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<!DOCTYPE html>
<html lang="en" data-content_root="./">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
<title>ProPhyle documentation contents — ProPhyle 0.3.3.2 documentation</title>
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<section id="prophyle-documentation-contents">
<span id="contents"></span><h1>ProPhyle documentation contents<a class="headerlink" href="#prophyle-documentation-contents" title="Link to this heading">¶</a></h1>
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<li class="toctree-l1"><a class="reference internal" href="example.html">1. Quick example</a></li>
<li class="toctree-l1"><a class="reference internal" href="requirements.html">2. Requirements</a></li>
<li class="toctree-l1"><a class="reference internal" href="install.html">3. Installing ProPhyle</a><ul>
<li class="toctree-l2"><a class="reference internal" href="install.html#installing-prophyle-using-bioconda">3.1. Installing ProPhyle using Bioconda</a></li>
<li class="toctree-l2"><a class="reference internal" href="install.html#installing-prophyle-using-pip">3.2. Installing ProPhyle using PIP</a></li>
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<li class="toctree-l1"><a class="reference internal" href="standard_db.html">4. Building a standard database</a><ul>
<li class="toctree-l2"><a class="reference internal" href="standard_db.html#downloading-genomes">4.1. Downloading genomes</a></li>
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<li class="toctree-l2"><a class="reference internal" href="custom_db.html#building-a-custom-database-with-user-provided-data">5.1. Building a custom database with user-provided data</a></li>
<li class="toctree-l2"><a class="reference internal" href="custom_db.html#building-a-custom-database-with-refseq-genomes-and-the-ncbi-taxonomy">5.2. Building a custom database with RefSeq genomes and the NCBI taxonomy</a></li>
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<li class="toctree-l1"><a class="reference internal" href="classify.html">6. Classifying reads</a></li>
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<li class="toctree-l2"><a class="reference internal" href="compress.html#decompression">7.2. Decompression</a></li>
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<li class="toctree-l1"><a class="reference internal" href="formats.html">8. File formats</a><ul>
<li class="toctree-l2"><a class="reference internal" href="formats.html#input-data-formats">8.1. Input data formats</a></li>
<li class="toctree-l2"><a class="reference internal" href="formats.html#assignments">8.2. Assignments</a></li>
<li class="toctree-l2"><a class="reference internal" href="formats.html#abundances-estimates-experimental">8.3. Abundances estimates (experimental)</a></li>
<li class="toctree-l2"><a class="reference internal" href="formats.html#internal-prophyle-formats">8.4. Internal ProPhyle formats</a></li>
</ul>
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<li class="toctree-l1"><a class="reference internal" href="cli.html">9. Command-line interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="cli.html#prophyle-the-main-program">9.1. ProPhyle – the main program</a></li>
<li class="toctree-l2"><a class="reference internal" href="cli.html#prophyle-assembler">9.2. <code class="docutils literal notranslate"><span class="pre">prophyle_assembler</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="cli.html#id1">9.3. <code class="docutils literal notranslate"><span class="pre">prophyle_index</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="cli.html#prophyle-assignment">9.4. <code class="docutils literal notranslate"><span class="pre">prophyle_assignment</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="cli.html#prophyle-propagation-makefile-py">9.5. <code class="docutils literal notranslate"><span class="pre">prophyle_propagation_makefile.py</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="cli.html#prophyle-propagation-preprocessing-py">9.6. <code class="docutils literal notranslate"><span class="pre">prophyle_propagation_preprocessing.py</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="cli.html#prophyle-propagation-postprocessing-py">9.7. <code class="docutils literal notranslate"><span class="pre">prophyle_propagation_postprocessing.py</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="cli.html#prophyle-validate-tree-py">9.8. <code class="docutils literal notranslate"><span class="pre">prophyle_validate_tree.py</span></code></a></li>
</ul>
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