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Consed/Phred/Phrap
IDEA - Interactive Display for Evolutionary Analyses Installed on genomes in /share/apps/idea.
Mr. Bayes
PAML Installed on genomes in /share/apps/paml/bin. Documentation is in /share/apps/paml/docs, and examples in /share/apps/paml/examples.
Paup is currently disabled while we determine its licensing status. If you would like to be consulted when/if we decide to purchase it, please let us know.
PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
Phylip Installed on genomes in /share/apps/phylip. Documentation is in /share/apps/phylip/docs.
RAxML is installed on phylocluster in /share/apps/RAxML/bin. Sample datasets are in /share/apps/RAxML/samples. The http://icwww.epfl.ch/~stamatak/index-Dateien/countManual7.0.4.php manual can be downloaded from http://icwww.epfl.ch/~stamatak/index-Dateien/countManual7.0.4.php here
Rosetta
SATe is installed on the clusters. To use it use this job script . Here are some instructions for doing this.
SEALS
tRNAscan is installed on Gutell Lab's gaon2 system in /share/apps. To use: To run type
/share/apps/tRNAscan/bin/setup.tRNAscan-SE
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