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---
layout: page
permalink: /software/index.html
title: Software
tags:
---
<div class="promoted">
<img src="/images/qiime_square.png">
QIIME: Quantitative Insights Into Microbial Ecology<br/>
(<a target="_blank" href="https://github.com/qiime/qiime">code</a> | <a target="_blank" href="http://qiime.org/">web</a> | <a target="_blank" href="http://blog.qiime.org/">blog</a> | <a target="_blank" href="http://forum.qiime.org/">forum</a> | <a target="_blank" href="http://www.nature.com/nmeth/journal/v7/n5/full/nmeth.f.303.html">paper</a>)
</div>
<div class="promoted centerPromoted">
<img src="/images/biom_logo.png">
BIOM: Biological Observation Matrix<br/>
(<a target="_blank" href="https://github.com/biom-format/biom-format">code</a> | <a target="_blank" href="http://www.biom-format.org/">web</a> | <a target="_blank" href="http://www.gigasciencejournal.com/content/1/1/7">paper</a>)
</div>
<div class="promoted">
<div class="promotedSpacer"></div>
PICRUST: Phylogenetic Investigation of Communities by Reconstruction of Unobserved STates<br/>
(<a target="_blank" href="https://github.com/picrust/picrust/">code</a> | <a target="_blank" href="http://picrust.github.io/picrust/">web</a>)
</div>
<div style="clear:both"></div>
<div>
PyCogent: Python Comparative Genomics Toolkit<br/>
(<a target="_blank" href="https://github.com/pycogent/pycogent/">code</a> | <a target="_blank" href="http://www.pycogent.org/">web</a> | <a target="_blank" href="http://pycogent.wordpress.com/">blog</a> | <a target="_blank" href="http://genomebiology.com/content/8/8/R171">paper</a>)
</div>
<div>
PrimerProspector<br/>
(<a target="_blank" href="http://sourceforge.net/projects/pprospector/">code</a> | <a target="_blank" href="http://pprospector.sourceforge.net/">web</a> | <a target="_blank" href="http://bioinformatics.oxfordjournals.org/content/early/2011/02/23/bioinformatics.btr087.abstract?sid=fd418a0c-ea5b-4116-9518-d1b5a9edb9f9">paper</a>)
</div>
<div>
PyNAST: Python Nearest Alignment Space Termination tool<br/>
(<a target="_blank" href="https://github.com/qiime/pynast/">code</a> | <a target="_blank" href="http://qiime.org/pynast/">web</a> | <a target="_blank" href="http://pynast.wordpress.com/">blog</a> | <a target="_blank" href="http://bioinformatics.oxfordjournals.org/content/26/2/266.long">paper</a>)
</div>
<div>
MutationFinder<br/>
(<a target="_blank" href="http://sourceforge.net/projects/mutationfinder/">code</a> | <a target="_blank" href="http://mutationfinder.sourceforge.net/">web</a> | <a target="_blank" href="http://bioinformatics.oxfordjournals.org/content/23/14/1862.long">paper</a>)
</div>