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software.html
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN"
"http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" >
<head>
<meta http-equiv="content-type" content="text/html; charset=iso-8859-1" />
<meta name="author" content="Lior Pachter" />
<meta name="keywords" content="Computational biology" />
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<title>Pachter Lab</title>
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<a href="http://www.caltech.edu/"><img src="Caltech_LOGO-WHITE-RGB.png" alt = "Caltech logo" width=150 /></a>
<p><span>Pachter Lab</span></p>
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<li><a href="index.html" title="Home">Home</a></li>
<li><a href="group.html" title="Group">Group</a></li>
<li><a href="research.html" title="Research" >Research</a></li>
<li><a href="software.html" title="Software" class="current-page">Software</a></li>
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<dl>
<dt>Software developed in the Pachter group and still under active development in the group</dt>
<ul>
<li>Software and scripts required to reproduce results of papers are hosted at the <a href="https://github.com/pachterlab">Pachter Lab GitHub Repository</a>.</li>
</ul>
</dl>
<dl>
<dt>Software developed in the Pachter group but now maintained/developed elsewhere</dt>
<ul>
<li><a href="http://atifrahman.github.io/SWALO/">SWALO</a> (2016) Scaffolding with assembly likelihood optimization (now supported by Atif Rahman)</li>
<li><a href="http://pachterlab.github.io/PROBer/">PROBer</a> (2015) Quantitative modeling of transcriptome-wide RNA structure-probing experiments (now supported by Bo Li)</li>
<li><a href="http://pachterlab.github.io/cgal/">CGAL</a> (2013) Computing genome assembly likelihoods (now supported by Atif Rahman)</li>
<li><a href="http://fsa.sourceforge.net">FSA</a> (2009) <b>F</b>ast <b>S</b>tatistical <b>A</b>lignment (now supported by <a href="https://www.linkedin.com/in/robert-k-bradley/">Robert Bradley</a> and his group at FHCRC)</li>
<li><a href="http://www.biostat.wisc.edu/~cdewey/mercator/">MERCATOR</a> (2004) Homology mapping (now supported by <a href="https://www.linkedin.com/in/colin-dewey-969971/">Colin Dewey</a> and his group at the University of Wisconsin)</li>
</ul>
</dl>
<dl>
<dt>Retired Software</dt>
These programs, originally developed in the Pachter group, are no longer under active development and are not being supported.
<ul>
<li><b>eXpress</b> (2012) Streaming quantification for high-throughput sequencing (recommended instead: <a href="http://pachterlab.github.io/kallisto/">kallisto</a>)</li>
<li><b>SysCall</b> (2011) Distinguishing heterozygous sites from systematic error in high-thoughput sequenced reads (archived <a href="http://pachterlab.github.io/SysCall/">here</a>)</li>
<li><b>ReadSpy</b> (2012) Assessment of uniformity in RNA-Seq reads</li>
<li><b>MetMap</b> (2010) Analysis of Methyl-Seq experiments</li>
<li><b>Cufflinks</b> (2010) Transcript assembly and abundance estimation for RNA-Seq (recommended instead: <a href="http://pachterlab.github.io/kallisto/">kallisto</a> and <a href="http://pachterlab.github.io/sleuth/">sleuth</a>)</li>
<li><b>Tophat</b> (2009) Splice junction mapper for short RNA-seq reads (archived <a href="https://ccb.jhu.edu/software/tophat/index.shtml">here</a>)</li>
<li><b>AMAP</b> (2007) Protein multiple alignment </li>
<li><b>GENEMAPPER</b> (2006) Reference based gene annotation (recommended instead: <a href="http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html"> an RNA-Seq experiment</a>)</li>
<li><b>MJOIN</b> (2006) Neighbor joining with subtree weights </li>
<li><b>PARALIGN</b> (2006) Alignment polytope construction </li>
<li><b>SLIM</b> (2003) Minimum network design for optimizing the search space for pair hidden Markov models </li>
<li><b>SLAM</b> (2003) Pairwise simultaneous alignment and gene finding (recommended instead: <a href="http://www.nature.com/nbt/journal/v28/n5/abs/nbt.1621.html">an RNA-Seq experiment</a>)</li>
<li><b>MAVID</b> (2003) Multiple alignment of large genomic sequences </li>
<li><b>VISTA</b> (2000) Visualization tool for global alignments</li>
</ul>
</dl>
</div>
</div>
</body>
</html>