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Consed/Phred/Phrap
IDEA - Interactive Display for Evolutionary Analyses Installed on genomes in /share/apps/idea.
Installed on clusters, but not currently active. This is a licensed product, so if someone wants to try it we can get a demo license, and then later a full license to continue using it.
The license terms are very strict. Academic usage does not mean imply non-commercial. If you are a student, and you wish to use the Intel compilers for coursework you can do so under the academic license. However, if you are being paid in any way for the work that you are using the compilers to produce, you no longer fall under the non-commerical license.
Mr. Bayes
PAML
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Installed on genomes in /share/apps/paml/bin. Documentation is in /share/apps/paml/docs, and examples in /share/apps/paml/examples.
Paup
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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
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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
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Installed on genomes in /share/apps/phylip. Documentation is in /share/apps/phylip/docs.
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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
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SATe is installed on the clusters. To use it use this job script . Here are some instructions for doing this.
SEALS
tRNAscan
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is installed on Gutell Lab's gaon2 system in /share/apps. To use:
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To run type
/share/apps/tRNAscan/bin/setup.tRNAscan-SE
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