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qiyunzhu committed Mar 26, 2024
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19 changes: 19 additions & 0 deletions docs/dev/_sources/generated/skbio.io.format.biom.rst.txt
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..
The extra blocks seem to be required for autosummary to populate our
docstrings correctly. In the original template, these would recusively call
autosummary again, but we already do that in the narratively convenient
places.
.. automodule:: skbio.io.format.biom












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<p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
<div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>

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<p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
<div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>

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1 change: 1 addition & 0 deletions docs/dev/generated/skbio.io.ClustalFormatError.html
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<p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
<div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>

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1 change: 1 addition & 0 deletions docs/dev/generated/skbio.io.EMBLFormatError.html
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<p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
<div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>

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1 change: 1 addition & 0 deletions docs/dev/generated/skbio.io.FASTAFormatError.html
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<p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
<div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>

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<p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
<div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>

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<p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
<div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>

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1 change: 1 addition & 0 deletions docs/dev/generated/skbio.io.FormatIdentificationWarning.html
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<p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
<div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>

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1 change: 1 addition & 0 deletions docs/dev/generated/skbio.io.GFF3FormatError.html
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<p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
<div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>

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1 change: 1 addition & 0 deletions docs/dev/generated/skbio.io.GenBankFormatError.html
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<p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
<div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>

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1 change: 1 addition & 0 deletions docs/dev/generated/skbio.io.IOSourceError.html
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<p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
<div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>

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1 change: 1 addition & 0 deletions docs/dev/generated/skbio.io.LSMatFormatError.html
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<p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
<div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>

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1 change: 1 addition & 0 deletions docs/dev/generated/skbio.io.NewickFormatError.html
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<p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
<div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>

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1 change: 1 addition & 0 deletions docs/dev/generated/skbio.io.OrdinationFormatError.html
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<p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
<div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>

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1 change: 1 addition & 0 deletions docs/dev/generated/skbio.io.PhylipFormatError.html
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<p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
<div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>

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1 change: 1 addition & 0 deletions docs/dev/generated/skbio.io.QSeqFormatError.html
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<p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
<div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>

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1 change: 1 addition & 0 deletions docs/dev/generated/skbio.io.QUALFormatError.html
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<p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
<div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>

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<p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
<div class="bd-toc-item navbar-nav"><ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.binary_dm.html">Simple binary dissimilarity matrix format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.binary_dm</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.biom.html">BIOM-Format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.biom</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast6.html">BLAST+6 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast6</span></code>)</a></li>
<li class="toctree-l1"><a class="reference internal" href="skbio.io.format.blast7.html">BLAST+7 format (<code class="xref py py-mod docutils literal notranslate"><span class="pre">skbio.io.format.blast7</span></code>)</a></li>

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