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<!DOCTYPE html>
<html lang="en" data-content_root="./">
<head>
<meta charset="utf-8" />
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<title>ProPhyle: DNA sequence classification — ProPhyle 0.3.3.2 documentation</title>
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<li><a href="http://github.com/prophyle/prophyle">Extend/Develop</a></li>
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<div style="color:white;font-size:240%">ProPhyle</div>
<div style="color:white;font-size:140%">DNA sequence classification</div>
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<h3>Navigation</h3>
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accesskey="I">index</a></li>
<li><a href="#">ProPhyle home</a> |</li>
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<div class="sphinxsidebarwrapper"><h3>Download</h3>
<p>Current version: <b><a href="https://github.com/prophyle/prophyle/releases/tag/0.3.3.2">0.3.3.2</a></b></p>
<p>Get ProPhyle from the <a href="https://pypi.python.org/pypi/prophyle">Python Package
Index</a>, install it with:</p>
<pre>pip install -U prophyle</pre>
<p>or from <a href="http://bioconda.github.io">BioConda</a>, install it with</p>
<pre>conda install prophyle</pre>
<p>or from <a href="http://doi.org/10.5281/zenodo.1045429">Zenodo</a>.</p>
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<h1>Welcome to ProPhyle</h1>
<p>
ProPhyle brings metagenomic classification <b>from clusters to laptops</b>. This is possible thanks to a novel indexing strategy,
based on the bottom-up propagation of k-mers in the phylogenetic/taxonomic tree, assembling contigs at each node and matching using a full-text search.
</p>
<p>Compared to other state-of-the-art classifiers, ProPhyle provides several unique features:
<img src="_static/prophyle_overview.jpg" style="float:right; width:250px" />
<ul>
<li><b>Low memory requirements.</b> Compared to Kraken, ProPhyle has 7x smaller memory footprint for index construction and 5x smaller footprint for querying, while providing a more expressive index.</li>
<li><b>Flexibility.</b> ProPhyle is easy to use with any user-provided phylogenetic trees and reference genomics sequences (e.g., reads or assemblies). It can classify short reads, long reads, or even assembled contigs.</li>
<li><b>Standard bioinformatics formats.</b> Newick/NHX is used for representing phylogenetic trees and SAM/BAM for reporting assignments.</li>
<li><b>Lossless k-mer indexing.</b> ProPhyle stores a list of all genomes containing a k-mer. The classification is, therefore, accurate even with trees containing similar genomes (e.g, phylogenetic trees for a single species).</li>
<li><b>Reproducibility.</b> ProPhyle is fully deterministic, with a mathematically well-defined behavior. Databases are versioned and distributed via Zenodo.</li>
</ul>
<h2 style="margin-bottom: 0">Documentation</h2>
<table class="contentstable">
<tr>
<td style="width:35%">
<p class="biglink"><a class="biglink" href="example.html">Quick example</a><br/>
<span class="linkdescr">5 minutes example</span></p>
</td><td>
<p class="biglink"><a class="biglink" href="contents.html">Contents</a><br/>
<span class="linkdescr">for a complete overview</span></p>
</td>
</tr><tr>
<td><p class="biglink"><a class="biglink" href="search.html">Search page</a><br/>
<span class="linkdescr">search the documentation</span></p>
</td><td>
<p class="biglink"><a class="biglink" href="https://github.com/prophyle/prophyle/releases">
Releases
</a><br/>
<span class="linkdescr">release history</span></p>
</td>
</tr>
</table>
<h2 style="margin-bottom: 0">Auxiliary tools</h2>
<table class="contentstable">
<tr>
<td style="width:35%">
<p class="biglink"><a class="biglink" href="http://github.com/prophyle/prophex">ProphEx</a><br/>
<span class="linkdescr">FM-index for rapid k-mer matching using simplitigs</span>
</p>
</td>
<td>
<p class="biglink"><a class="biglink" href="http://github.com/prophyle/prophasm">ProphAsm</a><br/>
<span class="linkdescr">representing k-mer sets via simplitigs</span>
</p>
</td>
</tr>
</table>
<h2>Cite</h2>
<div class="cit">
<p>
[1] K. Břinda, L. Lima, S. Pignotti, N. Quinones-Olvera, K. Salikhov,
R. Chikhi, G. Kucherov, Z. Iqbal, and M. Baym,
<b>Efficient and robust search of microbial genomes via phylogenetic compression,</b>
bioRxiv 2023.04.15.536996, 2023.
<a href="https://doi.org/10.1101/2023.04.15.536996">https://doi.org/10.1101/2023.04.15.536996</a>.
</p>
<p>
[2] Břinda K, Salikhov K, Pignotti S, Kucherov G.
<b>ProPhyle 0.3.1.0</b>, Zenodo, 2017.
<a href="http://doi.org/10.5281/zenodo.1045429">https://doi.org/10.5281/zenodo.1045429</a>.
</p>
<p>
[3] Břinda K, Salikhov K, Pignotti S, Kucherov G.
<b>ProPhyle: a phylogeny-based metagenomic classifier using the Burrows-Wheeler Transform.</b>
Poster at HiTSeq 2017.
<a href="http://doi.org/10.5281/zenodo.1045427">https://doi.org/10.5281/zenodo.1045427</a>
</p>
<p>
[4] Břinda K.
<b>Novel computational techniques for mapping and classifying Next-Generation Sequencing data.</b>
PhD Thesis, Université Paris-Est, 2016.
<a href="http://doi.org/10.5281/zenodo.1045317">https://doi.org/10.5281/zenodo.1045317</a>
</p>
<p>
[5] Salikhov K.
<b>Efficient algorithms and data structures for indexing DNA sequence data.</b>
PhD Thesis, Université Paris-Est, 2017.
</p>
</div>
<p style="font-size:90%">
[1] introduces phylogenetic compression, which is the fundamental concept behind ProPhyle,
[2] is the main reference for the entire ProPhyle package,
[3] contains a summary of the ProPhyle algorithm,
[4] provides a thorough description (see Chapter 12),
and [5] explains details of the BWT-indexing technique.
</p>
<h2>Authors</h2>
<ul>
<li><a href="http://brinda.eu">Karel Břinda</a> <<a href="mailto:karel.brinda@inria.fr">karel.brinda@inria.fr</a>></li>
<li>Kamil Salikhov <<a href="mailto:kamil.salikhov@univ-mlv.fr">kamil.salikhov@univ-mlv.fr</a>></li>
<li>Simone Pignotti <<a href="mailto:pignottisimone@gmail.com">pignottisimone@gmail.com</a>></li>
<li><a href="http://igm.univ-mlv.fr/~koutcher/">Gregory Kucherov</a> <<a href="mailto:gregory.kucherov@univ-mlv.fr">gregory.kucherov@univ-mlv.fr</a>></li>
</ul>
<div class="clearer"></div>
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</div>
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<div class="related" role="navigation" aria-label="Related">
<h3>Navigation</h3>
<ul>
<li class="right" style="margin-right: 10px">
<a href="genindex.html" title="General Index"
>index</a></li>
<li><a href="#">ProPhyle home</a> |</li>
<li><a href="contents.html">Documentation</a> »</li>
<li class="nav-item nav-item-this"><a href="">ProPhyle: DNA sequence classification</a></li>
</ul>
</div>
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© Copyright 2015-2024, Karel Břinda, Kamil Salikhov, Simone Pignotti, Gregory Kucherov.
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