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<h3>
Shayan Doust pushed to branch master
at <a href="https://salsa.debian.org/med-team/mmseqs2">Debian Med / mmseqs2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mmseqs2/commit/c82d0645d6c8cfdec5940e169cd9045666bc7558">c82d0645</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2019-07-19T15:24:20Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Include-binaries to reflect on some pptx and images
These are used to generate the PDF documentation hence source
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mmseqs2/commit/18e82408e17a45a4653d0d1b49a98b7ee5299288">18e82408</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2019-07-19T17:32:30Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Split optional files into mmseqs2-examples.
Files will be installed under /usr/share/doc/mmseqs2 as these are informational
</pre>
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<h4>19 changed files:</h4>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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debian/missing-sources/userguide/images/cluster-cascaded-clustering-workflow.png
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debian/missing-sources/userguide/images/cluster-mode-connectedcomp.png
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debian/missing-sources/userguide/images/cluster-mode-greedyincremental.png
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debian/missing-sources/userguide/images/cluster-mode-setcover.png
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debian/missing-sources/userguide/images/cluster-updating-workflow.png
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debian/missing-sources/userguide/images/kclust-supp-fig2-spc-vs-seqid.jpg
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debian/missing-sources/userguide/images/linclust-algorithm.png
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debian/missing-sources/userguide/images/mmseqs2-logo.png
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debian/missing-sources/userguide/images/mmseqs2-prefilter.png
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debian/missing-sources/userguide/images/mmseqs2-search.png
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debian/missing-sources/userguide/images/mmseqs2-sense.png
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debian/missing-sources/userguide/images/taxonomy-2blca-protocol.pptx
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debian/missing-sources/userguide/userguide.pdf
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debian/mmseqs2-examples.install
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debian/mmseqs2.install
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debian/source/include-binaries
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<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/mmseqs2/compare/636cb533cd08114d7628f033ab4463c0b6626079...18e82408e17a45a4653d0d1b49a98b7ee5299288#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4" style="width: 35px; color: rgba(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">@@ -4,10 +4,10 @@ Uploaders: Shayan Doust <hello@shayandoust.me></td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 12~),</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"><span class="idiff left right"> </span> cmake,</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"><span class="idiff left right"> </span> libgzstream-dev,</span>
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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC9" class="line" lang="plaintext"><span class="idiff left right"> </span> libzstd-dev,</span>
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<td class="diff-line-num new_line old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC10" class="line" lang="plaintext"><span class="idiff left right"> </span> zlib1g-dev</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"><span class="idiff left right"> </span> cmake,</span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC8" class="line" lang="plaintext"><span class="idiff left right"> </span> libgzstream-dev,</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"><span class="idiff left right"> </span> libzstd-dev,</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"><span class="idiff left right"> </span> zlib1g-dev</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Standards-Version: 4.3.0</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/mmseqs2</span>
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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(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="LC13" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/mmseqs2.git</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="26" style="width: 35px; color: rgba(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="26" style="width: 35px; color: rgba(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">@@ -26,3 +26,17 @@ Description: ultra fast and sensitive protein search and clustering.</td>
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<td class="diff-line-num old_line" data-linenumber="26" style="width: 35px; color: rgba(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="LC26" class="line" lang="plaintext"> MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it</span>
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<td class="diff-line-num old_line" data-linenumber="27" style="width: 35px; color: rgba(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="diff-line-num new_line" data-linenumber="27" style="width: 35px; color: rgba(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="LC27" class="line" lang="plaintext"> achieves almost the same sensitivity. It can perform profile searches</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> with the same sensitivity as PSI-BLAST at over 400 times its speed.</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">Package: mmseqs2-examples</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">Depends: ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">Recommends: mmseqs2</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">Description: optional resources for the mmseqs2 package</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> MMseqs2 (Many-against-Many sequence searching) is a software suite to</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> search and cluster huge proteins/nucleotide sequence sets. MMseqs2 is</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> open source GPL-licensed software implemented in C++ for Linux, MacOS,</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> and (as beta version, via cygwim) Windows. The software is designed to</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> run on multiple cores and servers and exhibits very good scalability.</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> achieves almost the same sensitivity. It can perform profile searches</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> with the same sensitivity as PSI-BLAST at over 400 times its speed.</span></pre>
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<a href="https://salsa.debian.org/med-team/mmseqs2/compare/636cb533cd08114d7628f033ab4463c0b6626079...18e82408e17a45a4653d0d1b49a98b7ee5299288#eadd6558d4bb49d31369a6f04aa859cc0c646a1b"><strong>debian/missing-sources/userguide/images/cluster-cascaded-clustering-workflow.png</strong></a>
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<a href="https://salsa.debian.org/med-team/mmseqs2/compare/636cb533cd08114d7628f033ab4463c0b6626079...18e82408e17a45a4653d0d1b49a98b7ee5299288#28cd5a83b18f69c457a05d07f182af5e4f623afa"><strong>debian/mmseqs2-examples.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">examples</span><span class="o" style="font-weight: 600;">/*</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mmseqs2</span><span class="o" style="font-weight: 600;">/</span><span class="nx">example</span><span class="o" style="font-weight: 600;">-</span><span class="nx">data</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="nx">data</span><span class="o" style="font-weight: 600;">/*</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mmseqs2</span><span class="o" style="font-weight: 600;">/</span><span class="nx">example</span><span class="o" style="font-weight: 600;">-</span><span class="nx">data</span></span></pre>
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<a href="https://salsa.debian.org/med-team/mmseqs2/compare/636cb533cd08114d7628f033ab4463c0b6626079...18e82408e17a45a4653d0d1b49a98b7ee5299288#e6ea635754248ef19ddbf9613e6c62a5311ac353"><strong>debian/mmseqs2.install</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="php"><span class="nx">obj</span><span class="o" style="font-weight: 600;">-</span><span class="nx">x86_64</span><span class="o" style="font-weight: 600;">-</span><span class="nx">linux</span><span class="o" style="font-weight: 600;">-</span><span class="nx">gnu</span><span class="o" style="font-weight: 600;">/</span><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">test</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mmseqs2</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="php"><span class="nx">util</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bash</span><span class="o" style="font-weight: 600;">-</span><span class="nx">completion</span><span class="o" style="font-weight: 600;">.</span><span class="nx">sh</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mmseqs2</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="php"><span class="nx">README</span><span class="o" style="font-weight: 600;">.</span><span class="nx">md</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mmseqs2</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="php"><span class="nx"><span class="idiff left">examples</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/*</span></span><span class="idiff"> </span><span class="nx"><span class="idiff">usr</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nx"><span class="idiff">share</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nx"><span class="idiff">doc</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nx"><span class="idiff">mmseqs2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nx"><span class="idiff">example</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="nx"><span class="idiff right">data</span></span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="php"><span class="nx">d<span class="idiff left">ata</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/*</span></span><span class="idiff"> </span><span class="nx"><span class="idiff">usr</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nx"><span class="idiff">share</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nx"><span class="idiff">doc</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nx"><span class="idiff">mmseqs2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nx"><span class="idiff">example</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="nx"><span class="idiff right">data</span></span></span></pre>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="php"><span class="nx"><span class="idiff left">debian</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nx"><span class="idiff">missing</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="nx"><span class="idiff">sources</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nx"><span class="idiff">userguide</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nx"><span class="idiff">userguide</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nx"><span class="idiff">pdf</span></span><span class="idiff"> </span><span class="nx"><span class="idiff">usr</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nx"><span class="idiff">share</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nx"><span class="idiff">doc</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nx"><span class="idiff right">mmseqs2</span></span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"><span class="nx">d<span class="idiff left">ebian</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nx"><span class="idiff">tmp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nx"><span class="idiff">usr</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nx"><span class="idiff">bin</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nx"><span class="idiff">mmseqs</span></span><span class="idiff"> </span><span class="nx"><span class="idiff">usr</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nx"><span class="idiff right">bin</span></span></span></pre>
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<a href="https://salsa.debian.org/med-team/mmseqs2/compare/636cb533cd08114d7628f033ab4463c0b6626079...18e82408e17a45a4653d0d1b49a98b7ee5299288#d0b2adb0358f0eab7dd3bb1849dd4e795a81f242"><strong>debian/source/include-binaries</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/missing-sources/userguide/images/cluster-mode-connectedcomp.png</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/missing-sources/userguide/images/kclust-supp-fig2-spc-vs-seqid.jpg</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">debian/missing-sources/userguide/images/mmseqs2-sense.png</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">debian/missing-sources/userguide/images/search-workflow.png</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">debian/missing-sources/userguide/images/mmseqs2-prefilter.png</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">debian/missing-sources/userguide/images/cluster-cascaded-clustering-workflow.png</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">debian/missing-sources/userguide/images/cluster-updating-workflow.png</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">debian/missing-sources/userguide/images/cluster-mode-setcover.png</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">debian/missing-sources/userguide/images/taxonomy-2blca-protocol.png</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">debian/missing-sources/userguide/images/mmseqs2-search.png</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">debian/missing-sources/userguide/images/cluster-mode-greedyincremental.png</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">debian/missing-sources/userguide/images/mmseqs2-logo.png</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">debian/missing-sources/userguide/images/linclust-algorithm.png</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">debian/missing-sources/userguide/images/taxonomy-2blca-protocol.pptx</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">debian/missing-sources/userguide/userguide.pdf</span></pre>
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