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Computational tools from various research groups

<h2>DNA Sequence Assembly & Analysis</h2>
<a href="http://popgen.dk/wiki/index.php/ANGSD" rel="external">ANGSD</a><br>
<a href="https://github.com/mojaveazure/angsd-wrapper" rel="external">ANGSD-wrapper</a><br>
<a href="https://github.com/pezmaster31/bamtools/wiki" rel="external">bamtools</a><br>
<a href="http://samtools.github.io/bcftools/" rel="external">bcftools</a><br>
<a href="https://github.com/arq5x/bedtools2/releases" rel="external">bedtools</a><br>
<a href="https://github.com/lh3/bioawk" rel="external">bioawk</a><br>
<a href="http://bowtie-bio.sourceforge.net/bowtie2/index.shtml" rel="external">Bowtie 2</a><br>
<a href="http://bio-bwa.sourceforge.net/" rel="external">BWA</a><br>
<a href="http://stephenslab.uchicago.edu/software.html" rel="external">fastPHASE and PHASE</a><br>
<a href="https://www.broadinstitute.org/gatk/" rel="external">Genome Analysis Toolkit (GATK)</a><br>
<a href="http://molpopgen.github.io/libsequence/" rel="external">libsequence</a><br>
<a href="http://www.novocraft.com/products/novoalign/" rel="external">Novoalign</a><br>
<a href="http://broadinstitute.github.io/picard/" rel="external">Picard</a><br>
<a href="http://droog.gs.washington.edu/polyphred/" rel="external">PolyPhred</a><br>
<a href="http://samtools.sourceforge.net/" rel="external">SAMtools</a><br>
<a href="https://github.com/vsbuffalo/scythe/blob/master/README.md" rel="external">Scythe</a><br>
<a href="https://github.com/vsbuffalo/seqqs" rel="external">seqqs</a><br>
<a href="https://github.com/lh3/seqtk" rel="external">seqtk</a><br>
<a href="https://vcftools.github.io/index.html" rel="external">VCFtools</a><br>

<h2>Genetic Assignment</h2>
<a href="http://www.genetics.ucla.edu/software/admixture/" rel="external">ADMIXTURE</a><br>
<a href="http://www.stanford.edu/group/rosenberglab/clumpp.html" rel="external">CLUMPP</a><br>
<a href="http://www.stanford.edu/group/rosenberglab/distruct.html" rel="external">distruct</a><br>
<a href="http://www.stanford.edu/group/rosenberglab/infocalc.html" rel="external">infocalc</a><br>
<a href="http://cbsuapps.tc.cornell.edu/InStruct.aspx" rel="external">InStruct</a><br>
<a href="http://stephenslab.uchicago.edu/software.html#scat" rel="external">SCAT</a><br>
<a href="http://pritchardlab.stanford.edu/structure.html" rel="external">Structure</a><br>
<a href="http://cteg.berkeley.edu/~structurama/" rel="external">Structurama</a><br>
<a href="http://membres-timc.imag.fr/Olivier.Francois/tess.html" rel="external">TESS</a><br>

<h2>Genotyping & SNP Data</h2>
<a href="http://alchemy.sourceforge.net/" rel="external">Alchemy</a><br>

<h2>Marker & QTL Analyses</h2>
<a href="http://www.evachan.org/" rel="external">Eva Chan's R Scripts</a><br>
<a href="https://cran.r-project.org/web/packages/hierfstat/index.html" rel="external">hierfstat</a><br>
<a href="https://cran.r-project.org/web/packages/LDheatmap/index.html" rel="external">LDHeatmap</a><br>
<a href="http://pngu.mgh.harvard.edu/~purcell/plink/" rel="external">plink</a><br>
<a href="http://www.rqtl.org/" rel="external">R/QTL</a><br>

<h2>Simulation Tools</h2>
<a href="http://molpopgen.github.io/fwdpp/" rel="external">fwdpp</a><br>
<a href="https://code.google.com/archive/p/macs/" rel="external">macs</a><br>
<a href="http://home.uchicago.edu/rhudson1/source/mksamples.html" rel="external">ms</a><br>
<a href="http://www.mabs.at/ewing/msms/index.shtml" rel="external">msms</a><br>
<a href="http://sfscode.sourceforge.net/SFS_CODE/index/index.html" rel="external">SFS_CODE</a><br>

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