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<!DOCTYPE html>
<html>
<head>
<meta charset='utf-8'>
<meta http-equiv="X-UA-Compatible" content="chrome=1">
<meta name="description" content="Rap-green : A phylogenetic tree analysis package (species/gene tree reconciliation, tree pattern matching, Javascript interfaces ...)">
<link rel="stylesheet" type="text/css" media="screen" href="stylesheets/stylesheet.css">
<title>Rap-green</title>
</head>
<body>
<!-- HEADER -->
<div id="header_wrap" class="outer">
<header class="inner">
<a id="forkme_banner" href="https://github.com/dufayard/rap-green">View on GitHub</a>
<img align="left" width="80px" src="images/LOGO_RAP.png">
<h1 id="project_title">Rap-green</h1>
<h2 id="project_tagline">A phylogenetic tree analysis package (species/gene tree reconciliation, tree pattern matching, Javascript interfaces ...)</h2>
<section id="downloads">
<a class="zip_download_link" href="https://github.com/dufayard/rap-green/zipball/master">Download this project as a .zip file</a>
<a class="tar_download_link" href="https://github.com/dufayard/rap-green/tarball/master">Download this project as a tar.gz file</a>
</section>
</header>
</div>
<!-- MAIN CONTENT -->
<div id="main_content_wrap" class="outer">
<section id="main_content" class="inner">
<p>RAP-Green is a new implementation and an improvment of the RAP software (<a href="http://pbil.univ-lyon1.fr/software/RAP/RAP.htm">http://pbil.univ-lyon1.fr/software/RAP/RAP.htm</a>), which permits to compare gene and species trees, infers duplication events, and provide confidence score in function conservation between genes.</p>
<p>Afterwards, it became a development plateform, to implement several phylogenetic tree analysis softwares.</p>
<p>RAP-Green includes also two graphical web interfaces : one to display phylogenetic trees, explore them and annotate them ; and another to explore a tree forest, using tree pattern matching, and a tree pattern daemon implemented in the Rap-Green java package.</p>
<hr>
<p><em>PLEASE CITE:</em></p>
<p><a href="http://bioinformatics.oxfordjournals.org/content/21/11/2596.short">http://bioinformatics.oxfordjournals.org/content/21/11/2596.short</a></p>
<hr>
<p><em>CONTACT</em></p>
<p>For general questions or comments, you can contact the project owner (jeanfrancois.dufayard <em>at</em> gmail.com)</p>
<hr>
<p><em>ABOUT TREE PATTERN MATCHING AND TREE DISPLAY</em></p>
<p>Tree pattern matching is a way to explore a large library of phylogenetic trees, extracting those which contain specific phylogenetic patterns.</p>
<p>Tree pattern matching facilities are in constant development, and are not intended to be easily installed and adapted to a tree repository. The installation of this system in your environment should be the occasion of a collaboration. </p>
<hr>
<p><em>ABOUT TREE RECONCILIATION:</em></p>
<p>Documentation is yet to be improved.</p>
<p>For a command line option description: <a href="https://github.com/dufayard/rap-green/wiki/%22RapGreen%22-reconciliation-command-line-documentation">here using GitHub wiki</a></p>
<p>For a code documentation: <a href="javadoc/index.html">here using HTML preview</a></p>
<hr>
<p>Project was formerly supported by <a href="http://www-helix.inrialpes.fr/old/">Helix INRIA project</a>, and <a href="http://lbbe.univ-lyon1.fr/">LBBE</a>, and is now supported by the <a href="http://umr-agap.cirad.fr/">UMR AGAP</a> (<a href="http://www.cirad.fr">CIRAD</a>) and project <a href="http://ancestrome.univ-lyon1.fr/">Ancestrome</a>.</p>
</section>
</div>
<!-- FOOTER -->
<div id="footer_wrap" class="outer">
<footer class="inner">
<p class="copyright">Rap-green maintained by <a href="https://github.com/dufayard">dufayard</a></p>
<p>Published with <a href="https://pages.github.com">GitHub Pages</a></p>
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