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<h3 style="margin-top: 20px; margin-bottom: 10px;">
Andreas Tille pushed to branch upstream at <a href="https://salsa.debian.org/med-team/mmseqs2">Debian Med / mmseqs2</a>
</h3>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
Commits:
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<ul>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/mmseqs2/-/commit/5717b94c98c58af93a84e6fe6755431b0dc641c8">5717b94c</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2025-10-19T21:04:08+02:00 </i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 18-8cc5c+ds</pre>
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src/workflow/EasyCluster.cpp
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src/workflow/EasyLinclust.cpp
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src/workflow/EasyRbh.cpp
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src/workflow/EasySearch.cpp
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src/workflow/EasyTaxonomy.cpp
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src/workflow/Linsearch.cpp
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src/workflow/Map.cpp
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src/workflow/PickConsensusRep.cpp
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src/workflow/Rbh.cpp
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src/workflow/Search.cpp
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src/workflow/Taxonomy.cpp
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util/build_osx.sh
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util/mmseqs_wrapper.bat
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util/update_libmarv.sh
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The diff was not included because it is too large.
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