<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN" "http://www.w3.org/TR/REC-html40/loose.dtd">
<html lang="en" style='--code-editor-font: var(--default-mono-font, "GitLab Mono"), JetBrains Mono, Menlo, DejaVu Sans Mono, Liberation Mono, Consolas, Ubuntu Mono, Courier New, andale mono, lucida console, monospace;'>
<head>
<meta content="text/html; charset=utf-8" http-equiv="Content-Type">
<title>
GitLab
</title>

<style data-premailer="ignore" type="text/css">
a { color: #1068bf; }
</style>


<style>img {
max-width: 100%; height: auto;
}
body {
font-size: .875rem;
}
body {
-webkit-text-shadow: rgba(255,255,255,.01) 0 0 1px;
}
body {
font-family: "GitLab Sans",-apple-system,BlinkMacSystemFont,"Segoe UI",Roboto,"Noto Sans",Ubuntu,Cantarell,"Helvetica Neue",sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol","Noto Color Emoji"; font-size: inherit;
}
</style>
</head>
<body style='font-size: inherit; -webkit-text-shadow: rgba(255,255,255,.01) 0 0 1px; font-family: "GitLab Sans",-apple-system,BlinkMacSystemFont,"Segoe UI",Roboto,"Noto Sans",Ubuntu,Cantarell,"Helvetica Neue",sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol","Noto Color Emoji";'>
<div class="content">

<h3 style="margin-top: 20px; margin-bottom: 10px;">
Charles Plessy pushed to branch master at <a href="https://salsa.debian.org/med-team/kalign">Debian Med / kalign</a>
</h3>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
Commits:
</h4>
<ul>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/kalign/-/commit/92b24cbdedc4743593efdb5cc7f04d46b39779d2">92b24cbd</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2026-02-27T16:41:36+09:00 </i>
</div>
<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
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/kalign/-/commit/ce28fe71f132ea819e72747073ba4068879b2719">ce28fe71</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2026-02-27T16:41:37+09:00 </i>
</div>
<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 3.5.1</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/kalign/-/commit/20deff66fa50de1ccd62b3f69174b976a71d5ae8">20deff66</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2026-02-27T16:41:39+09:00 </i>
</div>
<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;'>Update upstream source from tag 'upstream/3.5.1'

Update to upstream version '3.5.1'
with Debian dir cdac5fa5bca848ea6c76086cc04bef6720a42030</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/kalign/-/commit/9d2dbe8dfc7e6fe883ed56c18e1a8cbb02b122e2">9d2dbe8d</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2026-02-27T16:41:39+09:00 </i>
</div>
<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;'>Standards-Version: 4.7.3 (routine-update)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/kalign/-/commit/aebd0bf77cb0ab54230bfa910537674c339aae9e">aebd0bf7</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2026-02-27T16:41:41+09:00 </i>
</div>
<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;'>Remove Priority field to comply with Debian Policy 4.7.3 (routine- update)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/kalign/-/commit/d32a6b43078c80a74e1279966a259cd903315c71">d32a6b43</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2026-02-27T16:41:57+09:00 </i>
</div>
<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;'>Set upstream metadata fields: Documentation.

Changes-By: lintian-brush
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/kalign/-/commit/b354582ce9eb8e116e175cc0b802f9fbed11b424">b354582c</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2026-02-27T16:54:03+09:00 </i>
</div>
<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;'>cme fix dpkg-control --save
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/kalign/-/commit/3536d0e86b28ac6c4d18fe82f20ce2192896a82f">3536d0e8</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2026-02-27T17:00:15+09:00 </i>
</div>
<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;'>Relicensed to Apache 2.0
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/kalign/-/commit/ae4707100dec9ac79546c124906d3732d86c9815">ae470710</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2026-02-27T17:00:50+09:00 </i>
</div>
<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;'>Ready for upload and close upstream bug.
</pre>
</li>
</ul>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
150 changed files:
</h4>
<ul>
<li class="file-stats">
<a href="#92bd70280d1467b70554bf8720117ca458a91c68">
<span class="new-file">
+
.claude/commands/release.md
</span>
</a>
</li>
<li class="file-stats">
<a href="#d4df36a9401a00e7c140b834f312ba4ccc3da86d">
<span class="new-file">
+
.containerignore
</span>
</a>
</li>
<li class="file-stats">
<a href="#2988cbe972fe24aeb6ee4536af0d0adb14495729">
<span class="new-file">
+
.github/workflows/benchmark.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#9ae3f8f5993cde39520379ad6054df829e6c91a7">
.github/workflows/cmake.yml
</a>
</li>
<li class="file-stats">
<a href="#c3aa8b7f1c613e43d3bb9d5ac52ac6603d945e89">
.github/workflows/codeql-analysis.yml
</a>
</li>
<li class="file-stats">
<a href="#ceb0aadb3a092229876e4de4500aac9c2dff3627">
<span class="new-file">
+
.github/workflows/python.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#6cd2a502257ede524d220cea6700e2fa98f071aa">
<span class="new-file">
+
.github/workflows/wheels.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
.gitignore
</a>
</li>
<li class="file-stats">
<a href="#2f473ef69010f24d2546e13263bcc2c49befd2f3">
<span class="new-file">
+
CITATION.cff
</span>
</a>
</li>
<li class="file-stats">
<a href="#2d5d10cfc503b52b745a2f437966ee1b895371af">
<span class="new-file">
+
CLAUDE.md
</span>
</a>
</li>
<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
</a>
</li>
<li class="file-stats">
<a href="#3f454a98e586d1aa0d322e19afd5e67e08f2d3c8">
<span class="new-file">
+
CONTRIBUTING.md
</span>
</a>
</li>
<li class="file-stats">
<a href="#6156cd6ac57d8b88e473d9202392ec064b623c93">
COPYING
</a>
</li>
<li class="file-stats">
<a href="#00fe7828d56d7a3ee4030d6cea057cf13f50e70c">
ChangeLog
</a>
</li>
<li class="file-stats">
<a href="#a6ff37b281ae15403476fcd5ebb91d8d5df79d90">
<span class="new-file">
+
Containerfile
</span>
</a>
</li>
<li class="file-stats">
<a href="#f22631ab443033e7956e813e59aa95889374067a">
<span class="new-file">
+
Containerfile.downstream
</span>
</a>
</li>
<li class="file-stats">
<a href="#9e9332af7a93fc75d792aa2dd9c41d210dfc9def">
<span class="new-file">
+
README-python.md
</span>
</a>
</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
</li>
<li class="file-stats">
<a href="#3cf662f363bf6fc9d311532765a0ce2ef1502ac9">
<span class="new-file">
+
benchmarks/__init__.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#8fdc3d5a69280e50ad4b015de2d53b8a78240189">
<span class="new-file">
+
benchmarks/__main__.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#80f590d134b5906e0aba88b88d062dcd5c46f770">
<span class="new-file">
+
benchmarks/analysis.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#cdfc651bca91f9dc7e30538b6b6c2181635a7454">
<span class="new-file">
+
benchmarks/app.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#0cb564638ff659b6d7ff0d5177e296ae85264583">
<span class="new-file">
+
benchmarks/combined_improvements.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#e8a46a7a7f3e58e5434ef7f69099f56d0cea9bf2">
<span class="new-file">
+
benchmarks/datasets.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#f06d03baf5e5f73185b8c12de0ae36afc713811b">
<span class="new-file">
+
benchmarks/downstream/__init__.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#1f721b7e71819bba22a7401268d4adddcb116c64">
<span class="new-file">
+
benchmarks/downstream/__main__.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#df9b7672efe4499d7d2fe57d13635ddc20a1b84b">
<span class="new-file">
+
benchmarks/downstream/alignment_accuracy.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#5941c2590bdf25235b57318877c8d812c16061f1">
<span class="new-file">
+
benchmarks/downstream/calibration.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#c79c79c07850c272a77fbb18ba302a245343ecbe">
<span class="new-file">
+
benchmarks/downstream/figures.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#1c76255b83ee1d20d3dbe0ef89372469c36ab3b7">
<span class="new-file">
+
benchmarks/downstream/hmmer_detection.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#3c6cd7ae7897b14e73ffe0fcd14f44421a5702ca">
<span class="new-file">
+
benchmarks/downstream/phylo_accuracy.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#440c5e370a141d25f36c15cf3360a4c4d6343dc1">
<span class="new-file">
+
benchmarks/downstream/positive_selection.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#dfbe63dafd3281ef1242e1c59cad0cf65dec6080">
<span class="new-file">
+
benchmarks/downstream/provenance.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#f649cfef3e2cc2dc3d873f7bac8b9faabdbb9f93">
<span class="new-file">
+
benchmarks/downstream/simulation.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#a38387a96439c1ab88feacfeb4c607fca78c6411">
<span class="new-file">
+
benchmarks/downstream/utils.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#e9e728dfd174421f649e65cb15ff8fd21b31ae72">
<span class="new-file">
+
benchmarks/external_balibase.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#7441edae01731099a06261a43103ea0179e06b75">
<span class="new-file">
+
benchmarks/full_comparison.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#44fc0f9b82563c7d21b3672d916517c69d64175a">
<span class="new-file">
+
benchmarks/make_summary_figure.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#b94f933ff4b8190a6231143559121f7ea7715806">
<span class="new-file">
+
benchmarks/mumsa_plots.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#1a13a1e4604632cc294ba16e97f80c088a8eac1c">
<span class="new-file">
+
benchmarks/mumsa_precision.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#3763e51faf0958686b397267a770b702a216e996">
<span class="new-file">
+
benchmarks/runner.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#e4549b3393844df4c9f610a25913ba974ad18874">
<span class="new-file">
+
benchmarks/scoring.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#134b718924bf42ed608198fee3e0d7ad7e0c22af">
<span class="new-file">
+
benchmarks/vsm_ensemble_experiment.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#f3cea7d565868c92517c8ea6be3d0bcd1fa49eb5">
<span class="new-file">
+
build.zig
</span>
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
</a>
</li>
<li class="file-stats">
<a href="#5aaf1108b7746d548df6a3d1a75ba6040c3a8804">
lib/CMakeLists.txt
</a>
</li>
<li class="file-stats">
<a href="#956755a88873f7a02300f54ac049ac9a61460e69">
lib/include/kalign/kalign.h
</a>
</li>
<li class="file-stats">
<a href="#3c6c94de4b0b9193f71d2358511410567ca45d3a">
<span class="new-file">
+
lib/src/aln_apair_dist.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#601ff7fd77810ae32a4d0111f2bbe8f66a6a8ea4">
<span class="new-file">
+
lib/src/aln_apair_dist.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#667f15e714fc7fab386e1cf93e67f6b962161013">
lib/src/aln_controller.c
</a>
</li>
<li class="file-stats">
<a href="#4ad990417c2d5630c97db3f4c1d267c8003d502e">
lib/src/aln_mem.c
</a>
</li>
<li class="file-stats">
<a href="#7eb8bd5b27d0b3b81274e217dfd39bb94bd9027b">
lib/src/aln_param.c
</a>
</li>
<li class="file-stats">
<a href="#dfb3a29245fc15f2436fabfd1678fe4e1e7b1489">
lib/src/aln_param.h
</a>
</li>
<li class="file-stats">
<a href="#68293685a4775b75caa1fba94490abfa8cff5033">
lib/src/aln_profileprofile.c
</a>
</li>
<li class="file-stats">
<a href="#47f7a64dac6a15541344ff60c2a91cc353c6a8b0">
<span class="new-file">
+
lib/src/aln_refine.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#bd4b533c5913ce506c1930b13c634593fd5ad0e9">
<span class="new-file">
+
lib/src/aln_refine.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#573e1d796418f70113a5f4879f70b047cf778732">
lib/src/aln_run.c
</a>
</li>
<li class="file-stats">
<a href="#e6a6a87d05b916073dd58a93270060d218150a06">
lib/src/aln_run.h
</a>
</li>
<li class="file-stats">
<a href="#7e015d12bca99e88c4e9b046d647b87489f44a96">
lib/src/aln_seqprofile.c
</a>
</li>
<li class="file-stats">
<a href="#0ec6fa528c92b403b5647809e8389a4553e04d27">
lib/src/aln_seqseq.c
</a>
</li>
<li class="file-stats">
<a href="#61be5a8c4893df8c70084ac461e97053126d4559">
lib/src/aln_setup.c
</a>
</li>
<li class="file-stats">
<a href="#bab105e220808c45b01930cf94a49a0d89d25137">
lib/src/aln_setup.h
</a>
</li>
<li class="file-stats">
<a href="#4bac8909c8670d1d0750d0c0ff65fba3e10928f7">
lib/src/aln_struct.h
</a>
</li>
<li class="file-stats">
<a href="#bcd542b6d9fd6b4dd5763eb5a5d02c8a32b8c30f">
lib/src/aln_wrap.c
</a>
</li>
<li class="file-stats">
<a href="#c54c9366482b164568265f6622dc793003c94064">
lib/src/aln_wrap.h
</a>
</li>
<li class="file-stats">
<a href="#f09917e0725be335fed15fd342636159f3d48c91">
lib/src/alphabet.c
</a>
</li>
<li class="file-stats">
<a href="#041564a7289739d71e7c5478a364d526aaaa5f82">
lib/src/alphabet.h
</a>
</li>
<li class="file-stats">
<a href="#6e6ca1657be2a38ebcece21d3a51a3132542965b">
<span class="new-file">
+
lib/src/anchor_consistency.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#bd7088e8870239740aef081e72301e4da77a7cfc">
<span class="new-file">
+
lib/src/anchor_consistency.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#6c6874add6c04da1c822aa84ce8c04612ae6083b">
lib/src/bisectingKmeans.c
</a>
</li>
<li class="file-stats">
<a href="#89a396c2cd9dbd9ea2f4359c99df4eda0c662f52">
lib/src/bisectingKmeans.h
</a>
</li>
<li class="file-stats">
<a href="#0c789fe549db4caec9c26772672b182dc6cb0da1">
lib/src/bpm.c
</a>
</li>
<li class="file-stats">
<a href="#9ab5299497004052e01895f4babeed0ad313fa39">
lib/src/bpm.h
</a>
</li>
<li class="file-stats">
<a href="#764ad6e1fc8d50260ed117a99c847ba3cca57fca">
<span class="new-file">
+
lib/src/consensus_msa.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#2a29c929dd5003bb06d8dd04605b57329000f3cb">
<span class="new-file">
+
lib/src/consensus_msa.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#4847b3178adde5c0e2278fa1c3c753c463077f73">
<span class="new-file">
+
lib/src/ensemble.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#6d68164b572d2969e8577cc6899dcda1854bc77e">
<span class="new-file">
+
lib/src/ensemble.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#e38722192e3fd58c2ed688b66603e8272e494c50">
lib/src/euclidean_dist.c
</a>
</li>
<li class="file-stats">
<a href="#75f39fb0781741c412050f3fdc2af96cdbe50b28">
lib/src/euclidean_dist.h
</a>
</li>
<li class="file-stats">
<a href="#b0b23cc472379a6497c7b08e94bd200724dd2ee6">
lib/src/msa_alloc.c
</a>
</li>
<li class="file-stats">
<a href="#1c2350227626febbb164e84ea774b72ca602d7ca">
lib/src/msa_check.c
</a>
</li>
<li class="file-stats">
<a href="#1f0141a0630211b1bd70624b96adced057bb9fdd">
lib/src/msa_cmp.c
</a>
</li>
<li class="file-stats">
<a href="#7b3c001274fa9d18ff26861b6a1758955153a9a3">
lib/src/msa_cmp.h
</a>
</li>
<li class="file-stats">
<a href="#c23c0c7a5f0e119686be0021de1d329fb35ad1dc">
lib/src/msa_io.c
</a>
</li>
<li class="file-stats">
<a href="#3836b2cd2d2d7d89160c2329abefc09b429e8919">
lib/src/msa_op.c
</a>
</li>
<li class="file-stats">
<a href="#56bfbd07f24c128780063200710713e8f3ebf757">
lib/src/msa_struct.h
</a>
</li>
<li class="file-stats">
<a href="#eb6deed589b6c34f3e57cc375059bf82d0c67ddb">
lib/src/pick_anchor.c
</a>
</li>
<li class="file-stats">
<a href="#c416f7e7787f53649ea2612f309d1f827cf3afed">
<span class="new-file">
+
lib/src/poar.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#bd142abe177b6393b6fe2274aa697388dc7ded2f">
<span class="new-file">
+
lib/src/poar.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#b3154988ba638e181183927f9920a3f42be0cade">
lib/src/sequence_distance.c
</a>
</li>
<li class="file-stats">
<a href="#1484f7fb37276db196ca27137c181b2ac3d4297b">
lib/src/sequence_distance.h
</a>
</li>
<li class="file-stats">
<a href="#ab26a9baaccf7e6a519c41cb17b28e403b032ae7">
<span class="new-file">
+
lib/src/sp_score.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#5d4b12d85e55a0cfd2b9503dc794b7517d65c3a6">
<span class="new-file">
+
lib/src/sp_score.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#2a3e0cbaec2bcaa613852b619a102b4b9f91ef5d">
lib/src/task.c
</a>
</li>
<li class="file-stats">
<a href="#04e0dfbf68b1de483408a7212ae737d8907bdcec">
lib/src/task.h
</a>
</li>
<li class="file-stats">
<a href="#9ad12cd895e2c71913c665dc7fb65fed6d7a38c1">
lib/src/test.c
</a>
</li>
<li class="file-stats">
<a href="#f30d3b0dc9b2cce4e5ca7d7b220137f8ea2fc826">
lib/src/tldevel.c
</a>
</li>
<li class="file-stats">
<a href="#99eb2beba86dcdad4f1203fc03c1db73b833f54d">
lib/src/tldevel.h
</a>
</li>
<li class="file-stats">
<a href="#cf76c7aa031977e3328dbbbdabfe08e2ddb8c66b">
lib/src/tlmisc.c
</a>
</li>
<li class="file-stats">
<a href="#ce3be29cd9af225fce9105a723909ccaaf53f209">
lib/src/weave_alignment.c
</a>
</li>
<li class="file-stats">
<a href="#a36f72c41ac3a53dc89ab2ebd4f7da0c48af445c">
lib/src/weave_alignment.h
</a>
</li>
<li class="file-stats">
<a href="#5d07e7d72637aa0d59c89d381fe6dc4cf46e2491">
<span class="new-file">
+
pyproject.toml
</span>
</a>
</li>
<li class="file-stats">
<a href="#4c6e2c868cabb1d57f8b9d9b484491c8f90dff83">
<span class="new-file">
+
python-kalign/__init__.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc0c3b25c397885bf44e19f2806177f75289aabf">
<span class="new-file">
+
python-kalign/_core.cpp
</span>
</a>
</li>
<li class="file-stats">
<a href="#4a9a5f610b5e25c54516cd7438ea0990ed96d383">
<span class="new-file">
+
python-kalign/cli.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#9e3f0095256982f2228bb232e337847eb3c91700">
<span class="new-file">
+
python-kalign/io.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#fa5f083fe7a3d18a42220a798567141d769bedc2">
<span class="new-file">
+
python-kalign/py.typed
</span>
</a>
</li>
<li class="file-stats">
<a href="#38a6d795f7c33ad718ca5530156e6f1071865849">
<span class="new-file">
+
python-kalign/utils.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#f6d78aeba065070353a886d46d99fb334f4a350f">
scripts/balibase_test.org
</a>
</li>
<li class="file-stats">
<a href="#c9d71ea10de32de1c3a782e2cb3156ce0bbe784e">
scripts/benchmark.org
</a>
</li>
<li class="file-stats">
<a href="#716dea4717ab39505d2db02595a7875ffef7e357">
scripts/bralibase.org
</a>
</li>
<li class="file-stats">
<a href="#631c8d07f5ea23b9a9f6c57f5389dfcf94bc33b7">
src/CMakeLists.txt
</a>
</li>
<li class="file-stats">
<a href="#5bf1bea928976f53c109f8097d857fddbfac7fd8">
src/parameters.c
</a>
</li>
<li class="file-stats">
<a href="#c52aa08ec41825810398467572e8d6c8f4ab4408">
src/parameters.h
</a>
</li>
<li class="file-stats">
<a href="#830464862debacd7cdfde9fb2e1e7dae90d05037">
src/run_kalign.c
</a>
</li>
<li class="file-stats">
<a href="#8f13c3ee0e1cd30a8a84952efd02731156fac6f1">
src/run_reformat.c
</a>
</li>
<li class="file-stats">
<a href="#c62459b166a334e6529175340eedeee6977df0ca">
tests/CMakeLists.txt
</a>
</li>
<li class="file-stats">
<a href="#a276ae5cc2cddfa9f68f0accc1bbec7c604e60c0">
tests/dssim.c
</a>
</li>
<li class="file-stats">
<a href="#5fdfb9b08fb49b1e7d52dbc8209de0a48e4cab8c">
tests/dssim_test.c
</a>
</li>
<li class="file-stats">
<a href="#f536cf1caeacec2aaa74f1098d98547c15afe7e2">
<span class="new-file">
+
tests/kalign_api_test.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#6312b355e8a083efd669bf5a59a5218efa48a775">
<span class="new-file">
+
tests/kalign_ensemble_test.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#6fe20956e1e8d2ee6370bc737e04210a465c9cc2">
tests/kalign_lib_test.c
</a>
</li>
<li class="file-stats">
<a href="#a04099689cb93c07f39616bd0b81396d17726f4c">
tests/large_benchmark.c
</a>
</li>
<li class="file-stats">
<a href="#bd0dd3b674422c1399adc2e5c260712a31ea2a9b">
<span class="new-file">
+
tests/python/conftest.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#c4c9a26c8dcd337e1cae35af1438d2c8aa2309a6">
<span class="new-file">
+
tests/python/pytest.ini
</span>
</a>
</li>
<li class="file-stats">
<a href="#2bdb42e5bdff53eae827e5c50b4bd38f455b3a86">
<span class="new-file">
+
tests/python/test_basic_alignment.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#5272f747379e2e7f4526e0d725b0d8899a982c66">
<span class="new-file">
+
tests/python/test_cli.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#721a142d5bc3925ec4540a679c7c31808fdbadbc">
<span class="new-file">
+
tests/python/test_compare.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#79d32f0d3ed27ddb7798bdc696d08400a8e210f0">
<span class="new-file">
+
tests/python/test_data/dna_sequences.fasta
</span>
</a>
</li>
<li class="file-stats">
<a href="#639eaa364259637971639dbbb46d43873bff8eed">
<span class="new-file">
+
tests/python/test_data/invalid_sequences.fasta
</span>
</a>
</li>
<li class="file-stats">
<a href="#bf8d36ca03218260e03909fcef71496d3351c2bd">
<span class="new-file">
+
tests/python/test_data/protein_sequences.fasta
</span>
</a>
</li>
<li class="file-stats">
<a href="#20a6829c3bc09b915fe48f9ec15d46a383c8b01a">
<span class="new-file">
+
tests/python/test_data/rna_sequences.fasta
</span>
</a>
</li>
<li class="file-stats">
<a href="#46141437c02d798b78df7d984ec27b0fad7aba0c">
<span class="new-file">
+
tests/python/test_downstream_foundation.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#33984c7db2c89fe03529e07177b9328f4f3f8adb">
<span class="new-file">
+
tests/python/test_downstream_integration.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#c78de02b28bb5687587fcb171e8061ac6af524c8">
<span class="new-file">
+
tests/python/test_ecosystem_integration.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#688848b8453da74ee0a33e17e0d241b7fa087986">
<span class="new-file">
+
tests/python/test_ecosystem_real.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#ffff31e82c4256448bb7a699a9b05e665c840eb0">
<span class="new-file">
+
tests/python/test_edge_cases.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#5fb6a67012927d7f4e1187f1567c63ffa4cdd85e">
<span class="new-file">
+
tests/python/test_error_handling.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#4e3740ab93c1c956fb64bc08a31548c10e439c8b">
<span class="new-file">
+
tests/python/test_file_operations.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#f8b6511c7dde8a6521fd2ec9b29accb58e6825b9">
<span class="new-file">
+
tests/python/test_input_validation.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#34bad42c6d9e29127625c9d540afd1b9d0a34b0a">
<span class="new-file">
+
tests/python/test_integration.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#85fa5abd749a98763ac7023227905ab7754b0957">
<span class="new-file">
+
tests/python/test_modes.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#d65043c8f10052a3c34858d3ba32d04d0b29a2dc">
<span class="new-file">
+
tests/python/test_parameters.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#6b8fdb182c30f136b9408c87491f3b11e1408c9c">
<span class="new-file">
+
tests/python/test_performance.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#010a6d3100c0500f375a775d71fd6eb37a73a819">
<span class="new-file">
+
tests/python/test_sequence_types.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#424afb96c97076d9ae8980106a88c1032df467c5">
<span class="new-file">
+
tests/zig_test.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#8356d81e4534d6870d4e03761c963b3e292cdb5e">
<span class="new-file">
+
uv.lock
</span>
</a>
</li>
</ul>
<h5 style="margin-top: 10px; margin-bottom: 10px; font-size: .875rem;">
The diff was not included because it is too large.
</h5>

</div>
<div class="footer" style="margin-top: 10px;">
<p style="font-size: small; color: #626168;">

<br>
<a href="https://salsa.debian.org/med-team/kalign/-/compare/8b8bb89b976a9c7011570a1149fce3b6f22aef86...ae4707100dec9ac79546c124906d3732d86c9815">View it on GitLab</a>.
<br>
You're receiving this email because of your account on <a target="_blank" rel="noopener noreferrer" href="https://salsa.debian.org">salsa.debian.org</a>. <a href="https://salsa.debian.org/-/profile/notifications" target="_blank" rel="noopener noreferrer" class="mng-notif-link">Manage all notifications</a> · <a href="https://salsa.debian.org/help" target="_blank" rel="noopener noreferrer" class="help-link">Help</a>
<span style="color: transparent; font-size: 0; display: none; overflow: hidden; opacity: 0; width: 0; height: 0; max-width: 0; max-height: 0;">
Notification message regarding https://salsa.debian.org/med-team/kalign/-/compare/8b8bb89b976a9c7011570a1149fce3b6f22aef86...ae4707100dec9ac79546c124906d3732d86c9815 at 1772179755
</span>



</p>
</div>
</body>
</html>