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- ATLAS is a programming library which aims to provide very fast linear algebra routines.
Installed on phylocluster in /share/apps/atlas. On other clusters/systems may be installed in /usr/lib and /usr/include.h as part of the atlas-3.6.0 package. - Blast
- BEAST 1.8.0 was installed in phylocluster
- Bioconductor
- Bioperl
BioPython - Installed on clusters. Use /opt/rocks/bin/python as your python interpreter.
- BioMart Perl APIs
- NCBI Eutils
- Qiime 1.7.0 is installed on phylocluster.
- R
- Python
- Mathematica (installed in /share/apps/bin/math on phylocluster. Also installed is mash.pl a program which can be used to run .m files on the nodes. See http://ai.eecs.umich.edu/people/dreeves/mash/] for more details.)
- Mat-lab -UT has site-licensed Mat lab 2013.
- LAPACK is a set of libraries which allow common linear algebra procedures to be performed. LAPACK depends on BLAS for much of the low-level calculations.
- BLAS libraries are hardware tuned routines to work on matrices. Likely you would use this not by itself, but as part of ATLAS or LAPACK.
- Graphics programs
- BOOST libraries
- Phred, Phrap, Consed, cross_match, daev
- Picard
- Hmmer
- Data compression programs
- Clustering programs - MCL and usearch, uclust
- ssh - generating keys
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Transcriptome de novo assembly
ABI pipelines
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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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