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<!DOCTYPE html>
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<div id="sitetitle" class="sixteen columns"><a href="index.html">The Hahn Lab</a></div>
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<ul>
<li><a href="research.html">Research</a></li>
<li><a href="publications.html">Publications</a></li>
<li><a href="people.html">People</a></li>
<li><a href="software.html">Software</a></li>
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<div class="fourteen columns offset-by-one">
<h3>Software</h3>
<ul class="softwarelist">
<li><strong>Heterogeneity test: </strong> Coalescent test for differences in allele frequency distributions</li>
<ul>
<li><a href="Programs/make_trees.txt">[Download]</a> <a href="Htest.html">[Instructions]</a> <a href="publications.html#Heterogeneity">[Citation]</a></li>
<li></li>
</ul>
<li><strong>CAFE: </strong>Computational analysis of (gene) family evolution</li>
<ul>
<li> <strong>CAFE v5: </strong><a href="https://github.com/hahnlab/CAFE5">[Website]</a> <a href="publications.html#CAFE5">[Citation]</a></li>
<li></li>
</ul>
<li><strong>Dfoil: </strong>Introgression testing for a five-taxon phylogeny</li>
<ul>
<li><a href="http://www.github.com/jbpease/dfoil">[Download]</a> <a href="publications.html#dfoil">[Citation]</a></li>
</ul>
<li><strong>AGOUTI: </strong>Improving assembly and annotation using RNA-seq</li>
<ul>
<li><a href="http://www.github.com/svm-zhang/AGOUTI">[Download]</a> <a href="Programs/AGOUTI/agouti_example_fasta_gff.tar.gz">[Example assembly and annotation]</a> <a href="publications.html#AGOUTI">[Citation]</a></li>
</ul>
<li><strong>GRAMPA: </strong>Gene-tree reconciliation algorithm using MUL-trees for polyploid analysis</li>
<ul>
<li><a href="http://www.github.com/gwct/grampa">[Download]</a> <a href="publications.html#GRAMPA">[Citation]</a></li>
<li></li>
</ul>
<li><strong>TEFLoN: </strong>Transposable element frequency and location navigator</li>
<ul>
<li><a href="http://www.github.com/jradrion/TEFLoN">[Download]</a> <a href="publications.html#TEFLoN">[Citation]</a></li>
<li></li>
</ul>
<li><strong>PePo: </strong>Probabilities of hemiplasy versus probabilities of homoplasy</li>
<ul>
<li><a href="https://github.com/guerreror/pepo">[Download]</a> <a href="publications.html#PePo">[Citation]</a></li>
<li></li>
</ul>
<li><strong>Referee: </strong>Genome assembly quality scores</li>
<ul>
<li><a href="https://gwct.github.io/referee/">[Download]</a> <a href="publications.html#Referee">[Citation]</a></li>
<li></li>
</ul>
<li><strong>HeIST: </strong>Hemiplasy Inference Tool (for discrete traits)</li>
<ul>
<li><a href="https://github.com/mhibbins/HeIST">[Download]</a> <a href="publications.html#Heist">[Citation]</a></li>
<li></li>
</ul>
<li><strong>sCF: </strong>Site concordance factors</li>
<ul>
<li><a href="https://iqtree.github.io/">[Download]</a> <a href="publications.html#sCF">[Citation (parsimony version)]</a> <a href="publications.html#sCFl">[Citation (likelihood version)]</a></li>
<li></li>
</ul>
<li><strong>CAGEE: </strong>Computational Analysis of Gene Expression Evolution</li>
<ul>
<li><a href="https://github.com/hahnlab/CAGEE">[Website]</a> <a href="publications.html#CAGEE">[Citation]</a></li>
<li></li>
</ul>
<li><strong>seastaR: </strong>Construct a phylogenetic covariance matrix with discordance</li>
<ul>
<li><a href="https://github.com/larabreithaupt/seastaR">[Download]</a> <a href="publications.html#seastaR">[Citation]</a></li>
<li></li>
</ul>
<li><strong>phyloGAN: </strong>Phylogenetic generative adversarial network</li>
<ul>
<li><a href="https://github.com/meganlsmith/phyloGAN/">[Download]</a> <a href="publications.html#phyloGAN">[Citation]</a></li>
<li></li>
</ul>
<li><strong>NoDEAR: </strong>No Disequilibrium Estimation of Accurate Recombination</li>
<ul>
<li><a href="https://github.com/smishra677/nodear">[Download]</a> <a href="publications.html#NoDEAR">[Citation]</a></li>
<li></li>
</ul>
<li><strong>reconcILS: </strong>Gene tree-species tree reconciliation with ILS</li>
<ul>
<li><a href="https://github.com/smishra677/reconcILS">[Download]</a> <a href="https://www.biorxiv.org/content/10.1101/2023.11.03.565544v4">[Citation]</a></li>
<li></li>
</ul>
<li><strong>dupcoal: </strong>Coalescent simulator with duplication and loss under the MSC-DL model</li>
<ul>
<li><a href="https://github.com/meganlsmith/dupcoal">[Download]</a> <a href="https://www.biorxiv.org/content/10.1101/2023.11.03.565544v4">[Citation]</a></li>
<li></li>
</ul>
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