• ECDFBiologyPackages

This list was sent by Chris Kant. It is not clear which are needed on the ECDF.

Sequence Searching

• BLAST http://www.ncbi.nlm.nih.gov/blast/download.shtml

• hmmer http://hmmer.janelia.org (enable-pvm for clusters)

• SAM http://www.cse.ucsc.edu/compbio/HMM-apps/T02-query.html (query entry no download)

• BLAT http://www.kentinformatics.com/products.html (is this freeware)

• SAHA2 http://www.sanger.ac.uk/Software/analysis/SSAHA/

• WU http://blast.wustl.edu/

• ESTScan http://estscan.sourceforge.net/

• Emboss http://www.emboss.org

• FAST ??? Toomany fasts

Sequence Database (is this software?)

• Pfam http://www.sanger.ac.uk/Software/Pfam/

Sequence Alignment

• ClustalW http://www.ebi.ac.uk/clustalw/

• Muscle http://www.drive5.com/muscle

• ProbCons http://probcons.stanford.edu

• PartialOrderAlignment(POA) http://www.bioinformatics.ucla.edu/poa

Protein Structure Prediction

• Amber http://amber.scripps.edu (license costs 400 dollars)

• Modeller http://salilab.org/modeller(register for license)

Protein Function Analysis

• Sifter http://sifter.berkeley.edu/

Crystalography/NMR Software

• ZDOCK http://zdock.bu.edu/ (this is a site for queries)

Gene Prediction Tools

• GeneScan http://genes.mit.edu/GENSCAN.html(signed license needed)

RNA Secondary Structure Prediction

• Mfold http://www.bioinfo.rpi.edu/%7Ezukerm/export/mfold-3.html (replaced by UNAfold whose functionality can be extended with glut/OpenGL, GD Library, gnuplot)

• RNAVienna Package http://www.tbi.univie.ac.at/~ivo/RNA/

• RNAMotif http://www.scripps.edu/mb/case/casegr-sh-3.5.html(GNU License)

In-House Software Requirements

• Perl + BioPerl http://www.bioperl.org/

• Python + BioPython http://www.biopython.org

• C, C++

• Java + BioJava http://www.biojava.org

  • BioPerl, BioPython and BioJava are installed from associated Wikis

Bayesian Inference of Phylogeny

• MrBayes http://mrbayes.csit.fsu.edu/ can use MPI

• BayesPhylogenies http://www.evolution.rdg.ac.uk/BayesPhy.html

• PAUP http://paup.csit.fsu.edu/ (a cost is involved at the moment, but a GNU licence version is expected last summer

• PhyML http://atgc.lirmm.fr/phyml/

• Modeltest http://darwin.uvigo.es/software/modeltest.html a script that runs paup; it would help if it could launch 50 instances and do its model testing in parallel)

• PAML http://abacus.gene.ucl.ac.uk/software/paml.html

• Beast java http://www.beastsoftware.org/

• Structure java ????

• HyPhy http://www.hyphy.org/ (said to be parallelised for

clusters)

Statistics

• R http://www.r-project.org http://www.bioconductor.org/ Mathematics

• Mathematica http://www.wolfram.com/GridMathemica is available at http://www.wolfram.com/products/gridmathematica/whatis.html

See also [: ECDF Biology CMS call 437178:ECDF Biology CMS call 437178]