" lang="perl">          <span class="nv" style="color: #008080;">$isoform_mapping</span><span class="p">{</span><span class="nv" style="color: #008080;">$<span class="idiff left">file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff right">$</span>curLine</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$iso</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="2662" 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">
2662
</td>
<td class="new_line diff-line-num" data-linenumber="2900" 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">
2900
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2900" class="line" lang="perl"></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="2663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2663
</td>
<td class="new_line diff-line-num old" data-linenumber="2901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC2663" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">found isoform '</span><span class="si" style="color: #d14;">$curLine</span><span class="s2" style="color: #d14;">' => '</span><span class="si" style="color: #d14;">$iso</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="2664" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2901" 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">
2901
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2901" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">found isoform '</span><span class="si" style="color: #d14;"><span class="idiff left">$file</span></span><span class="s2" style="color: #d14;"><span class="idiff right"> </span></span><span class="si" style="color: #d14;">$curLine</span><span class="s2" style="color: #d14;">' => '</span><span class="si" style="color: #d14;">$iso</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="2664" 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">
2664
</td>
<td class="new_line diff-line-num" data-linenumber="2902" 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">
2902
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<pre style="margin: 0;"> <span id="LC2902" class="line" lang="perl">        <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="2665" 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">
2665
</td>
<td class="new_line diff-line-num" data-linenumber="2903" 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">
2903
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2903" class="line" lang="perl">        <span class="nv" style="color: #008080;">$curLine</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/[\r\n]+$//</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">#chomp only removes last \n newline, now also \r are removed and all occurences</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="2666" 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">
2666
</td>
<td class="new_line diff-line-num" data-linenumber="2904" 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">
2904
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2904" class="line" lang="perl">        <span class="nv" style="color: #008080;">$curLine</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/^>//</span><span class="p">;</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="2667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2667
</td>
<td class="new_line diff-line-num" data-linenumber="2905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2905
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2905" class="line" lang="perl">        <span class="nv" style="color: #008080;">$curLine</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/\s.*//</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="2668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2668
</td>
<td class="new_line diff-line-num old" data-linenumber="2906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2668" class="line" lang="perl">        <span class="nv" style="color: #008080;">$isoform_mapping_ncbiuniprot_correction</span><span class="p">{</span><span class="nv" style="color: #008080;">&convertUniprotAndNCBI</span><span class="p">(</span><span class="nv" style="color: #008080;">$curLine</span><span class="p">)}</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$curLine</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="2669" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2906" 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">
2906
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2906" class="line" lang="perl">        <span class="nv" style="color: #008080;">$isoform_mapping_ncbiuniprot_correction</span><span class="p">{</span><span class="nv" style="color: #008080;"><span class="idiff left">$file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;">&convertUniprotAndNCBI</span><span class="p">(</span><span class="nv" style="color: #008080;">$curLine</span><span class="p">)}</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$<span class="idiff">file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff right">$</span>curLine</span><span class="p">;</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="2669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2669
</td>
<td class="new_line diff-line-num" data-linenumber="2907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2907
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2907" class="line" lang="perl"></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="2670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2670
</td>
<td class="new_line diff-line-num" data-linenumber="2908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2908
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2908" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$isoform</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">trinity</span><span class="p">"){</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="2671" 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">
2671
</td>
<td class="new_line diff-line-num" data-linenumber="2909" 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">
2909
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2909" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2675" 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="2913" 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">@@ -2675,9 +2913,11 @@ sub read_details {</td>
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<td class="old_line diff-line-num" data-linenumber="2675" 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">
2675
</td>
<td class="new_line diff-line-num" data-linenumber="2913" 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">
2913
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2913" class="line" lang="perl">          <span class="nv" style="color: #008080;">$curLine</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/^>//</span><span class="p">;</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="2676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2676
</td>
<td class="new_line diff-line-num" data-linenumber="2914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2914
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2914" class="line" lang="perl">          <span class="nv" style="color: #008080;">$curLine</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/\s.*//</span><span class="p">;</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="2677" 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">
2677
</td>
<td class="new_line diff-line-num" data-linenumber="2915" 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">
2915
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<pre style="margin: 0;"> <span id="LC2915" class="line" lang="perl">          <span class="nv" style="color: #008080;">$iso</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/^>//</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="2678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2678
</td>
<td class="new_line diff-line-num old" data-linenumber="2916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC2678" class="line" lang="perl">          <span class="nv" style="color: #008080;">$isoform_mapping</span><span class="p">{</span><span class="nv" style="color: #008080;">$curLine</span><span class="p">}</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$iso</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="2679" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2916" 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">
2916
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<pre style="margin: 0;">+<span id="LC2916" class="line" lang="perl">          <span class="nv" style="color: #008080;">$isoform_mapping</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$curLine</span><span class="p">}</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$iso</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="2679" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2917" 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">
2917
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2917" class="line" lang="perl"></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="2679" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2918" 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">
2918
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2918" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#print STDERR "DEBUG::1) ".$file." ".$curLine."\n";</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="2679" 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">
2679
</td>
<td class="new_line diff-line-num" data-linenumber="2919" 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">
2919
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<pre style="margin: 0;"> <span id="LC2919" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="2680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2680
</td>
<td class="new_line diff-line-num old" data-linenumber="2920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC2680" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">found isoform '</span><span class="si" style="color: #d14;">$curLine</span><span class="s2" style="color: #d14;">' => '</span><span class="si" style="color: #d14;">$iso</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="2681" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2920" 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">
2920
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2920" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">found isoform '</span><span class="si" style="color: #d14;"><span class="idiff left">$file</span></span><span class="s2" style="color: #d14;"><span class="idiff right"> </span></span><span class="si" style="color: #d14;">$curLine</span><span class="s2" style="color: #d14;">' => '</span><span class="si" style="color: #d14;">$iso</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="2681" 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">
2681
</td>
<td class="new_line diff-line-num" data-linenumber="2921" 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">
2921
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<pre style="margin: 0;"> <span id="LC2921" class="line" lang="perl">        <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="2682" 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">
2682
</td>
<td class="new_line diff-line-num" data-linenumber="2922" 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">
2922
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<pre style="margin: 0;"> <span id="LC2922" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$isoform</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">ncbi</span><span class="p">"){</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="2683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2683
</td>
<td class="new_line diff-line-num" data-linenumber="2923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2923
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<pre style="margin: 0;"> <span id="LC2923" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$curLine</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/gene:([^ ]+).*isoform/i</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$curLine</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/isoform.*Acc:MGI:([0-9])/i</span><span class="p">){</span></span>
</pre>
</td>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2685,14 +2925,14 @@ sub read_details {</td>
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<td class="old_line diff-line-num" data-linenumber="2685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2685
</td>
<td class="new_line diff-line-num" data-linenumber="2925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2925
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<pre style="margin: 0;"> <span id="LC2925" class="line" lang="perl">          <span class="nv" style="color: #008080;">$curLine</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/[\r\n]+$//</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">#chomp only removes last \n newline, now also \r are removed and all occurences</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="2686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2686
</td>
<td class="new_line diff-line-num" data-linenumber="2926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2926
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<pre style="margin: 0;"> <span id="LC2926" class="line" lang="perl">          <span class="nv" style="color: #008080;">$curLine</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/^>//</span><span class="p">;</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="2687" 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">
2687
</td>
<td class="new_line diff-line-num" data-linenumber="2927" 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">
2927
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2927" class="line" lang="perl">          <span class="nv" style="color: #008080;">$curLine</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/\s.*//</span><span class="p">;</span></span>
</pre>
</td>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="2688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2688
</td>
<td class="new_line diff-line-num old" data-linenumber="2928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2688" class="line" lang="perl">          <span class="nv" style="color: #008080;">$isoform_mapping</span><span class="p">{</span><span class="nv" style="color: #008080;">$curLine</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$iso</span><span class="p">;</span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="2689" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2928" 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">
2928
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2928" class="line" lang="perl">          <span class="nv" style="color: #008080;">$isoform_mapping</span><span class="p">{</span><span class="nv" style="color: #008080;">$<span class="idiff left">file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff right">$</span>curLine</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$iso</span><span class="p">;</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="2689" 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">
2689
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<td class="new_line diff-line-num" data-linenumber="2929" 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">
2929
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2929" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="2690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2690
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<td class="new_line diff-line-num old" data-linenumber="2930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC2690" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">found isoform '</span><span class="si" style="color: #d14;">$curLine</span><span class="s2" style="color: #d14;">' => '</span><span class="si" style="color: #d14;">$iso</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="2691" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="2930" 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">
2930
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2930" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">found isoform '</span><span class="si" style="color: #d14;"><span class="idiff left">$file</span></span><span class="s2" style="color: #d14;"><span class="idiff right"> </span></span><span class="si" style="color: #d14;">$curLine</span><span class="s2" style="color: #d14;">' => '</span><span class="si" style="color: #d14;">$iso</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="2691" 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">
2691
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<td class="new_line diff-line-num" data-linenumber="2931" 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">
2931
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2931" class="line" lang="perl">        <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="2692" 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">
2692
</td>
<td class="new_line diff-line-num" data-linenumber="2932" 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">
2932
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2932" class="line" lang="perl">        <span class="nv" style="color: #008080;">$curLine</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/[\r\n]+$//</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">#chomp only removes last \n newline, now also \r are removed and all occurences</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="2693" 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">
2693
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<td class="new_line diff-line-num" data-linenumber="2933" 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">
2933
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2933" class="line" lang="perl">        <span class="nv" style="color: #008080;">$curLine</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/^>//</span><span class="p">;</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="2694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2694
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<td class="new_line diff-line-num" data-linenumber="2934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2934
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2934" class="line" lang="perl">        <span class="nv" style="color: #008080;">$curLine</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/\s.*//</span><span class="p">;</span></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="2695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2695
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<td class="new_line diff-line-num old" data-linenumber="2935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC2695" class="line" lang="perl">        <span class="nv" style="color: #008080;">$isoform_mapping_ncbiuniprot_correction</span><span class="p">{</span><span class="nv" style="color: #008080;">$<span class="idiff left">curLine</span></span><span class="p"><span class="idiff">}</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">=</span></span><span class="nv" style="color: #008080;">$curLine</span><span class="p">;</span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="2696" 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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<td class="new_line diff-line-num new" data-linenumber="2935" 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">
2935
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<pre style="margin: 0;">+<span id="LC2935" class="line" lang="perl">        <span class="nv" style="color: #008080;">$isoform_mapping_ncbiuniprot_correction</span><span class="p">{</span><span class="nv" style="color: #008080;">$<span class="idiff left">file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">$curLine</span></span><span class="p"><span class="idiff">}</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="nv" style="color: #008080;"><span class="idiff">$file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">.</span></span><span class="nv" style="color: #008080;">$curLine</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="2696" 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">
2696
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<td class="new_line diff-line-num" data-linenumber="2936" 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">
2936
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<pre style="margin: 0;"> <span id="LC2936" class="line" lang="perl">      <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="2697" 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">
2697
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<td class="new_line diff-line-num" data-linenumber="2937" 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">
2937
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2937" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="2698" 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">
2698
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<td class="new_line diff-line-num" data-linenumber="2938" 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="LC2938" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$checkfasta</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">exists</span><span class="p">(</span><span class="nv" style="color: #008080;">$allowedAlphabet</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">$blastmode</span><span class="p">})</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$cur_gene_is_valid</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="k" style="font-weight: 600;">last</span><span class="p">;}</span></span>
</pre>
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<li id="e6d14c79cd4fd6390fadb1ca94af0c36b0671d26">
<a href="https://salsa.debian.org/med-team/proteinortho/-/commit/3746e15da8bc7609707daf904845cd274344cd8f#e6d14c79cd4fd6390fadb1ca94af0c36b0671d26"><strong>proteinorthoHelper.html</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="248" 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="248" 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">@@ -248,6 +248,16 @@ The resulting proteinortho command (replace proteinortho with 'perl proteinortho</td>
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<td class="new_line diff-line-num" data-linenumber="248" 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="LC248" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fb-number form-group field-cov"</span><span class="nt" style="color: #000080;">><label</span> <span class="na" style="color: #008080;">for=</span><span class="s" style="color: #d14;">"cov"</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fb-number-label"</span><span class="nt" style="color: #000080;">><b></span>-cov<span class="nt" style="color: #000080;"></b></span> : min. coverage of best blast alignments in %<span class="nt" style="color: #000080;"></label><br></span><span class="ni" style="color: #800080;">&nbsp;&nbsp;&nbsp;&nbsp;</span><span class="nt" style="color: #000080;"><input</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"number"</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"form-control"</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"cov"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"50"</span> <span class="na" style="color: #008080;">min=</span><span class="s" style="color: #d14;">"0"</span> <span class="na" style="color: #008080;">step=</span><span class="s" style="color: #d14;">"any"</span> <span class="na" style="color: #008080;">max=</span><span class="s" style="color: #d14;">"100"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"cov"</span><span class="nt" style="color: #000080;">></div></span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fb-text form-group field-subparaBlast"</span><span class="nt" style="color: #000080;">><label</span> <span class="na" style="color: #008080;">for=</span><span class="s" style="color: #d14;">"subparaBlast"</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fb-text-label"</span><span class="nt" style="color: #000080;">><b></span>-subparaBlast<span class="nt" style="color: #000080;"></b></span> : additional parameters for the search tool(-p). Careful when changing -p, then this option may lead to errors.<span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"tooltip-element"</span> <span class="na" style="color: #008080;">tooltip=</span><span class="s" style="color: #d14;">"example -subpara='-seg no' for -p=blastp+ or -subpara='--more-sensitive' for -p=diamond. Do not use '=' here!"</span><span class="nt" style="color: #000080;">></span>?<span class="nt" style="color: #000080;"></span></label><br></span><span class="ni" style="color: #800080;">&nbsp;&nbsp;&nbsp;&nbsp;</span>'<span class="nt" style="color: #000080;"><input</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"text"</span> <span class="na" style="color: #008080;">pattern=</span><span class="s" style="color: #d14;">"[^'=]+"</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"form-control"</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"subparaBlast"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"subparaBlast"</span> <span class="na" style="color: #008080;">title=</span><span class="s" style="color: #d14;">"example -subpara='-seg no' or -subpara='--more-sensitive' for diamond. Do not use '=' here!"</span><span class="nt" style="color: #000080;">></span>'<span class="nt" style="color: #000080;"></div></span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fb-checkbox"</span><span class="nt" style="color: #000080;">><input</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"additionalFlags1[]"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"checkfasta"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"checkfasta"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"checkbox"</span><span class="nt" style="color: #000080;">><label</span> <span class="na" style="color: #008080;">for=</span><span class="s" style="color: #d14;">"additionalFlags1-6"</span><span class="nt" style="color: #000080;">><b></span>-checkfasta<span class="nt" style="color: #000080;"></b></span> : checks if the given algorithm (-p) can process the input fasta file.<span class="nt" style="color: #000080;"></label></div></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="html"><span class="nt" style="color: #000080;"><br></span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="252" 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="LC252" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fb-radio-group form-group field-isoform"</span><span class="nt" style="color: #000080;">><label</span> <span class="na" style="color: #008080;">for=</span><span class="s" style="color: #d14;">"isoform"</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fb-radio-group-label"</span><span class="nt" style="color: #000080;">><b></span>-isoform<span class="nt" style="color: #000080;"></b></span> : Enables the isoform processing.<span class="nt" style="color: #000080;"></label></span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="253" 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="LC253" class="line" lang="html">  <span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"radio-group"</span><span class="nt" style="color: #000080;">></span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="254" 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="LC254" class="line" lang="html">      <span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fb-radio"</span><span class="nt" style="color: #000080;">><input</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"isoform"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"isoform-no"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"blastn"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"radio"</span> <span class="na" style="color: #008080;">checked</span><span class="nt" style="color: #000080;">><label</span> <span class="na" style="color: #008080;">for=</span><span class="s" style="color: #d14;">"isoform-no"</span><span class="nt" style="color: #000080;">></span>disabled<span class="nt" style="color: #000080;"></label></div></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="html">      <span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fb-radio"</span><span class="nt" style="color: #000080;">><input</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"isoform"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"isoform-0"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"blastn"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"radio"</span><span class="nt" style="color: #000080;">><label</span> <span class="na" style="color: #008080;">for=</span><span class="s" style="color: #d14;">"isoform-0"</span><span class="nt" style="color: #000080;">></span>ncbi (Different proteins have the same gene id. The word isoform is mandatory!)<span class="nt" style="color: #000080;"></label></div></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="html">    <span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fb-radio"</span><span class="nt" style="color: #000080;">><input</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"isoform"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"isoform-1"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"blastp"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"radio"</span><span class="nt" style="color: #000080;">><label</span> <span class="na" style="color: #008080;">for=</span><span class="s" style="color: #d14;">"isoform-1"</span><span class="nt" style="color: #000080;">></span>uniprot (Isoforms are specified in uniprot style using the '*_additional.fa' files, just add these files to the analysis)<span class="nt" style="color: #000080;"></label></div></span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="257" 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="LC257" class="line" lang="html">    <span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"fb-radio"</span><span class="nt" style="color: #000080;">><input</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"isoform"</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"isoform-2"</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"tblastx"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"radio"</span><span class="nt" style="color: #000080;">><label</span> <span class="na" style="color: #008080;">for=</span><span class="s" style="color: #d14;">"isoform-2"</span><span class="nt" style="color: #000080;">></span>trinity (Isoforms are given in the trinity ids TRINITY_DN1000_c115_g5_i1 -> isoform 1)<span class="nt" style="color: #000080;"></label></div></span> </span>
</pre>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="html">  <span class="nt" style="color: #000080;"></div></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="html"><span class="nt" style="color: #000080;"></div></span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="html"></span>
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="html"><span class="nt" style="color: #000080;"><br><hr></span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="html"><span class="nt" style="color: #000080;"><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">""</span><span class="nt" style="color: #000080;">><h2</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"control-5359817"</span><span class="nt" style="color: #000080;">><b></span>Synteny<span class="nt" style="color: #000080;"></b></span> options (optional, step 2)<span class="nt" style="color: #000080;"></h2></div></span></span>
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="html"><span class="nt" style="color: #000080;"><hr><br></span></span>
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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">@@ -324,6 +334,15 @@ run into smaller chunks, use the -jobs=<strong>M</strong>/<strong>N</strong> opt</td>
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="html"></span>
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="html">    <span class="kd" style="font-weight: 600;">var</span> <span class="nx">output</span><span class="o" style="font-weight: 600;">=</span><span class="dl">"</span><span class="s2" style="color: #d14;">proteinortho</span><span class="dl">"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="html"></span>
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<td class="old_line diff-line-num new" data-linenumber="327" 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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<td class="new_line diff-line-num new" data-linenumber="337" 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="LC337" class="line" lang="html">    <span class="kd" style="font-weight: 600;">var</span> <span class="nx">isoformno</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">document</span><span class="p">.</span><span class="nx">getElementById</span><span class="p">(</span><span class="dl">'</span><span class="s1" style="color: #d14;">isoform-no</span><span class="dl">'</span><span class="p">).</span><span class="nx">checked</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="327" 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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<td class="new_line diff-line-num new" data-linenumber="338" 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="LC338" class="line" lang="html">    <span class="kd" style="font-weight: 600;">var</span> <span class="nx">isoform0</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">document</span><span class="p">.</span><span class="nx">getElementById</span><span class="p">(</span><span class="dl">'</span><span class="s1" style="color: #d14;">isoform-0</span><span class="dl">'</span><span class="p">).</span><span class="nx">checked</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="327" 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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<td class="new_line diff-line-num new" data-linenumber="339" 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="LC339" class="line" lang="html">    <span class="kd" style="font-weight: 600;">var</span> <span class="nx">isoform1</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">document</span><span class="p">.</span><span class="nx">getElementById</span><span class="p">(</span><span class="dl">'</span><span class="s1" style="color: #d14;">isoform-1</span><span class="dl">'</span><span class="p">).</span><span class="nx">checked</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="327" 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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<td class="new_line diff-line-num new" data-linenumber="340" 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="LC340" class="line" lang="html">    <span class="kd" style="font-weight: 600;">var</span> <span class="nx">isoform2</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">document</span><span class="p">.</span><span class="nx">getElementById</span><span class="p">(</span><span class="dl">'</span><span class="s1" style="color: #d14;">isoform-2</span><span class="dl">'</span><span class="p">).</span><span class="nx">checked</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="327" 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="LC341" class="line" lang="html"></span>
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<td class="old_line diff-line-num new" data-linenumber="327" 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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<td class="new_line diff-line-num new" data-linenumber="342" 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="LC342" class="line" lang="html">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nx">isoform0</span><span class="p">){</span><span class="nx">output</span><span class="o" style="font-weight: 600;">+=</span><span class="dl">"</span><span class="s2" style="color: #d14;"> -isoform=ncbi</span><span class="dl">"</span><span class="p">;}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="327" 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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<td class="new_line diff-line-num new" data-linenumber="343" 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="LC343" class="line" lang="html">    <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nx">isoform1</span><span class="p">){</span><span class="nx">output</span><span class="o" style="font-weight: 600;">+=</span><span class="dl">"</span><span class="s2" style="color: #d14;"> -isoform=uniprot</span><span class="dl">"</span><span class="p">;}</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="344" 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="LC344" class="line" lang="html">    <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nx">isoform2</span><span class="p">){</span><span class="nx">output</span><span class="o" style="font-weight: 600;">+=</span><span class="dl">"</span><span class="s2" style="color: #d14;"> -isoform=trinity</span><span class="dl">"</span><span class="p">;}</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="345" 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="LC345" class="line" lang="html"></span>
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="html">    <span class="kd" style="font-weight: 600;">var</span> <span class="nx">step0</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">document</span><span class="p">.</span><span class="nx">getElementById</span><span class="p">(</span><span class="dl">'</span><span class="s1" style="color: #d14;">step-0</span><span class="dl">'</span><span class="p">).</span><span class="nx">checked</span><span class="p">;</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="html">    <span class="kd" style="font-weight: 600;">var</span> <span class="nx">step1</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">document</span><span class="p">.</span><span class="nx">getElementById</span><span class="p">(</span><span class="dl">'</span><span class="s1" style="color: #d14;">step-1</span><span class="dl">'</span><span class="p">).</span><span class="nx">checked</span><span class="p">;</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="html">    <span class="kd" style="font-weight: 600;">var</span> <span class="nx">step2</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">document</span><span class="p">.</span><span class="nx">getElementById</span><span class="p">(</span><span class="dl">'</span><span class="s1" style="color: #d14;">step-2</span><span class="dl">'</span><span class="p">).</span><span class="nx">checked</span><span class="p">;</span></span>
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<br>
</li>
<li id="d0cbc2488744231506d0c284dad99f8cc4078553">
<a href="https://salsa.debian.org/med-team/proteinortho/-/commit/3746e15da8bc7609707daf904845cd274344cd8f#d0cbc2488744231506d0c284dad99f8cc4078553"><strong>src/proteinortho2xml.pl</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15" 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="15" 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">@@ -15,6 +15,7 @@ my $po_file = $ARGV[0];</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$cur_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="16" 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="LC16" class="line" lang="perl"></span>
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<td class="old_line diff-line-num" data-linenumber="17" 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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<td class="new_line diff-line-num" data-linenumber="17" 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="LC17" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@species</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="18" 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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<td class="new_line diff-line-num new" data-linenumber="18" 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="LC18" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@species_num_prots</span><span class="p">;</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$headerisset</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">%protID2id</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$orthologygroup</span><span class="o" style="font-weight: 600;">=</span><span class="p">"";</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="115" 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="116" 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">@@ -115,6 +116,8 @@ if($po_file=~m/proteinortho-graph/){</td>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="perl">     <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$line</span><span class="p">)</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$line</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">#</span><span class="p">"){</span> </span>
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<td class="new_line diff-line-num" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="perl">         <span class="nb" style="color: #0086b3;">chomp</span><span class="p">(</span><span class="nv" style="color: #008080;">$line</span><span class="p">);</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="118" 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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<td class="new_line diff-line-num new" data-linenumber="119" 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="LC119" class="line" lang="perl">         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$headerisset</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[ERROR] header is missing.</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="nb" style="color: #0086b3;">die</span><span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="118" 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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<td class="new_line diff-line-num new" data-linenumber="120" 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="LC120" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="118" 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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<td class="new_line diff-line-num" data-linenumber="121" 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="LC121" class="line" lang="perl">                 <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$curorthologygroup</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"";</span> <span class="c1" style="color: #998; font-style: italic;"># create template orthology group</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="perl">                 <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@linesplt</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="sr" style="color: #009926;">/\t/</span><span class="p">,</span><span class="nv" style="color: #008080;">$line</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;"># -> first 3 cols are number of species/genes and the algebraic connectivity of the given group</span></span>
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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">@@ -131,6 +134,7 @@ if($po_file=~m/proteinortho-graph/){</td>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="perl">                                 <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$j</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: #008080;">@linesplt2</span><span class="p">)</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$j</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$j</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="perl">                                         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="nv" style="color: #008080;">$linesplt2</span><span class="p">[</span><span class="nv" style="color: #008080;">$j</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">*</span><span class="p">"</span> <span class="p">){</span><span class="k" style="font-weight: 600;">next</span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="perl">                                         <span class="c1" style="color: #998; font-style: italic;"># $linesplt2[$j] is a protein (name like tr|A8JEJ4|A8JEJ4_CHLRE) of the current ortho group</span></span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="perl">                                         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nb" style="color: #0086b3;">exists</span><span class="p">(</span><span class="nv" style="color: #008080;">$protID2id</span><span class="p">{</span><span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">#</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$linesplt2</span><span class="p">[</span><span class="nv" style="color: #008080;">$j</span><span class="p">]})){</span> <span class="c1" style="color: #998; font-style: italic;"># map down to a integer A8JEJ4->0 ...</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="144" 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="148" 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">@@ -144,6 +148,8 @@ if($po_file=~m/proteinortho-graph/){</td>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="perl">                                         <span class="nv" style="color: #008080;">$protId</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/^[sptr]{2}\|//g</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># protein names can be 'sp|O08314|TGT_HELPY' -> 'O08314'</span></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="perl">                                         <span class="nv" style="color: #008080;">$protId</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/\|[^|]+$//g</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># protein names can be 'sp|O08314|TGT_HELPY' -> 'O08314'</span></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="perl">                                         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@species_num_prots</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@linesplt</span><span class="p">){</span> <span class="nv" style="color: #008080;">@species_num_prots</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span><span class="nv" style="color: #008080;">x</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@linesplt</span><span class="p">)</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="perl">                                         <span class="nv" style="color: #008080;">$species_num_prots</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">3</span><span class="p">]</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="perl">                                         <span class="nv" style="color: #008080;">$species</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">3</span><span class="p">]</span><span class="o" style="font-weight: 600;">.=</span><span class="p">"</span><span class="se" style="color: #d14;">\t\t\t\t</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">'</span><span class="s1" style="color: #d14;"><gene id="</span><span class="p">'</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$protID2id</span><span class="p">{</span><span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">#</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$linesplt2</span><span class="p">[</span><span class="nv" style="color: #008080;">$j</span><span class="p">]}</span><span class="o" style="font-weight: 600;">.</span><span class="p">'</span><span class="s1" style="color: #d14;">" protId="</span><span class="p">'</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$protId</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">/></span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="perl">                                         <span class="nv" style="color: #008080;">$curorthologygroup</span><span class="o" style="font-weight: 600;">.=</span><span class="p">"</span><span class="se" style="color: #d14;">\t\t\t</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">'</span><span class="s1" style="color: #d14;"><geneRef id="</span><span class="p">'</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$protID2id</span><span class="p">{</span><span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">#</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$linesplt2</span><span class="p">[</span><span class="nv" style="color: #008080;">$j</span><span class="p">]}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">/></span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="perl">                                 <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="153" 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="159" 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">@@ -153,6 +159,7 @@ if($po_file=~m/proteinortho-graph/){</td>
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="perl">                         <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="perl">                 <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="perl">                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$orthologygroup</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span><span class="nv" style="color: #008080;">$orthologygroup</span><span class="o" style="font-weight: 600;">.=</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="156" 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="LC162" class="line" lang="perl">                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$con</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">NA</span><span class="p">"){</span><span class="nv" style="color: #008080;">$con</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;">-1</span><span class="p">"}</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="perl">                 <span class="nv" style="color: #008080;">$orthologygroup</span><span class="o" style="font-weight: 600;">.=</span><span class="p">"</span><span class="se" style="color: #d14;">\t\t</span><span class="s2" style="color: #d14;"><orthologGroup id=</span><span class="se" style="color: #d14;">\"</span><span class="si" style="color: #d14;">$cur_id</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">></span><span class="se" style="color: #d14;">\n\t\t\t</span><span class="s2" style="color: #d14;"><score id=</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">algcon</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;"> value=</span><span class="se" style="color: #d14;">\"</span><span class="si" style="color: #d14;">$con</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">/></span><span class="se" style="color: #d14;">\n</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$curorthologygroup</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\t\t</span><span class="s2" style="color: #d14;"></orthologGroup></span><span class="p">";</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="158" 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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<td class="new_line diff-line-num" data-linenumber="165" 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="LC165" class="line" lang="perl">                 <span class="nv" style="color: #008080;">$cur_id</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$cur_id</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="196" 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="203" 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">@@ -196,25 +203,30 @@ print "\n\t<notes>\n\t\tProteinortho OrthoXML file.\n\t</notes>\n";</td>
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$po_file</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">m/proteinortho-graph/</span><span class="p">){</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="perl"> <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$cur_species</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">keys</span> <span class="nv" style="color: #008080;">%species_graph</span><span class="p">){</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="198" 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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<td class="new_line diff-line-num" data-linenumber="205" 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="LC205" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="perl">         <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: #008080;">$species_graph</span><span class="p">{</span><span class="nv" style="color: #008080;">$cur_species</span><span class="p">}{"</span><span class="s2" style="color: #d14;">header</span><span class="p">"};</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="200" 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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<td class="new_line diff-line-num new" data-linenumber="206" 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="LC206" class="line" lang="perl">         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nb" style="color: #0086b3;">keys</span> <span class="nv" style="color: #008080;">%</span><span class="p">{</span><span class="nv" style="color: #008080;">$species_graph</span><span class="p">{</span><span class="nv" style="color: #008080;">$cur_species</span><span class="p">}}</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="200" 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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<td class="new_line diff-line-num new" data-linenumber="207" 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="LC207" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="200" 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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<td class="new_line diff-line-num new" data-linenumber="208" 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">
208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="perl">                 <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: #008080;">$species_graph</span><span class="p">{</span><span class="nv" style="color: #008080;">$cur_species</span><span class="p">}{"</span><span class="s2" style="color: #d14;">header</span><span class="p">"};</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="200" 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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<td class="new_line diff-line-num new" data-linenumber="209" 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">
209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="200" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="210" 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">
210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="perl">                 <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$prot</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">keys</span> <span class="nv" style="color: #008080;">%</span><span class="p">{</span><span class="nv" style="color: #008080;">$species_graph</span><span class="p">{</span><span class="nv" style="color: #008080;">$cur_species</span><span class="p">}}){</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="200" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="211" 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">
211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="perl">                         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$prot</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">header</span><span class="p">"){</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="200" 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">
200
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<td class="new_line diff-line-num" data-linenumber="212" 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">
212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
201
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<td class="new_line diff-line-num old" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC201" class="line" lang="perl">         <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$prot</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">keys</span> <span class="nv" style="color: #008080;">%</span><span class="p">{</span><span class="nv" style="color: #008080;">$species_graph</span><span class="p">{</span><span class="nv" style="color: #008080;">$cur_species</span><span class="p">}}){</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
202
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<td class="new_line diff-line-num old" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC202" class="line" lang="perl">                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$prot</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">header</span><span class="p">"){</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="203" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="213" 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">
213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="perl">                         <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$prot_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$prot</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="203" 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">
203
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<td class="new_line diff-line-num" data-linenumber="214" 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">
214
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC214" class="line" lang="perl"></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
204
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<td class="new_line diff-line-num old" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC204" class="line" lang="perl">                 <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$prot_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$prot</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="205" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="215" 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">
215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="perl">                         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$prot</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">m/^[^\|]+\|([^\|]+)\|[^\|]+/</span><span class="p">){</span> <span class="c1" style="color: #998; font-style: italic;"># extract the true name (A8JEJ4)</span></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="205" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="216" 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">
216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="perl">                                 <span class="nv" style="color: #008080;">$prot_id</span><span class="o" style="font-weight: 600;">=</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="205" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="217" 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">
217
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC217" class="line" lang="perl">                         <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="205" 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">
205
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<td class="new_line diff-line-num" data-linenumber="218" 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">
218
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC218" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
206
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<td class="new_line diff-line-num old" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC206" class="line" lang="perl">                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$prot</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">m/^[^\|]+\|([^\|]+)\|[^\|]+/</span><span class="p">){</span> <span class="c1" style="color: #998; font-style: italic;"># extract the true name (A8JEJ4)</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
207
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<td class="new_line diff-line-num old" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC207" class="line" lang="perl">                         <span class="nv" style="color: #008080;">$prot_id</span><span class="o" style="font-weight: 600;">=</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="208" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="219" 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="LC219" class="line" lang="perl">                         <span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\t\t\t\t</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">'</span><span class="s1" style="color: #d14;"><gene id="</span><span class="p">'</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$protID2id</span><span class="p">{</span><span class="nv" style="color: #008080;">$cur_species</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">#</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$prot</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">'</span><span class="s1" style="color: #d14;">" protId="</span><span class="p">'</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$prot_id</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">/></span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="208" 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">
208
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220
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="perl">                 <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="209" 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">
209
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<td class="new_line diff-line-num" data-linenumber="221" 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">
221
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
210
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<td class="new_line diff-line-num old" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="perl">                 <span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\t\t\t<span class="idiff left">\t</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">'</span></span><span class="s1" style="color: #d14;"><span class="idiff"><gene id="</span></span><span class="p"><span class="idiff">'</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">$protID2id</span></span><span class="p"><span class="idiff">{</span></span><span class="nv" style="color: #008080;"><span class="idiff">$cur_species</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">#</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">$prot</span></span><span class="p"><span class="idiff">}</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">'</span></span><span class="s1" style="color: #d14;"><span class="idiff">" protId="</span></span><span class="p"><span class="idiff">'</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">$prot_id</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\"</span></span><span class="s2" style="color: #d14;"><span class="idiff right">/</span>></span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="211" 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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<td class="new_line diff-line-num new" data-linenumber="222" 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="LC222" class="line" lang="perl">                 <span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s2" style="color: #d14;"><span class="idiff left"></genes></span></span><span class="se" style="color: #d14;"><span class="idiff">\n\t\t</span></span><span class="s2" style="color: #d14;"><span class="idiff"></database></span></span><span class="se" style="color: #d14;"><span class="idiff">\n\t</span></span><span class="s2" style="color: #d14;"><span class="idiff right"></species</span>></span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="211" 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">
211
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<td class="new_line diff-line-num" data-linenumber="223" 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">
223
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="perl">         <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC212" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="perl">         <span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s2" style="color: #d14;"></genes></span><span class="se" style="color: #d14;">\n\t\t</span><span class="s2" style="color: #d14;"></database></span><span class="se" style="color: #d14;">\n\t</span><span class="s2" style="color: #d14;"></species></span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="214" 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">
214
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<td class="new_line diff-line-num" data-linenumber="224" 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">
224
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="perl"> <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="215" 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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<td class="new_line diff-line-num" data-linenumber="225" 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="LC225" class="line" lang="perl"><span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
216
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<td class="new_line diff-line-num old" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC216" class="line" lang="perl"> <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$cur_species</span> <span class="p">(</span><span class="nv" style="color: #008080;">@species</span><span class="p">){</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC217" class="line" lang="perl">         <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: #008080;">$cur_species</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s2" style="color: #d14;"></genes></span><span class="se" style="color: #d14;">\n\t\t</span><span class="s2" style="color: #d14;"></database></span><span class="se" style="color: #d14;">\n\t</span><span class="s2" style="color: #d14;"></species></span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="218" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="226" 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">
226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="perl"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@species</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="218" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="227" 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">
227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="perl">         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$species_num_prots</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="218" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="228" 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">
228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="perl">                 <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: #008080;">$species</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s2" style="color: #d14;"></genes></span><span class="se" style="color: #d14;">\n\t\t</span><span class="s2" style="color: #d14;"></database></span><span class="se" style="color: #d14;">\n\t</span><span class="s2" style="color: #d14;"></species></span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="218" 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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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="perl">         <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="218" 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">
218
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230
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="perl"> <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="219" 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">
219
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231
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="perl"><span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="220" 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">
220
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<td class="new_line diff-line-num" data-linenumber="232" 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">
232
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC232" class="line" lang="perl"></span>
</pre>
</td>
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</table>
<br>
</li>
<li id="3439148ea7017354388f7c55043cc84986c1c394">
<a href="https://salsa.debian.org/med-team/proteinortho/-/commit/3746e15da8bc7609707daf904845cd274344cd8f#3439148ea7017354388f7c55043cc84986c1c394"><strong>src/proteinortho_grab_proteins.pl</strong></a>
<hr>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="28" 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="28" 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">@@ -28,12 +28,18 @@</td>
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<td class="old_line diff-line-num" data-linenumber="28" 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">
28
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<td class="new_line diff-line-num" data-linenumber="28" 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">
28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @author Paul Klemm</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="29" 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">
29
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<td class="new_line diff-line-num" data-linenumber="29" 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">
29
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC29" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @email klemmp@staff.uni-marburg.de</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="30" 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">
30
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<td class="new_line diff-line-num" data-linenumber="30" 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">
30
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC30" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @company Bioinformatics, University of Leipzig</span></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
31
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<td class="new_line diff-line-num old" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC31" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @version <span class="idiff left right">5</span></span></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num old" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
32
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<td class="new_line diff-line-num old" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC32" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @date <span class="idiff left right">1-29</span>-2021</span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="33" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="31" 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">
31
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC31" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @version <span class="idiff left right">6</span></span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="33" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="32" 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">
32
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC32" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @date <span class="idiff left right">2-10</span>-2021</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="33" 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">
33
</td>
<td class="new_line diff-line-num" data-linenumber="33" 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">
33
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC33" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="34" 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">
34
</td>
<td class="new_line diff-line-num" data-linenumber="34" 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">
34
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC34" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" 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">
35
</td>
<td class="new_line diff-line-num" 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">
35
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC35" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="36" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="36" 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">
36
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC36" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="36" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="37" 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">
37
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC37" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">threads</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="36" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="38" 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">
38
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC38" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">threads::</span><span class="nv" style="color: #008080;">shared</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" 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">
36
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<td class="new_line diff-line-num" data-linenumber="39" 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">
39
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC39" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">POSIX</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="37" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="40" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC40" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">File::</span><span class="nv" style="color: #008080;">Basename</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="37" 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="LC41" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Thread::</span><span class="nv" style="color: #008080;">Queue</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$QUEUE</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Thread::</span><span class="nv" style="color: #008080;">Queue</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">();</span>    <span class="c1" style="color: #998; font-style: italic;"># A new empty queue</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$usage</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><<'ENDUSAGE';</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="perl"><span class="s" style="color: #d14;">proteinortho_grab_proteins.pl        greps all genes/proteins of a given fasta file</span></span>
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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">@@ -48,9 +54,13 @@ proteinortho_grab_proteins.pl (options) QUERY FASTA1 (FASTA2 ...)</td>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="perl"><span class="s" style="color: #d14;">   FASTA*  fasta file(s) (database)</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="perl"><span class="s" style="color: #d14;">   (options):</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="perl"><span class="s" style="color: #d14;">           -tofiles, -t  print everything to files instead of stdout files are called OrthoGroup**.fasta for a proteinortho.tsv file</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="perl"><span class="s" style="color: #d14;">           -tofiles, -t  print everything to files instead of stdout files are called OrthoGroup.fasta for a proteinortho.tsv file</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="perl"><span class="s" style="color: #d14;">           -tofiles=DIR  additionally specifies a output directory for the OrthoGroup files</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="perl"><span class="s" style="color: #d14;">           -E            enables regex matching otherwise the string is escaped (e.g. | -> \|)</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="perl"><span class="s" style="color: #d14;">           -exact        search patters are extended with a \b, that indicates end of word.</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="perl"><span class="s" style="color: #d14;">           -cpus=INT     the number of parallel open files for reading, this is strictly limited by the I/O bandwith (default:1).</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="perl"><span class="s" style="color: #d14;">                         for fast SSD drives, you can increase this to gain speed.</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="perl"><span class="s" style="color: #d14;">           -minprot=X    if you give a proteinortho.tsv file, this filters out groups with less than X proteins (default:0).</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="perl"><span class="s" style="color: #d14;">           -source, -s   adds the filename (FASTA1,...) to the found gene-name</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="perl"><span class="s" style="color: #d14;">           -F=s          char delimiter for multiple identifier if QUERY is a string input (default: ',')</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="perl"><span class="s" style="color: #d14;">           -isoform      if you use proteinortho with --isoform option, then you need to set this option here too. </span></span>
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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">@@ -98,28 +108,37 @@ DESCRIPTION</td>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="perl"><span class="s" style="color: #d14;"> </span></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="perl"><span class="s" style="color: #d14;">ENDUSAGE</span></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="perl"></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$query</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$help</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$tofiles</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$isoform</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$justid</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$prefix</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;">></span><span class="p">";</span></span>
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<td class="old_line diff-line-num old" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$doregex</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$source</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$exact</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$del</span><span class="o" style="font-weight: 600;">=</span><span class="p">'</span><span class="s1" style="color: #d14;">,</span><span class="p">';</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@ARGV_copy</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">@ARGV</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="perl"></span>
</pre>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@ARGV_copyiddone</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="nv" style="color: #008080;">x</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: #008080;">@ARGV_copy</span><span class="p">));</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$ARGV_copyiddone_counter</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: #008080;">@ARGV_copy</span><span class="p">);</span></span>
</pre>
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111
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC111" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="115" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="112" 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">
112
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC112" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="115" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="113" 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">
113
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC113" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$query</span><span class="p">;</span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="115" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="114" 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">
114
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC114" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$help</span><span class="p">;</span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="115" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="115" 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">
115
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC115" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$tofiles</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;">-1</span><span class="p">";</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="115" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="116" 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">
116
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC116" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$isoform</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="115" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="117" 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">
117
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC117" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$justid</span><span class="p">;</span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="115" 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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<td class="new_line diff-line-num new" data-linenumber="118" 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">
118
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC118" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$prefix</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;">></span><span class="p">";</span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="115" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="119" 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">
119
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC119" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$doregex</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="115" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="120" 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">
120
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC120" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$source</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="115" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="121" 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">
121
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC121" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$exact</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="115" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="122" 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">
122
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC122" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$del</span><span class="o" style="font-weight: 600;">=</span><span class="p">'</span><span class="s1" style="color: #d14;">,</span><span class="p">';</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="115" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="123" 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">
123
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC123" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">@ARGV_copy</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">@ARGV</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="115" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="124" 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">
124
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC124" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$ignoreWarning</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="115" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="125" 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">
125
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC125" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$minprot</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="115" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="126" 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">
126
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC126" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$cpus</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="115" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="127" 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">
127
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC127" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="115" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="128" 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">
128
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC128" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">@ARGV_copyiddone</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="nv" style="color: #008080;">x</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: #008080;">@ARGV_copy</span><span class="p">));</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="115" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="129" 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">
129
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC129" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$ARGV_copyiddone_counter</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: #008080;">@ARGV_copy</span><span class="p">);</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
115
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<td class="new_line diff-line-num" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="perl"><span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$v</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$v</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@ARGV_copy</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$v</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="116" 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">
116
</td>
<td class="new_line diff-line-num" data-linenumber="131" 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">
131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="perl"> <span class="nv" style="color: #008080;">$ARGV_copyiddone</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</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>
</pre>
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<td class="old_line diff-line-num" data-linenumber="117" 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">
117
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<td class="new_line diff-line-num" data-linenumber="132" 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">
132
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC132" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV_copy</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/--?(help|h)$/</span><span class="p">){</span><span class="nv" style="color: #008080;">$help</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
118
</td>
<td class="new_line diff-line-num old" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC118" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV_copy</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?(tofiles|t)$/</span><span class="p">){</span><span class="nv" style="color: #008080;">$tofiles</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="119" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="133" 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">
133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV_copy</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?(tofiles|t)$/</span><span class="p">){</span><span class="nv" style="color: #008080;">$tofiles</span><span class="o" style="font-weight: 600;">=</span><span class="p">"";}</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="119" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="134" 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">
134
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC134" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV_copy</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?(tofiles|t)=(.*)$/</span><span class="p">){</span><span class="nv" style="color: #008080;">$tofiles</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;">$2/</span><span class="p">";}</span></span>
</pre>
</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
119
</td>
<td class="new_line diff-line-num" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
135
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC135" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV_copy</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?(source|s)$/</span><span class="p">){</span><span class="nv" style="color: #008080;">$source</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>
</pre>
</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
120
</td>
<td class="new_line diff-line-num" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
136
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC136" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV_copy</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?F=(.*)$/</span><span class="p">){</span><span class="nv" style="color: #008080;">$del</span><span class="o" style="font-weight: 600;">=</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="121" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="137" 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">
137
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC137" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV_copy</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?minprots?=(.*)$/</span><span class="p">){</span><span class="nv" style="color: #008080;">$minprot</span><span class="o" style="font-weight: 600;">=</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="121" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="138" 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">
138
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC138" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV_copy</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?cpus?=(.*)$/</span><span class="p">){</span><span class="nv" style="color: #008080;">$cpus</span><span class="o" style="font-weight: 600;">=</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
121
</td>
<td class="new_line diff-line-num" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
139
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC139" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV_copy</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?E$/</span><span class="p">){</span><span class="nv" style="color: #008080;">$doregex</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
122
</td>
<td class="new_line diff-line-num" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
140
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC140" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV_copy</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?isoform$/</span><span class="p">){</span><span class="nv" style="color: #008080;">$isoform</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="123" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="141" 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">
141
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC141" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV_copy</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?ignoreWarning$/</span><span class="p">){</span><span class="nv" style="color: #008080;">$ignoreWarning</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="123" 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">
123
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<td class="new_line diff-line-num" data-linenumber="142" 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">
142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV_copy</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?exact$/</span><span class="p">){</span><span class="nv" style="color: #008080;">$exact</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="124" 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">
124
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<td class="new_line diff-line-num" data-linenumber="143" 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">
143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV_copy</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^-.+/</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: #008080;">$usage</span><span class="p">;</span> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">ERROR: invalid option </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$ARGV_copy</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">!</span><span class="se" style="color: #d14;">\n\n</span><span class="p">";</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
125
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<td class="new_line diff-line-num" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: #008080;">$query</span><span class="p">)){</span><span class="nv" style="color: #008080;">$query</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$ARGV_copy</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">];}</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -144,8 +163,7 @@ if($fail){</td>
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<td class="old_line diff-line-num" data-linenumber="144" 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">
144
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<td class="new_line diff-line-num" data-linenumber="163" 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">
163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="145" 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">
145
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<td class="new_line diff-line-num" data-linenumber="164" 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">
164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="perl"><span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="146" 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">
146
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<td class="new_line diff-line-num" data-linenumber="165" 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">
165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="perl"></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
147
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<td class="new_line diff-line-num old" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC147" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">%qdata</span><span class="p">;</span></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
148
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<td class="new_line diff-line-num old" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># my $qdata_count = {};</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="149" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="166" 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">
166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">%qdata</span><span class="p">;</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="149" 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">
149
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<td class="new_line diff-line-num" data-linenumber="167" 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">
167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="150" 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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<td class="new_line diff-line-num" data-linenumber="168" 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">
168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$orthogroupcounter</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
151
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<td class="new_line diff-line-num" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$genecounter</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="157" 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="175" 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">@@ -157,6 +175,7 @@ for(my $v = 0 ; $v < scalar @ARGV_copy ; $v++){</td>
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157
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<td class="new_line diff-line-num" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="perl"> <span class="nv" style="color: #008080;">$numOfFastas</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="158" 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">
158
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<td class="new_line diff-line-num" 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">
176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="perl"><span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="159" 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">
159
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<td class="new_line diff-line-num" data-linenumber="177" 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">
177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">@filenames</span><span class="p">;</span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="160" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="178" 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">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">@thread_return</span> <span class="p">:</span><span class="nv" style="color: #008080;">shared</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">("")</span><span class="nv" style="color: #008080;">x$cpus</span><span class="p">;</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
160
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<td class="new_line diff-line-num" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="perl"></span>
</pre>
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$foundHeader</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="162" 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">
162
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="164" 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="183" 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">@@ -164,14 +183,16 @@ my $foundHeader=0;</td>
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164
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<td class="new_line diff-line-num" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
165
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<td class="new_line diff-line-num" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">processLine</span><span class="p">{</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
166
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$line</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="168" 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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<td class="new_line diff-line-num new" data-linenumber="186" 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="LC186" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$prefix<span class="idiff left right">_group</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
168
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<td class="new_line diff-line-num" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="perl"> <span class="nv" style="color: #008080;">$line</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/[\r\n]+$//</span><span class="p">;</span> </span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@sp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="sr" style="color: #009926;">/\t/</span><span class="p">,</span><span class="nv" style="color: #008080;">$line</span><span class="p">);</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="172" 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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<td class="new_line diff-line-num" data-linenumber="191" 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="LC191" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$line</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">#</span><span class="p">"){</span><span class="nv" style="color: #008080;">$foundHeader</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span><span class="nv" style="color: #008080;">@filenames</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">@sp</span><span class="p">;</span> <span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="173" 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">
173
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<td class="new_line diff-line-num" data-linenumber="192" 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">
192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: #008080;">@sp</span><span class="p">)</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">3</span><span class="p">){</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
174
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<td class="new_line diff-line-num old" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="perl">         <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$v</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$v</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@sp</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$v</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="175" 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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<td class="new_line diff-line-num new" data-linenumber="193" 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="LC193" class="line" lang="perl">         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="nv" style="color: #008080;">@sp</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$sp</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: #008080;">$minprot</span> <span class="p">){</span><span class="nv" style="color: #008080;">$orthogroupcounter</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="k" style="font-weight: 600;">next</span><span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="175" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="194" 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">
194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="175" 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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<td class="new_line diff-line-num new" data-linenumber="195" 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="LC195" class="line" lang="perl">         <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$v</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$v</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@sp</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$v</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="perl">                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$sp</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">*</span><span class="p">"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$sp</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">""){</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="perl">                 <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@spp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="s2" style="color: #d14;">,</span><span class="p">",</span><span class="nv" style="color: #008080;">$sp</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]);</span></span>
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="perl"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -180,16 +201,17 @@ sub processLine{</td>
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="perl">                         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$spp</span><span class="p">[</span><span class="nv" style="color: #008080;">$vv</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">*</span><span class="p">"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$spp</span><span class="p">[</span><span class="nv" style="color: #008080;">$vv</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">""){</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
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181
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="perl">                         <span class="nv" style="color: #008080;">$spp</span><span class="p">[</span><span class="nv" style="color: #008080;">$vv</span><span class="p">]</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/^\(//</span><span class="p">;</span><span class="nv" style="color: #008080;">$spp</span><span class="p">[</span><span class="nv" style="color: #008080;">$vv</span><span class="p">]</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/\)$//</span><span class="p">;</span></span>
</pre>
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182
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<td class="new_line diff-line-num" data-linenumber="203" 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">
203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="perl">                         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nb" style="color: #0086b3;">exists</span> <span class="nv" style="color: #008080;">$filenames</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]){</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="perl">                                 <span class="nv" style="color: #008080;">$filenames</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="p">""</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="perl">                         <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="186" 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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<td class="new_line diff-line-num new" data-linenumber="204" 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="LC204" class="line" lang="perl">                         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nb" style="color: #0086b3;">exists</span> <span class="nv" style="color: #008080;">$filenames</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]){</span> <span class="nv" style="color: #008080;">$filenames</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="p">""</span> <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="186" 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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<td class="new_line diff-line-num new" data-linenumber="205" 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="LC205" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="186" 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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<td class="new_line diff-line-num new" data-linenumber="206" 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="LC206" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#print join (",",@filenames)."\n";die;</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="186" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="207" 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">
207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#print STDERR $filenames[$v].":>".$spp[$vv]."<\n";</span></span>
</pre>
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<td class="old_line diff-line-num" 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">
186
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<td class="new_line diff-line-num" data-linenumber="208" 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">
208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="perl">                         <span class="nv" style="color: #008080;">$qdata</span><span class="p">{</span><span class="nv" style="color: #008080;">$filenames</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]}{</span><span class="nv" style="color: #008080;">$spp</span><span class="p">[</span><span class="nv" style="color: #008080;">$vv</span><span class="p">]}</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$prefix</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.OrthoGroup</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$orthogroupcounter</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="188" 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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<td class="new_line diff-line-num new" data-linenumber="209" 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="LC209" class="line" lang="perl">                         <span class="nv" style="color: #008080;">$qdata</span><span class="p">{</span><span class="nv" style="color: #008080;">$filenames</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]}{</span><span class="nv" style="color: #008080;">$spp</span><span class="p">[</span><span class="nv" style="color: #008080;">$vv</span><span class="p">]}</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$prefix<span class="idiff left right">_group</span></span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.OrthoGroup</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$orthogroupcounter</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="perl">                         <span class="nv" style="color: #008080;">$genecounter</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="189" 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">
189
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<td class="new_line diff-line-num" data-linenumber="211" 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">
211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="perl">                 <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="190" 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">
190
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<td class="new_line diff-line-num" data-linenumber="212" 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">
212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="perl">         <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="191" 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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<td class="new_line diff-line-num new" data-linenumber="213" 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="LC213" class="line" lang="perl">         <span class="nv" style="color: #008080;">$orthogroupcounter</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
</pre>
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191
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<td class="new_line diff-line-num" data-linenumber="214" 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">
214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="perl"> <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="perl"> <span class="nv" style="color: #008080;">$orthogroupcounter</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="perl"><span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="perl"></span>
</pre>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="perl"><span class="k" style="font-weight: 600;">unless</span><span class="p">(</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$FH</span><span class="p">,'</span><span class="s1" style="color: #d14;"><</span><span class="p">',</span><span class="nv" style="color: #008080;">$query</span><span class="p">))</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="206" 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="228" 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">@@ -206,9 +228,9 @@ unless(open(my $FH,'<',$query)) {</td>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="perl">         <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="207" 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="LC229" class="line" lang="perl"> <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="208" 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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<td class="new_line diff-line-num" data-linenumber="230" 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="LC230" class="line" lang="perl"><span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$isoform</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$exact</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[<span class="idiff left right">STDERR</span>] WARNING The -isoform option is not compatible with -exact if a proteinortho file is given. -exact is now unset.</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="nv" style="color: #008080;">$exact</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;}</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$isoform</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$exact</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[<span class="idiff left right">STDERR</span>] WARNING The -exact option is mandatory if a proteinortho file is given. -exact is now set.</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="nv" style="color: #008080;">$exact</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$doregex</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[<span class="idiff left right">STDERR</span>] WARNING The -E option is not allowed if a proteinortho file is given. -E is now unset.</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="nv" style="color: #008080;">$doregex</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;}</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="212" 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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<td class="new_line diff-line-num new" data-linenumber="231" 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="LC231" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$isoform</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$exact</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[<span class="idiff left right">proteinortho_grab_proteins.pl</span>] WARNING The -isoform option is not compatible with -exact if a proteinortho file is given. -exact is now unset.</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="nv" style="color: #008080;">$exact</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;}</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$isoform</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$exact</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[<span class="idiff left right">proteinortho_grab_proteins.pl</span>] WARNING The -exact option is mandatory if a proteinortho file is given. -exact is now set.</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="nv" style="color: #008080;">$exact</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="212" 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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<td class="new_line diff-line-num new" data-linenumber="233" 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="LC233" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$doregex</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[<span class="idiff left right">proteinortho_grab_proteins.pl</span>] WARNING The -E option is not allowed if a proteinortho file is given. -E is now unset.</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="nv" style="color: #008080;">$doregex</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;}</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="213" 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="LC235" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$query_basename</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$query</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="214" 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="LC236" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$query_basename</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/\/([^\/]+)$/</span><span class="p">){</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="217" 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="239" 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">@@ -217,167 +239,185 @@ unless(open(my $FH,'<',$query)) {</td>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="218" 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="LC240" class="line" lang="perl"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="o" style="font-weight: 600;"><</span><span class="nv" style="color: #008080;">$FH</span><span class="o" style="font-weight: 600;">></span><span class="p">){</span> <span class="nv" style="color: #008080;">&processLine</span><span class="p">(</span><span class="vg" style="color: #008080;">$_</span><span class="p">,</span> <span class="nv" style="color: #008080;">$query_basename</span><span class="p">)</span> <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">close</span><span class="p">(</span><span class="nv" style="color: #008080;">$FH</span><span class="p">);</span></span>
</pre>
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<td class="new_line diff-line-num old" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[<span class="idiff left right">STDERR</span>] Done reading the query </span><span class="si" style="color: #d14;">$query</span><span class="s2" style="color: #d14;"> file. Now I know </span><span class="si" style="color: #d14;">$orthogroupcounter</span><span class="s2" style="color: #d14;"> groups with </span><span class="si" style="color: #d14;">$genecounter</span><span class="s2" style="color: #d14;"> genes/proteins in total.</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="221" 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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<td class="new_line diff-line-num new" data-linenumber="242" 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="LC242" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[<span class="idiff left right">proteinortho_grab_proteins.pl</span>] Done reading the query </span><span class="si" style="color: #d14;">$query</span><span class="s2" style="color: #d14;"> file. Now I know </span><span class="si" style="color: #d14;">$orthogroupcounter</span><span class="s2" style="color: #d14;"> groups with </span><span class="si" style="color: #d14;">$genecounter</span><span class="s2" style="color: #d14;"> genes/proteins in total.</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="221" 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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<td class="new_line diff-line-num" data-linenumber="243" 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="LC243" class="line" lang="perl"><span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="222" 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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<td class="new_line diff-line-num" data-linenumber="244" 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="LC244" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="224" 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="LC245" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="nv" style="color: #008080;">$foundHeader</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$numOfFastas</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$genecounter</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">20</span><span class="p">){</span></span>
</pre>
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<td class="new_line diff-line-num old" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">WARNING : The header of the proteinortho file is missing, this can increase the runtime dramatically. Please include the first line (starting with '#'), to accelerate this program.</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;"><span class="idiff left right">$NC</span></span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="226" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="246" 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">
246
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC246" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">WARNING : The header of the proteinortho file is missing, this can increase the runtime dramatically. Please include the first line (starting with '#'), to accelerate this program.</span><span class="se" style="color: #d14;">\n\n</span><span class="p">";</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="226" 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">
226
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<td class="new_line diff-line-num" data-linenumber="247" 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">
247
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC247" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">sleep</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
</pre>
</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="227" 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">
227
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<td class="new_line diff-line-num" data-linenumber="248" 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">
248
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC248" class="line" lang="perl"><span class="p">}</span></span>
</pre>
</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="228" 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">
228
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<td class="new_line diff-line-num" data-linenumber="249" 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">
249
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC249" class="line" lang="perl"></span>
</pre>
</td>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
229
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<td class="new_line diff-line-num old" data-linenumber="250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC229" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="nv" style="color: #008080;">$tofiles</span><span class="o" style="font-weight: 600;"><span class="idiff left">==</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="nv" style="color: #008080;">$orthogroupcounter</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">100</span><span class="p">)</span> <span class="p">){</span></span>
</pre>
</td>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
230
</td>
<td class="new_line diff-line-num old" data-linenumber="250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC230" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">!!!</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">WARNING : This call will produce </span><span class="si" style="color: #d14;">$orthogroupcounter</span><span class="s2" style="color: #d14;"> files (one for each orthology group) !</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">In the *.html file you can individually extract single groups by clicking on the front part of a row.</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;"><span class="idiff left right">$NC</span></span><span class="p">";</span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="231" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="250" 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">
250
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC250" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="nv" style="color: #008080;">$tofiles</span><span class="idiff left"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">ne</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">-1</span></span><span class="p"><span class="idiff">"</span></span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="nv" style="color: #008080;">$orthogroupcounter</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">100</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="nv" style="color: #008080;"><span class="idiff">$ignoreWarning</span></span><span class="idiff right"> </span><span class="p">){</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="231" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="251" 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">
251
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC251" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">!!!</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">WARNING : This call will produce </span><span class="si" style="color: #d14;">$orthogroupcounter</span><span class="s2" style="color: #d14;"> files (one for each orthology group) !</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">In the *.html file you can individually extract single groups by clicking on the front part of a row.</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="231" 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">
231
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<td class="new_line diff-line-num" data-linenumber="252" 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">
252
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC252" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Press 'strg+c' to prevent me from proceeding or wait 20 seconds to continue...</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">!!!</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
</pre>
</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="232" 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">
232
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<td class="new_line diff-line-num" data-linenumber="253" 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">
253
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC253" class="line" lang="perl">         <span class="nb" style="color: #0086b3;">sleep</span> <span class="mi" style="color: #099;">20</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="233" 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">
233
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<td class="new_line diff-line-num" data-linenumber="254" 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">
254
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC254" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Well then, proceeding...</span><span class="se" style="color: #d14;">\n\n</span><span class="p">";</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="234" 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">
234
</td>
<td class="new_line diff-line-num" data-linenumber="255" 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">
255
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC255" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">sleep</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="235" 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">
235
</td>
<td class="new_line diff-line-num" data-linenumber="256" 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">
256
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC256" class="line" lang="perl"><span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="236" 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">
236
</td>
<td class="new_line diff-line-num" data-linenumber="257" 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">
257
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC257" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
237
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<td class="new_line diff-line-num old" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC237" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$cur_gene</span><span class="o" style="font-weight: 600;">=</span><span class="p">"";</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
238
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<td class="new_line diff-line-num old" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC238" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$cur_gene_filename</span><span class="o" style="font-weight: 600;">=</span><span class="p">"";</span></span>
</pre>
</td>
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239
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">%cur_gene_firsttime</span><span class="p">;</span></span>
</pre>
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240
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<td class="new_line diff-line-num old" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC240" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$genecounterfound</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
241
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<td class="new_line diff-line-num old" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC241" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$basename</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"";</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="242" 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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<td class="new_line diff-line-num new" data-linenumber="258" 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">
258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="perl"><span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$v</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$v</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@ARGV_copy</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$v</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV_copyiddone</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]){</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span> <span class="nv" style="color: #008080;">$QUEUE</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">enqueue</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV_copy</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">])</span> <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="242" 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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<td class="new_line diff-line-num new" data-linenumber="259" 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">
259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="perl"><span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: #008080;">$cpus</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span><span class="nv" style="color: #008080;">$QUEUE</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">enqueue</span><span class="p">(</span><span class="nb" style="color: #0086b3;">undef</span><span class="p">)}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="242" 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">
242
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<td class="new_line diff-line-num" data-linenumber="260" 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">
260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
243
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<td class="new_line diff-line-num old" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC243" class="line" lang="perl"><span class="k" style="font-weight: 600;"><span class="idiff left">my</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$fastai</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">;</span></span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="244" 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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<td class="new_line diff-line-num new" data-linenumber="261" 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">
261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="perl"><span class="k" style="font-weight: 600;"><span class="idiff left">for</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">my</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$cpus</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">++</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">threads</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="nv" style="color: #008080;"><span class="idiff">create</span></span><span class="p"><span class="idiff">('</span></span><span class="s1" style="color: #d14;"><span class="idiff">worker</span></span><span class="p"><span class="idiff">')</span></span><span class="idiff"> </span><span class="p"><span class="idiff">}</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># spawn a thread for each core</span></span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="244" 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">
244
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<td class="new_line diff-line-num" data-linenumber="262" 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">
262
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC262" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC245" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">%foundIDs</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="246" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="263" 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">
263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">%cache_files</span><span class="p">;</span></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="246" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="264" 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">
264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">%master</span><span class="p">;</span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="246" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="265" 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">
265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$genecounterfound</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="246" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="266" 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">
266
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC266" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">%genefound</span><span class="p">;</span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="246" 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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<td class="new_line diff-line-num new" data-linenumber="267" 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">
267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="perl"><span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$t</span> <span class="p">(</span><span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">list</span><span class="p">())</span> <span class="p">{</span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="246" 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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<td class="new_line diff-line-num new" data-linenumber="268" 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">
268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="perl"> <span class="nv" style="color: #008080;">$t</span><span class="o" style="font-weight: 600;">-></span><span class="nb" style="color: #0086b3;">join</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="246" 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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<td class="new_line diff-line-num new" data-linenumber="269" 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">
269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="s2" style="color: #d14;">$;$;</span><span class="p">",</span><span class="nv" style="color: #008080;">$thread_return</span><span class="p">[</span><span class="nv" style="color: #008080;">$t</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">tid</span><span class="p">]);</span> <span class="c1" style="color: #998; font-style: italic;"># await thread</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="246" 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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<td class="new_line diff-line-num new" data-linenumber="270" 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">
270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$first</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">shift</span> <span class="nv" style="color: #008080;">@ret</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="246" 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">
246
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<td class="new_line diff-line-num" data-linenumber="271" 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">
271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
247
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<td class="new_line diff-line-num old" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="perl"><span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$v</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$v</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@ARGV_copy</span> <span class="p">;</span> <span class="nv" style="color: #008080;">$v</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="248" 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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<td class="new_line diff-line-num new" data-linenumber="272" 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">
272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="perl"> <span class="nv" style="color: #008080;">$genecounterfound</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="s2" style="color: #d14;">$;</span><span class="p">",</span><span class="nv" style="color: #008080;">$first</span><span class="p">);</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="248" 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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<td class="new_line diff-line-num new" data-linenumber="273" 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">
273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">map</span> <span class="p">{</span> <span class="nv" style="color: #008080;">$genefound</span><span class="p">{</span><span class="vg" style="color: #008080;">$_</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="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="s2" style="color: #d14;">$;</span><span class="p">",</span><span class="nv" style="color: #008080;">$first</span><span class="p">);</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="248" 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">
248
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<td class="new_line diff-line-num" data-linenumber="274" 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">
274
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
249
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<td class="new_line diff-line-num old" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC249" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV_copyiddone</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]){</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="250" 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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<td class="new_line diff-line-num new" data-linenumber="275" 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">
275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="perl"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@ret</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="250" 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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<td class="new_line diff-line-num new" data-linenumber="276" 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">
276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="perl">         <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: #008080;">$key</span><span class="p">,</span><span class="nv" style="color: #008080;">$load</span><span class="p">)</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="s2" style="color: #d14;">$;</span><span class="p">",</span><span class="nv" style="color: #008080;">$ret</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]);</span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="250" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="277" 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">
277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="perl">         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nb" style="color: #0086b3;">exists</span> <span class="nv" style="color: #008080;">$master</span><span class="p">{</span><span class="nv" style="color: #008080;">$key</span><span class="p">}){</span><span class="nv" style="color: #008080;">$master</span><span class="p">{</span><span class="nv" style="color: #008080;">$key</span><span class="p">}</span><span class="o" style="font-weight: 600;">=</span><span class="p">""}</span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="250" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="278" 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">
278
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC278" class="line" lang="perl">         <span class="nv" style="color: #008080;">$master</span><span class="p">{</span><span class="nv" style="color: #008080;">$key</span><span class="p">}</span><span class="o" style="font-weight: 600;">.=</span><span class="nv" style="color: #008080;">$load</span><span class="p">;</span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="250" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="279" 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">
279
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC279" class="line" lang="perl"> <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="250" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="280" 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">
280
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC280" class="line" lang="perl"><span class="p">}</span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="250" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="281" 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">
281
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC281" class="line" lang="perl"><span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$key</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">keys</span> <span class="nv" style="color: #008080;">%master</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$tofiles</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">-1</span><span class="p">"){</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="283" 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">
283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="perl">         <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$FHOUT</span><span class="p">,"</span><span class="s2" style="color: #d14;">></span><span class="si" style="color: #d14;">$key</span><span class="p">");</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="250" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="284" 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">
284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="perl">         <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: #008080;">$FHOUT</span> <span class="nv" style="color: #008080;">$master</span><span class="p">{</span><span class="nv" style="color: #008080;">$key</span><span class="p">};</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="250" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="285" 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">
285
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC285" class="line" lang="perl">         <span class="nb" style="color: #0086b3;">close</span><span class="p">(</span><span class="nv" style="color: #008080;">$FHOUT</span><span class="p">);</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="250" 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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<td class="new_line diff-line-num new" data-linenumber="286" 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">
286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="250" 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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<td class="new_line diff-line-num new" data-linenumber="287" 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="LC287" class="line" lang="perl">         <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: #008080;">$master</span><span class="p">{</span><span class="nv" style="color: #008080;">$key</span><span class="p">};</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="250" 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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<td class="new_line diff-line-num new" data-linenumber="288" 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">
288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="perl"> <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="250" 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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<td class="new_line diff-line-num new" data-linenumber="289" 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">
289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="perl"><span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="250" 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">
250
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<td class="new_line diff-line-num" data-linenumber="290" 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">
290
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
251
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<td class="new_line diff-line-num old" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[STDERR] (</span><span class="si" style="color: #d14;">$fastai</span><span class="s2" style="color: #d14;">/</span><span class="si" style="color: #d14;">$numOfFastas</span><span class="s2" style="color: #d14;">) : </span><span class="p">";</span><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$basename</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Done reading </span><span class="si" style="color: #d14;">$basename</span><span class="s2" style="color: #d14;">. </span><span class="p">"}</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Start reading the fasta file </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nv" style="color: #008080;">$ARGV_copy</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">])</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC252" class="line" lang="perl"> <span class="nv" style="color: #008080;">$fastai</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="253" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="291" 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">
291
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC291" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">worker</span> <span class="p">{</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="253" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="292" 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">
292
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC292" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">local</span> <span class="nv" style="color: #008080;">$SIG</span><span class="p">{</span><span class="nv" style="color: #008080;">KILL</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">sub </span><span class="p">{</span> <span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nb" style="color: #0086b3;">exit</span> <span class="p">};</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="253" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="293" 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">
293
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC293" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$tid</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">tid</span><span class="p">();</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="253" 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">
253
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<td class="new_line diff-line-num" data-linenumber="294" 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">
294
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC294" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
254
</td>
<td class="new_line diff-line-num old" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC254" class="line" lang="perl"> <span class="nv" style="color: #008080;">$basename</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$ARGV_copy</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">];</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
255
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<td class="new_line diff-line-num old" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC255" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$basename</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/\/([^\/]+)$/</span><span class="p">){</span></span>
</pre>
</td>
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256
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<td class="new_line diff-line-num old" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC256" class="line" lang="perl">         <span class="nv" style="color: #008080;">$basename</span><span class="o" style="font-weight: 600;">=</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
257
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<td class="new_line diff-line-num old" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC257" class="line" lang="perl"> <span class="p">}</span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="258" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="295" 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">
295
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC295" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@genefound</span><span class="p">;</span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="258" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="296" 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">
296
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC296" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">%cache</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="258" 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">
258
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<td class="new_line diff-line-num" data-linenumber="297" 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">
297
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC297" class="line" lang="perl"></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
259
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<td class="new_line diff-line-num old" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC259" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$FH</span><span class="p">,'</span><span class="s1" style="color: #d14;"><</span><span class="p">',</span><span class="nv" style="color: #008080;">$ARGV_copy</span><span class="p">[</span><span class="nv" style="color: #008080;">$v</span><span class="p">]);</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
260
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<td class="new_line diff-line-num old" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC260" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$geneprintswitch</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
</td>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
261
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<td class="new_line diff-line-num old" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC261" class="line" lang="perl"> </span>
</pre>
</td>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
262
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<td class="new_line diff-line-num old" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC262" class="line" lang="perl"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="o" style="font-weight: 600;"><</span><span class="nv" style="color: #008080;">$FH</span><span class="o" style="font-weight: 600;">></span><span class="p">){</span></span>
</pre>
</td>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
263
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<td class="new_line diff-line-num old" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC263" class="line" lang="perl">         <span class="vg" style="color: #008080;">$_</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/[\r\n]+$//</span><span class="p">;</span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="264" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="298" 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">
298
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC298" class="line" lang="perl"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$job</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$QUEUE</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">dequeue</span><span class="p">()){</span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="264" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="299" 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">
299
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC299" class="line" lang="perl">         </span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="264" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="300" 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">
300
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC300" class="line" lang="perl">         <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$cur_gene_filename</span><span class="o" style="font-weight: 600;">=</span><span class="p">"";</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="264" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="301" 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">
301
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC301" class="line" lang="perl">         <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">%cur_gene_firsttime</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="264" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="302" 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">
302
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC302" class="line" lang="perl">         <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$cur_gene</span><span class="o" style="font-weight: 600;">=</span><span class="p">"";</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="264" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="303" 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">
303
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC303" class="line" lang="perl">         <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$basename</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">basename</span><span class="p">(</span><span class="nv" style="color: #008080;">$job</span><span class="p">);</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="264" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="304" 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">
304
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC304" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="264" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="305" 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">
305
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC305" class="line" lang="perl">         <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[proteinortho_grab_proteins.pl] Start processing the fasta file </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nv" style="color: #008080;">$job</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> (tid=</span><span class="si" style="color: #d14;">$tid</span><span class="s2" style="color: #d14;">)</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
</pre>
</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="264" 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">
264
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<td class="new_line diff-line-num" data-linenumber="306" 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">
306
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC306" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
265
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<td class="new_line diff-line-num old" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC265" class="line" lang="perl">         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="vg" style="color: #008080;">$_</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">""</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">length</span> <span class="vg" style="color: #008080;">$_</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="vg" style="color: #008080;">$_</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">#</span><span class="p">"){</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="266" 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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<td class="new_line diff-line-num new" data-linenumber="307" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC307" class="line" lang="perl">         <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$FH</span><span class="p">,'</span><span class="s1" style="color: #d14;"><</span><span class="p">',</span><span class="nv" style="color: #008080;">$job</span><span class="p">);</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="266" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="308" 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">
308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="perl">         <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$geneprintswitch</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="266" 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">
266
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<td class="new_line diff-line-num" data-linenumber="309" 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">
309
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="perl">         </span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
267
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<td class="new_line diff-line-num old" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="perl">         <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$curLine</span><span class="o" style="font-weight: 600;">=</span><span class="vg" style="color: #008080;">$_</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
268
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<td class="new_line diff-line-num old" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC268" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
269
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<td class="new_line diff-line-num old" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC269" class="line" lang="perl">         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$curLine</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="nv" style="color: #008080;">$prefix</span> <span class="p">){</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
270
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<td class="new_line diff-line-num old" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC270" class="line" lang="perl">                 <span class="nv" style="color: #008080;">$geneprintswitch</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
271
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<td class="new_line diff-line-num old" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC271" class="line" lang="perl"></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
272
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<td class="new_line diff-line-num old" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC272" class="line" lang="perl">                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$cur_gene</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
273
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<td class="new_line diff-line-num old" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC273" class="line" lang="perl">                         <span class="nv" style="color: #008080;">$cur_gene_filename</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/\\b//g</span><span class="p">;</span></span>
</pre>
</td>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
274
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<td class="new_line diff-line-num old" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC274" class="line" lang="perl">                         <span class="nv" style="color: #008080;">$cur_gene_filename</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/[^a-zA-Z0-9.]//g</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
275
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<td class="new_line diff-line-num old" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC275" class="line" lang="perl">                         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$tofiles</span><span class="p">){</span> <span class="c1" style="color: #998; font-style: italic;"># print to files</span></span>
</pre>
</td>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
276
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<td class="new_line diff-line-num old" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC276" class="line" lang="perl">                                 <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$writemodus</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;">>></span><span class="p">";</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
277
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<td class="new_line diff-line-num old" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC277" class="line" lang="perl">                                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nb" style="color: #0086b3;">exists</span> <span class="nv" style="color: #008080;">$cur_gene_firsttime</span><span class="p">{</span><span class="nv" style="color: #008080;">$cur_gene_filename</span><span class="p">}){</span><span class="nv" style="color: #008080;">$writemodus</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;">></span><span class="p">";</span><span class="nv" style="color: #008080;">$cur_gene_firsttime</span><span class="p">{</span><span class="nv" style="color: #008080;">$cur_gene_filename</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>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC278" class="line" lang="perl">                                 <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="nv" style="color: #008080;">$FHOUT</span><span class="p">,</span><span class="nv" style="color: #008080;">$writemodus</span><span class="p">,</span><span class="nv" style="color: #008080;">$cur_gene_filename</span><span class="p">);</span></span>
</pre>
</td>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="perl">                                 <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: #008080;">$FHOUT</span> <span class="nv" style="color: #008080;">$cur_gene</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
280
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<td class="new_line diff-line-num old" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC280" class="line" lang="perl">                                 <span class="nb" style="color: #0086b3;">close</span><span class="p">(</span><span class="nv" style="color: #008080;">$FHOUT</span><span class="p">);</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC281" class="line" lang="perl">                         <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
282
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<td class="new_line diff-line-num old" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC282" class="line" lang="perl">                                 <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: #008080;">$cur_gene</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
283
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<td class="new_line diff-line-num old" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC283" class="line" lang="perl">                         <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
284
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<td class="new_line diff-line-num old" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC284" class="line" lang="perl">                         <span class="nv" style="color: #008080;">$cur_gene</span><span class="o" style="font-weight: 600;">=</span><span class="p">"";</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
285
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<td class="new_line diff-line-num old" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC285" class="line" lang="perl">                 <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="286" 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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<td class="new_line diff-line-num new" data-linenumber="310" 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">
310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="perl">         <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="o" style="font-weight: 600;"><</span><span class="nv" style="color: #008080;">$FH</span><span class="o" style="font-weight: 600;">></span><span class="p">){</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="286" 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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<td class="new_line diff-line-num new" data-linenumber="311" 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">
311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="perl">                 <span class="vg" style="color: #008080;">$_</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/[\r\n]+$//</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="286" 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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<td class="new_line diff-line-num new" data-linenumber="312" 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">
312
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC312" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="286" 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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<td class="new_line diff-line-num new" data-linenumber="313" 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">
313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="perl">                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="vg" style="color: #008080;">$_</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">""</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">length</span> <span class="vg" style="color: #008080;">$_</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="vg" style="color: #008080;">$_</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">#</span><span class="p">"){</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="286" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="314" 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">
314
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC314" class="line" lang="perl">                 </span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="286" 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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<td class="new_line diff-line-num new" data-linenumber="315" 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">
315
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC315" class="line" lang="perl">                 <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$curLine</span><span class="o" style="font-weight: 600;">=</span><span class="vg" style="color: #008080;">$_</span><span class="p">;</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="286" 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">
286
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<td class="new_line diff-line-num" data-linenumber="316" 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">
316
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC316" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
287
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<td class="new_line diff-line-num old" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC287" class="line" lang="perl">                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;"><span class="idiff left">$exact</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">exists</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$qdata</span></span><span class="p"><span class="idiff">{</span></span><span class="nv" style="color: #008080;"><span class="idiff">$basename</span></span><span class="p"><span class="idiff right">}</span>){</span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="288" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="317" 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">
317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="perl">                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">substr</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$curLine</span></span><span class="p"><span class="idiff">,</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">eq</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$prefix</span></span><span class="idiff right"> </span><span class="p">){</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="288" 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">
288
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<td class="new_line diff-line-num" data-linenumber="318" 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">
318
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC318" class="line" lang="perl"></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
289
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<td class="new_line diff-line-num old" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC289" class="line" lang="perl">                         <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$genename</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$curLine</span><span class="p">;</span></span>
</pre>
</td>
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<td class="new_line diff-line-num old" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="perl">                         <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@arr</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="s2" style="color: #d14;"> </span><span class="p">",</span><span class="nv" style="color: #008080;">$genename</span><span class="p">);</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
291
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<td class="new_line diff-line-num old" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="perl">                         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: #008080;">@arr</span><span class="p">)</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">){</span><span class="nv" style="color: #008080;">$genename</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$arr</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];}</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
292
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<td class="new_line diff-line-num old" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="perl">                         <span class="nv" style="color: #008080;">$genename</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/^>//</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="293" 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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<td class="new_line diff-line-num new" data-linenumber="319" 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">
319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="perl">                         <span class="nv" style="color: #008080;">$geneprintswitch</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="293" 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">
293
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<td class="new_line diff-line-num" data-linenumber="320" 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="LC320" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="perl">                         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">exists</span> <span class="nv" style="color: #008080;">$qdata</span><span class="p">{</span><span class="nv" style="color: #008080;">$basename</span><span class="p">}{</span><span class="nv" style="color: #008080;">$genename</span><span class="p">}){</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="295" 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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<td class="new_line diff-line-num new" data-linenumber="321" 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="LC321" class="line" lang="perl">                         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$cur_gene</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="295" 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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<td class="new_line diff-line-num new" data-linenumber="322" 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="LC322" class="line" lang="perl">                                 <span class="nv" style="color: #008080;">$cur_gene_filename</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/\\b//g</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="295" 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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<td class="new_line diff-line-num new" data-linenumber="323" 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="LC323" class="line" lang="perl">                                 <span class="nv" style="color: #008080;">$cur_gene_filename</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/[^a-zA-Z0-9.]//g</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="295" 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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<td class="new_line diff-line-num" data-linenumber="324" 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="LC324" class="line" lang="perl">                                 </span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="perl">                                 <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$headerstr</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$curLine</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="perl">                                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$source</span><span class="p">){</span><span class="nv" style="color: #008080;">$headerstr</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$headerstr</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$basename</span><span class="p">;}</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="298" 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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<td class="new_line diff-line-num new" data-linenumber="325" 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">
325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="perl">                                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nb" style="color: #0086b3;">exists</span> <span class="nv" style="color: #008080;">$cache</span><span class="p">{(</span><span class="nv" style="color: #008080;">$tofiles</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">-1</span><span class="p">"</span> <span class="p">?</span> <span class="nv" style="color: #008080;">$tofiles</span> <span class="p">:</span> <span class="p">""</span> <span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$cur_gene_filename</span><span class="p">}){</span><span class="nv" style="color: #008080;">$cache</span><span class="p">{(</span><span class="nv" style="color: #008080;">$tofiles</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">-1</span><span class="p">"</span> <span class="p">?</span> <span class="nv" style="color: #008080;">$tofiles</span> <span class="p">:</span> <span class="p">""</span> <span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$cur_gene_filename</span><span class="p">}</span><span class="o" style="font-weight: 600;">=</span><span class="p">""}</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="298" 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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<td class="new_line diff-line-num new" data-linenumber="326" 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">
326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="perl">                                 <span class="nv" style="color: #008080;">$cache</span><span class="p">{(</span><span class="nv" style="color: #008080;">$tofiles</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">-1</span><span class="p">"</span> <span class="p">?</span> <span class="nv" style="color: #008080;">$tofiles</span> <span class="p">:</span> <span class="p">""</span> <span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$cur_gene_filename</span><span class="p">}</span> <span class="o" style="font-weight: 600;">.=</span> <span class="nv" style="color: #008080;">$cur_gene</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="298" 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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<td class="new_line diff-line-num new" data-linenumber="327" 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="LC327" class="line" lang="perl">                         </span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="298" 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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<td class="new_line diff-line-num new" data-linenumber="328" 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="LC328" class="line" lang="perl">                                 <span class="nv" style="color: #008080;">$cur_gene</span><span class="o" style="font-weight: 600;">=</span><span class="p">"";</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="perl">                         <span class="p">}</span></span>
</pre>
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330
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="perl">                                 <span class="nv" style="color: #008080;">$cur_gene</span><span class="o" style="font-weight: 600;">.=</span><span class="nv" style="color: #008080;">$headerstr</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="perl">                                 <span class="nv" style="color: #008080;">$cur_gene_filename</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$qdata</span><span class="p">{</span><span class="nv" style="color: #008080;">$basename</span><span class="p">}{</span><span class="nv" style="color: #008080;">$genename</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.fasta</span><span class="p">";</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="perl">                                 <span class="nv" style="color: #008080;">$geneprintswitch</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="perl">                                 <span class="nv" style="color: #008080;">$genecounterfound</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="303" 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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<td class="new_line diff-line-num new" data-linenumber="331" 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">
331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="perl">                         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$exact</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">exists</span> <span class="nv" style="color: #008080;">$qdata</span><span class="p">{</span><span class="nv" style="color: #008080;">$basename</span><span class="p">}){</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="303" 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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<td class="new_line diff-line-num" data-linenumber="332" 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">
332
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="perl">                                 <span class="nb" style="color: #0086b3;">delete</span> <span class="nv" style="color: #008080;">$qdata</span><span class="p">{</span><span class="nv" style="color: #008080;">$basename</span><span class="p">}{</span><span class="nv" style="color: #008080;">$genename</span><span class="p">};</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="perl">                         <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="306" 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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<td class="new_line diff-line-num new" data-linenumber="333" 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">
333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="perl">                                 <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$genename</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$curLine</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="306" 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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<td class="new_line diff-line-num new" data-linenumber="334" 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">
334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="perl">                                 <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@arr</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">split</span><span class="p">("</span><span class="s2" style="color: #d14;"> </span><span class="p">",</span><span class="nv" style="color: #008080;">$genename</span><span class="p">);</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="306" 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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<td class="new_line diff-line-num new" data-linenumber="335" 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">
335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="perl">                                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: #008080;">@arr</span><span class="p">)</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">){</span><span class="nv" style="color: #008080;">$genename</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$arr</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];}</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="306" 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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<td class="new_line diff-line-num new" data-linenumber="336" 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">
336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="perl">                                 <span class="nv" style="color: #008080;">$genename</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/^>//</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="306" 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">
306
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<td class="new_line diff-line-num" data-linenumber="337" 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">
337
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC337" class="line" lang="perl"></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
307
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<td class="new_line diff-line-num old" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC307" class="line" lang="perl">                 <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;"># fallback, if the basename (filename) does not exists, try all </span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="308" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="338" 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">
338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="perl">                                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">exists</span> <span class="nv" style="color: #008080;">$qdata</span><span class="p">{</span><span class="nv" style="color: #008080;">$basename</span><span class="p">}{</span><span class="nv" style="color: #008080;">$genename</span><span class="p">}){</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="308" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="339" 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">
339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="perl">                                 </span>
</pre>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="perl">                                         <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$headerstr</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$curLine</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="perl">                                         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$source</span><span class="p">){</span><span class="nv" style="color: #008080;">$headerstr</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$headerstr</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$basename</span><span class="p">;}</span></span>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="perl"></span>
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="perl">                         <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$filename</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">keys</span> <span class="nv" style="color: #008080;">%qdata</span><span class="p">)</span> <span class="p">{</span> </span>
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="perl">                                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$geneprintswitch</span><span class="p">){</span><span class="k" style="font-weight: 600;">last</span><span class="p">;}</span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="perl">                                 <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$key</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">keys</span> <span class="nv" style="color: #008080;">%</span><span class="p">{</span><span class="nv" style="color: #008080;">$qdata</span><span class="p">{</span><span class="nv" style="color: #008080;">$filename</span><span class="p">}})</span> <span class="p">{</span> </span>
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="perl">                                         <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$regexv</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$key</span><span class="p">;</span> </span>
</pre>
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="perl">                                         <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$curLine_test</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$curLine</span><span class="p">;</span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="perl">                                         </span>
</pre>
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="perl">                                         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$doregex</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$exact</span><span class="p">){</span><span class="nv" style="color: #008080;">$regexv</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">quotemeta</span><span class="p">(</span><span class="nv" style="color: #008080;">$regexv</span><span class="p">);}</span></span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="perl">                                         <span class="nv" style="color: #008080;">$cur_gene</span><span class="o" style="font-weight: 600;">.=</span><span class="nv" style="color: #008080;">$headerstr</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="perl">                                         <span class="nv" style="color: #008080;">$cur_gene_filename</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$qdata</span><span class="p">{</span><span class="nv" style="color: #008080;">$basename</span><span class="p">}{</span><span class="nv" style="color: #008080;">$genename</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.fasta</span><span class="p">";</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="316" 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="LC345" class="line" lang="perl">                                         <span class="nv" style="color: #008080;">$geneprintswitch</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="316" 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="LC346" class="line" lang="perl">                                         <span class="nb" style="color: #0086b3;">push</span><span class="p">(</span><span class="nv" style="color: #008080;">@genefound</span><span class="p">,</span><span class="nv" style="color: #008080;">$genename</span><span class="p">);</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="perl">                                 <span class="p">}</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="perl"></span>
</pre>
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="perl">                                         <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$test_match</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="perl">                                         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$exact</span> <span class="p">){</span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="perl">                                                 </span>
</pre>
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320
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="perl">                                                 <span class="c1" style="color: #998; font-style: italic;"># use regular expression</span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="perl">                                                 <span class="nv" style="color: #008080;">$test_match</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$curLine_test</span> <span class="o" style="font-weight: 600;">=~</span> <span class="nv" style="color: #008080;">$regexv</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="322" 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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<td class="new_line diff-line-num new" data-linenumber="349" 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="LC349" class="line" lang="perl">                         <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;"># fallback, if the basename (filename) does not exists, try all </span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="perl"></span>
</pre>
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="perl">                                         <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="perl">                                                 </span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="perl">                                                 <span class="c1" style="color: #998; font-style: italic;"># directly compare starting with first 5 character of fasta entry as offset</span></span>
</pre>
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<td class="new_line diff-line-num old" data-linenumber="351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="perl">                                                 <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># start at 1 -> fasta entries starts with ">"</span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="perl">                                                 <span class="k" style="font-weight: 600;">while</span><span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="p">(</span> <span class="nv" style="color: #008080;">$test_match</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$curLine</span><span class="p">,</span><span class="nv" style="color: #008080;">$offset</span><span class="p">,</span><span class="nb" style="color: #0086b3;">length</span> <span class="nv" style="color: #008080;">$key</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="nv" style="color: #008080;">$key</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$offset</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">5</span> <span class="p">){</span></span>
</pre>
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="perl">                                                         <span class="nv" style="color: #008080;">$offset</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="perl">                                                 <span class="p">}</span> </span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
330
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<td class="new_line diff-line-num old" data-linenumber="351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="perl">                                         <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="331" 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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<td class="new_line diff-line-num new" data-linenumber="351" 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">
351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="perl">                                 <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$filename</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">keys</span> <span class="nv" style="color: #008080;">%qdata</span><span class="p">)</span> <span class="p">{</span> </span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="331" 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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<td class="new_line diff-line-num new" data-linenumber="352" 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">
352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="perl">                                         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$geneprintswitch</span><span class="p">){</span><span class="k" style="font-weight: 600;">last</span><span class="p">;}</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="331" 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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<td class="new_line diff-line-num new" data-linenumber="353" 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">
353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="perl">                                         <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$key</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">keys</span> <span class="nv" style="color: #008080;">%</span><span class="p">{</span><span class="nv" style="color: #008080;">$qdata</span><span class="p">{</span><span class="nv" style="color: #008080;">$filename</span><span class="p">}})</span> <span class="p">{</span> </span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
331
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<td class="new_line diff-line-num" data-linenumber="354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
354
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="perl">                                         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="idiff left"> </span><span class="nv" style="color: #008080;"><span class="idiff">$test_match</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">){</span></span></span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="perl">                                         <span class="idiff left">       </span><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">defined</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$qdata</span></span><span class="p"><span class="idiff">{</span></span><span class="nv" style="color: #008080;"><span class="idiff">$filename</span></span><span class="p"><span class="idiff">}{</span></span><span class="nv" style="color: #008080;"><span class="idiff">$key</span></span><span class="p"><span class="idiff">}){</span></span><span class="k" style="font-weight: 600;"><span class="idiff">next</span></span><span class="p"><span class="idiff right">}</span></span></span>
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="perl"></span>
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<td class="new_line diff-line-num old" data-linenumber="357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="perl">                                                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$qdata</span><span class="p">{</span><span class="nv" style="color: #008080;">$filename</span><span class="p">}{</span><span class="nv" style="color: #008080;">$key</span><span class="p">}</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">""){</span></span>
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<td class="new_line diff-line-num old" data-linenumber="357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="perl">                                                         <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[STDERR] WARNING The input (</span><span class="si" style="color: #d14;">$key</span><span class="s2" style="color: #d14;">) was found multiple times in the fasta files </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$exact</span> <span class="p">?</span> <span class="p">"</span><span class="s2" style="color: #d14;">(maybe try --exact).</span><span class="p">"</span> <span class="p">:</span> <span class="p">"</span><span class="s2" style="color: #d14;">.</span><span class="p">")</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="perl">                                                 <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$regexv</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$key</span><span class="p">;</span> </span>
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="perl">                                                 <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$curLine_test</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$curLine</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="perl">                                                 </span>
</pre>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="perl">                                                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$doregex</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$exact</span><span class="p">){</span><span class="nv" style="color: #008080;">$regexv</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">quotemeta</span><span class="p">(</span><span class="nv" style="color: #008080;">$regexv</span><span class="p">);}</span></span>
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="perl"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="perl">                                                 <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$test_match</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="perl">                                                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$exact</span> <span class="p">){</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="perl">                                                         </span>
</pre>
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="perl">                                                         <span class="c1" style="color: #998; font-style: italic;"># use regular expression</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="perl">                                                         <span class="nv" style="color: #008080;">$test_match</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$curLine_test</span> <span class="o" style="font-weight: 600;">=~</span> <span class="nv" style="color: #008080;">$regexv</span><span class="p">;</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="perl"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="perl">                                                 <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="perl">                                                         </span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="perl">                                                         <span class="c1" style="color: #998; font-style: italic;"># directly compare starting with first 5 character of fasta entry as offset</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="perl">                                                         <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># start at 1 -> fasta entries starts with ">"</span></span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="perl">                                                         <span class="k" style="font-weight: 600;">while</span><span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="p">(</span> <span class="nv" style="color: #008080;">$test_match</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$curLine</span><span class="p">,</span><span class="nv" style="color: #008080;">$offset</span><span class="p">,</span><span class="nb" style="color: #0086b3;">length</span> <span class="nv" style="color: #008080;">$key</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="nv" style="color: #008080;">$key</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$offset</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">5</span> <span class="p">){</span></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="perl">                                                                 <span class="nv" style="color: #008080;">$offset</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="perl">                                                         <span class="p">}</span> </span>
</pre>
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336
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375
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="perl">                                                 <span class="p">}</span></span>
</pre>
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337
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376
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="perl"></span>
</pre>
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338
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="perl">                                                 <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$headerstr</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$curLine</span><span class="p">;</span></span>
</pre>
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339
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="perl">                                                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$source</span><span class="p">){</span><span class="nv" style="color: #008080;">$headerstr</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$headerstr</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$basename</span><span class="p">;}</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="perl">                                                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="nv" style="color: #008080;">$test_match</span> <span class="p">){</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="perl"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="perl">                                                         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="nv" style="color: #008080;">$qdata</span><span class="p">{</span><span class="nv" style="color: #008080;">$filename</span><span class="p">}{</span><span class="nv" style="color: #008080;">$key</span><span class="p">}</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">""){</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="perl">                                                                 <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[proteinortho_grab_proteins.pl] WARNING The input (</span><span class="si" style="color: #d14;">$key</span><span class="s2" style="color: #d14;">) was found multiple times in the fasta files </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$exact</span> <span class="p">?</span> <span class="p">"</span><span class="s2" style="color: #d14;">(maybe try --exact).</span><span class="p">"</span> <span class="p">:</span> <span class="p">"</span><span class="s2" style="color: #d14;">.</span><span class="p">")</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="381" 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">
381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="perl">                                                         <span class="p">}</span></span>
</pre>
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340
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<td class="new_line diff-line-num" data-linenumber="382" 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">
382
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="perl"></span>
</pre>
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341
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<td class="new_line diff-line-num old" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="perl">                                                 <span class="nv" style="color: #008080;">$cur_gene</span><span class="o" style="font-weight: 600;">.=</span><span class="nv" style="color: #008080;">$headerstr</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span>  </span>
</pre>
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="perl">                                                 <span class="nv" style="color: #008080;">$cur_gene_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$qdata</span><span class="p">{</span><span class="nv" style="color: #008080;">$filename</span><span class="p">}{</span><span class="nv" style="color: #008080;">$key</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.fasta</span><span class="p">";</span></span>
</pre>
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343
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<td class="new_line diff-line-num old" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="perl">                                                 <span class="nv" style="color: #008080;">$geneprintswitch</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
344
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<td class="new_line diff-line-num old" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="perl">                                                 <span class="nv" style="color: #008080;">$genecounterfound</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="345" 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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<td class="new_line diff-line-num new" data-linenumber="383" 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">
383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="perl">                                                         <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$headerstr</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$curLine</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="345" 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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<td class="new_line diff-line-num new" data-linenumber="384" 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">
384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="perl">                                                         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$source</span><span class="p">){</span><span class="nv" style="color: #008080;">$headerstr</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$headerstr</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$basename</span><span class="p">;}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="345" 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">
345
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<td class="new_line diff-line-num" data-linenumber="385" 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">
385
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="346" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
346
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<td class="new_line diff-line-num old" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="perl">                                                 <span class="nb" style="color: #0086b3;">delete</span> <span class="nv" style="color: #008080;">$qdata</span><span class="p">{</span><span class="nv" style="color: #008080;">$filename</span><span class="p">}{</span><span class="nv" style="color: #008080;">$key</span><span class="p">};</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="347" 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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<td class="new_line diff-line-num new" data-linenumber="386" 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">
386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="perl">                                                         <span class="nv" style="color: #008080;">$cur_gene</span><span class="o" style="font-weight: 600;">.=</span><span class="nv" style="color: #008080;">$headerstr</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span>  </span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="347" 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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<td class="new_line diff-line-num new" data-linenumber="387" 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">
387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="perl">                                                         <span class="nv" style="color: #008080;">$cur_gene_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$qdata</span><span class="p">{</span><span class="nv" style="color: #008080;">$filename</span><span class="p">}{</span><span class="nv" style="color: #008080;">$key</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.fasta</span><span class="p">";</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="347" 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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<td class="new_line diff-line-num new" data-linenumber="388" 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">
388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="perl">                                                         <span class="nv" style="color: #008080;">$geneprintswitch</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="347" 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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<td class="new_line diff-line-num new" data-linenumber="389" 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">
389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="perl">                                                         <span class="nb" style="color: #0086b3;">push</span><span class="p">(</span><span class="nv" style="color: #008080;">@genefound</span><span class="p">,</span><span class="nv" style="color: #008080;">$key</span><span class="p">);</span></span>
</pre>
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347
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<td class="new_line diff-line-num" data-linenumber="390" 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">
390
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC390" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
348
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<td class="new_line diff-line-num old" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC348" class="line" lang="perl">                                                 <span class="k" style="font-weight: 600;">last</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="349" 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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<td class="new_line diff-line-num new" data-linenumber="391" 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">
391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="perl">                                                         <span class="k" style="font-weight: 600;">last</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="349" 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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<td class="new_line diff-line-num new" data-linenumber="392" 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">
392
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC392" class="line" lang="perl">                                                 <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="349" 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">
349
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<td class="new_line diff-line-num" data-linenumber="393" 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">
393
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC393" class="line" lang="perl">                                         <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="350" 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">
350
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<td class="new_line diff-line-num" data-linenumber="394" 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">
394
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC394" class="line" lang="perl">                                 <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
351
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<td class="new_line diff-line-num old" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC351" class="line" lang="perl">                         <span class="p">}</span>  </span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
352
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<td class="new_line diff-line-num old" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC352" class="line" lang="perl">                 <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="353" 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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<td class="new_line diff-line-num new" data-linenumber="395" 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">
395
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC395" class="line" lang="perl">                         <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="353" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="396" 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">
396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="perl">                 <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$geneprintswitch</span><span class="p">){</span> <span class="nv" style="color: #008080;">$cur_gene</span><span class="o" style="font-weight: 600;">.=</span><span class="nv" style="color: #008080;">$curLine</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">"</span> <span class="p">}</span> <span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="353" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="397" 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">
397
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC397" class="line" lang="perl">         <span class="p">}</span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="353" 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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<td class="new_line diff-line-num new" data-linenumber="398" 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">
398
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC398" class="line" lang="perl">         <span class="nb" style="color: #0086b3;">close</span><span class="p">(</span><span class="nv" style="color: #008080;">$FH</span><span class="p">);</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="353" 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">
353
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<td class="new_line diff-line-num" data-linenumber="399" 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">
399
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC399" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
354
</td>
<td class="new_line diff-line-num old" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC354" class="line" lang="perl">         <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
355
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<td class="new_line diff-line-num old" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC355" class="line" lang="perl">                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$geneprintswitch</span><span class="p">){</span></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
356
</td>
<td class="new_line diff-line-num old" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC356" class="line" lang="perl">                         <span class="nv" style="color: #008080;">$cur_gene</span><span class="o" style="font-weight: 600;">.=</span><span class="nv" style="color: #008080;">$curLine</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
357
</td>
<td class="new_line diff-line-num old" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC357" class="line" lang="perl">                 <span class="p">}</span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="358" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="400" 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">
400
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC400" class="line" lang="perl">         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$cur_gene</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="358" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="401" 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">
401
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC401" class="line" lang="perl">                 <span class="nv" style="color: #008080;">$cur_gene_filename</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/\\b//g</span><span class="p">;</span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="358" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="402" 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">
402
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC402" class="line" lang="perl">                 <span class="nv" style="color: #008080;">$cur_gene_filename</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/[^a-zA-Z0-9.]//g</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="358" 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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<td class="new_line diff-line-num new" data-linenumber="403" 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">
403
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC403" class="line" lang="perl"></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="358" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="404" 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">
404
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC404" class="line" lang="perl">                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nb" style="color: #0086b3;">exists</span> <span class="nv" style="color: #008080;">$cache</span><span class="p">{(</span><span class="nv" style="color: #008080;">$tofiles</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">-1</span><span class="p">"</span> <span class="p">?</span> <span class="nv" style="color: #008080;">$tofiles</span> <span class="p">:</span> <span class="p">""</span> <span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$cur_gene_filename</span><span class="p">}){</span><span class="nv" style="color: #008080;">$cache</span><span class="p">{(</span><span class="nv" style="color: #008080;">$tofiles</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">-1</span><span class="p">"</span> <span class="p">?</span> <span class="nv" style="color: #008080;">$tofiles</span> <span class="p">:</span> <span class="p">""</span> <span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$cur_gene_filename</span><span class="p">}</span><span class="o" style="font-weight: 600;">=</span><span class="p">""}</span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="358" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="405" 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">
405
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC405" class="line" lang="perl">                 <span class="nv" style="color: #008080;">$cache</span><span class="p">{(</span><span class="nv" style="color: #008080;">$tofiles</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">-1</span><span class="p">"</span> <span class="p">?</span> <span class="nv" style="color: #008080;">$tofiles</span> <span class="p">:</span> <span class="p">""</span> <span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$cur_gene_filename</span><span class="p">}</span> <span class="o" style="font-weight: 600;">.=</span> <span class="nv" style="color: #008080;">$cur_gene</span><span class="p">;</span></span>
</pre>
</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="358" 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">
358
</td>
<td class="new_line diff-line-num" data-linenumber="406" 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">
406
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC406" class="line" lang="perl">         <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="359" 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">
359
</td>
<td class="new_line diff-line-num" data-linenumber="407" 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">
407
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC407" class="line" lang="perl"> <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
360
</td>
<td class="new_line diff-line-num old" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC360" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">close</span><span class="p">(</span><span class="nv" style="color: #008080;">$FH</span><span class="p">);</span></span>
</pre>
</td>
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<td class="old_line diff-line-num old" data-linenumber="361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
361
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<td class="new_line diff-line-num old" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC361" class="line" lang="perl"><span class="p">}</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="362" 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">
362
</td>
<td class="new_line diff-line-num" data-linenumber="408" 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">
408
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC408" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
363
</td>
<td class="new_line diff-line-num old" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC363" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$cur_gene</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>
</pre>
</td>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
364
</td>
<td class="new_line diff-line-num old" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC364" class="line" lang="perl"> <span class="nv" style="color: #008080;">$cur_gene_filename</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/\\b//g</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
365
</td>
<td class="new_line diff-line-num old" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC365" class="line" lang="perl"> <span class="nv" style="color: #008080;">$cur_gene_filename</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/[^a-zA-Z0-9.]//g</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
366
</td>
<td class="new_line diff-line-num old" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC366" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$tofiles</span><span class="p">){</span> <span class="c1" style="color: #998; font-style: italic;"># print to files</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
367
</td>
<td class="new_line diff-line-num old" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC367" class="line" lang="perl">         <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$writemodus</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;">>></span><span class="p">";</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
368
</td>
<td class="new_line diff-line-num old" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC368" class="line" lang="perl">         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nb" style="color: #0086b3;">exists</span> <span class="nv" style="color: #008080;">$cur_gene_firsttime</span><span class="p">{</span><span class="nv" style="color: #008080;">$cur_gene_filename</span><span class="p">}){</span><span class="nv" style="color: #008080;">$writemodus</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;">></span><span class="p">";</span><span class="nv" style="color: #008080;">$cur_gene_firsttime</span><span class="p">{</span><span class="nv" style="color: #008080;">$cur_gene_filename</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>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
369
</td>
<td class="new_line diff-line-num old" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC369" class="line" lang="perl">         <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="nv" style="color: #008080;">$FHOUT</span><span class="p">,</span><span class="nv" style="color: #008080;">$writemodus</span><span class="p">,</span><span class="nv" style="color: #008080;">$cur_gene_filename</span><span class="p">);</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
370
</td>
<td class="new_line diff-line-num old" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC370" class="line" lang="perl">         <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: #008080;">$FHOUT</span> <span class="nv" style="color: #008080;">$cur_gene</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
371
</td>
<td class="new_line diff-line-num old" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC371" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
372
</td>
<td class="new_line diff-line-num old" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC372" class="line" lang="perl">         <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: #008080;">$cur_gene</span><span class="p">;</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
373
</td>
<td class="new_line diff-line-num old" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC373" class="line" lang="perl"> <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
374
</td>
<td class="new_line diff-line-num old" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC374" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">close</span><span class="p">(</span><span class="nv" style="color: #008080;">$FHOUT</span><span class="p">);</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="375" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="409" 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">
409
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC409" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$ret</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">join</span><span class="p">("</span><span class="s2" style="color: #d14;">$;</span><span class="p">",</span><span class="nv" style="color: #008080;">@genefound</span><span class="p">);</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="375" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="410" 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">
410
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC410" class="line" lang="perl"> <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$key</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">keys</span> <span class="nv" style="color: #008080;">%cache</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: #008080;">$ret</span><span class="o" style="font-weight: 600;">.=</span><span class="p">"</span><span class="s2" style="color: #d14;">$;$;</span><span class="si" style="color: #d14;">$key</span><span class="s2" style="color: #d14;">$;</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$cache</span><span class="p">{</span><span class="nv" style="color: #008080;">$key</span><span class="p">}</span> <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="375" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="411" 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">
411
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC411" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="375" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="412" 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">
412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="perl"> <span class="nv" style="color: #008080;">$thread_return</span><span class="p">[</span><span class="nv" style="color: #008080;">$tid</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$ret</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="375" 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">
375
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<td class="new_line diff-line-num" data-linenumber="413" 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">
413
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC413" class="line" lang="perl"><span class="p">}</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="376" 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">
376
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<td class="new_line diff-line-num" data-linenumber="414" 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">
414
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC414" class="line" lang="perl"></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="377" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="415" 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">
415
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC415" class="line" lang="perl"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="377" 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">
377
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<td class="new_line diff-line-num" data-linenumber="416" 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">
416
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<pre style="margin: 0;"> <span id="LC416" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$genecounter</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nv" style="color: #008080;">$genecounterfound</span><span class="p">){</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
378
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<td class="new_line diff-line-num old" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC378" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[STDERR] WARNING The input (</span><span class="si" style="color: #d14;">$query</span><span class="s2" style="color: #d14;">) contains </span><span class="si" style="color: #d14;">$genecounter</span><span class="s2" style="color: #d14;"> queries, but I extracted </span><span class="si" style="color: #d14;">$genecounterfound</span><span class="s2" style="color: #d14;"> entries out of the fasta(s).</span><span class="p">";</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
379
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<td class="new_line diff-line-num old" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC379" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$exact</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;"> If this is not desired, please consider using the -exact option</span><span class="p">";}</span><span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$genecounter</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$genecounterfound</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">-> This should not have happen, maybe some fasta files are missing as input?</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">(If you cannot solve this error, please send a report to incoming+paulklemm-phd-proteinortho-7278443-issue-</span><span class="se" style="color: #d14;">\@</span><span class="s2" style="color: #d14;">incoming.gitlab.com or visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Codes for more help. Further more all mails to lechner</span><span class="se" style="color: #d14;">\@</span><span class="s2" style="color: #d14;">staff.uni-marburg.de are welcome)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>
</pre>
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380
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<td class="new_line diff-line-num old" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC380" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="381" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="417" 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">
417
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC417" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[proteinortho_grab_proteins.pl] WARNING The input (</span><span class="si" style="color: #d14;">$query</span><span class="s2" style="color: #d14;">) contains </span><span class="si" style="color: #d14;">$genecounter</span><span class="s2" style="color: #d14;"> queries, but I extracted </span><span class="si" style="color: #d14;">$genecounterfound</span><span class="s2" style="color: #d14;"> entries out of the fasta(s).</span><span class="p">";</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="381" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="418" 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">
418
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC418" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$exact</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;"> If this is not desired, please consider using the -exact option</span><span class="p">";}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="381" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="419" 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">
419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#elsif($genecounter > $genecounterfound){print STDERR "\n-> This should not have happen, maybe some fasta files are missing as input?\n(If you cannot solve this error, please send a report to incoming+paulklemm-phd-proteinortho-7278443-issue-\@incoming.gitlab.com or visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Codes for more help. Further more all mails to lechner\@staff.uni-marburg.de are welcome)\n";}</span></span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="381" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="420" 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">
420
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC420" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n\n</span><span class="p">";</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="381" 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">
381
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<td class="new_line diff-line-num" data-linenumber="421" 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">
421
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC421" class="line" lang="perl"></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="382" 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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<td class="new_line diff-line-num" data-linenumber="422" 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">
422
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC422" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$genecounterfound</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: #008080;">$genecounter</span><span class="p">){</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="383" 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">
383
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<td class="new_line diff-line-num" data-linenumber="423" 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">
423
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC423" class="line" lang="perl">         <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">The following ids were not found:</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
</pre>
</td>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="387" 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="427" 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">@@ -387,11 +427,27 @@ if($genecounter != $genecounterfound){</td>
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387
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<td class="new_line diff-line-num" data-linenumber="427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
427
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC427" class="line" lang="perl">                         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">10</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: #008080;">$counter</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span><span class="k" style="font-weight: 600;">last</span><span class="p">}</span></span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="388" 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">
388
</td>
<td class="new_line diff-line-num" data-linenumber="428" 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">
428
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC428" class="line" lang="perl">                         <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="nv" style="color: #008080;">$key</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span> </span>
</pre>
</td>
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<td class="old_line diff-line-num" data-linenumber="389" 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">
389
</td>
<td class="new_line diff-line-num" data-linenumber="429" 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">
429
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC429" class="line" lang="perl">                 <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
390
</td>
<td class="new_line diff-line-num old" data-linenumber="430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC390" class="line" lang="perl">                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">10</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: #008080;">$counter</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;"> ...</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="k" style="font-weight: 600;">last</span><span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="391" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="430" 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">
430
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC430" class="line" lang="perl">                 <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">10</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: #008080;">$counter</span><span class="p">){</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="391" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="431" 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">
431
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC431" class="line" lang="perl">                         <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;"> ...</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span>              </span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="391" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="432" 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">
432
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC432" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="391" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="433" 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">
433
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC433" class="line" lang="perl">                         <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="nv" style="color: #008080;">FH</span><span class="p">,"</span><span class="s2" style="color: #d14;">>missing_ids.txt</span><span class="p">");</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="391" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="434" 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">
434
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC434" class="line" lang="perl">                         <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$filenamee</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">keys</span> <span class="nv" style="color: #008080;">%qdata</span><span class="p">)</span> <span class="p">{</span> </span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="391" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="435" 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">
435
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC435" class="line" lang="perl">                                 <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$keyy</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">keys</span> <span class="nv" style="color: #008080;">%</span><span class="p">{</span><span class="nv" style="color: #008080;">$qdata</span><span class="p">{</span><span class="nv" style="color: #008080;">$filenamee</span><span class="p">}})</span> <span class="p">{</span> </span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="391" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="436" 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">
436
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC436" class="line" lang="perl">                                         <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nb" style="color: #0086b3;">exists</span> <span class="nv" style="color: #008080;">$genefound</span><span class="p">{</span><span class="nv" style="color: #008080;">$keyy</span><span class="p">}){</span> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: #008080;">FH</span> <span class="p">"</span><span class="si" style="color: #d14;">$keyy</span><span class="se" style="color: #d14;">\n</span><span class="p">"</span> <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="391" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="437" 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">
437
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC437" class="line" lang="perl">                                 <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="391" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="438" 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">
438
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC438" class="line" lang="perl">                         <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="391" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="439" 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">
439
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC439" class="line" lang="perl">                         <span class="nb" style="color: #0086b3;">close</span><span class="p">(</span><span class="nv" style="color: #008080;">FH</span><span class="p">);</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="391" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="440" 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">
440
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC440" class="line" lang="perl">                         <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">I produced a file containing all missing ids in the current working directory (missing_ids.txt)</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="391" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="441" 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">
441
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC441" class="line" lang="perl"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="391" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="442" 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">
442
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC442" class="line" lang="perl">                         <span class="k" style="font-weight: 600;">last</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="391" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="443" 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">
443
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC443" class="line" lang="perl">                 <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="391" 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">
391
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<td class="new_line diff-line-num" data-linenumber="444" 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">
444
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC444" class="line" lang="perl">         <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
392
</td>
<td class="new_line diff-line-num old" data-linenumber="445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC392" class="line" lang="perl">         <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Please make sure that the upper ids are part of the given fasta files (try searching these in the given fasta files) !</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="393" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="445" 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">
445
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC445" class="line" lang="perl">         <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Please make sure that those ids are part of the given fasta files (try searching these in the given fasta files) !</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="393" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="446" 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">
446
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC446" class="line" lang="perl"> <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="393" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="447" 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">
447
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC447" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$genecounterfound</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="393" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="448" 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">
448
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC448" class="line" lang="perl">         <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">If you used the --isoform option in proteinortho, then please set -isoform here too (no need to specify the isoform type, e.g. uniprot)!</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
</pre>
</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="393" 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">
393
</td>
<td class="new_line diff-line-num" data-linenumber="449" 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">
449
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC449" class="line" lang="perl"> <span class="p">}</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="394" 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">
394
</td>
<td class="new_line diff-line-num" data-linenumber="450" 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">
450
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC450" class="line" lang="perl"> </span>
</pre>
</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="395" 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">
395
</td>
<td class="new_line diff-line-num" data-linenumber="451" 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">
451
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC451" class="line" lang="perl"><span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
396
</td>
<td class="new_line diff-line-num old" data-linenumber="452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
 
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC396" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[<span class="idiff left right">STDERR</span>] All entries of the query are found in the fasta(s).</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="397" 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">
 
</td>
<td class="new_line diff-line-num new" data-linenumber="452" 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">
452
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC452" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[<span class="idiff left right">proteinortho_grab_proteins.pl</span>] All entries of the query are found in the fasta(s).</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num" data-linenumber="397" 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">
397
</td>
<td class="new_line diff-line-num" data-linenumber="453" 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">
453
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC453" class="line" lang="perl"><span class="p">}</span></span></pre>
</td>
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