3.1. List of packages present in the Bio Roll

The Bio Roll contains a suite of Bio-informatics applications, most commonly in use by the bio-informatics community. The list of applications is as follows:

• HMMER - http://hmmer.janelia.org/

• NCBI BLAST - From National Center for Biotechnology Information - www.ncbi.nlm.nih.gov/BLAST/

• MpiBLAST - From Los Alamos National Laboratory - http://mpiblast.lanl.gov/

• biopython - www.biopython.org

• ClustalW - From the European BioInformatics Institute - http://www.ebi.ac.uk/clustalw/

• MrBayes - From School of Computational Science at the Florida State University - http://mrbayes.csit.fsu.edu/

• T_Coffee - From Information Genomique et Structurale at Centre National de la Recherche Scientifique - The T-Coffee Home Page

• Emboss - From European Molecular Biology Institute - http://emboss.sourceforge.net/

• Phylip - From the Dept. of Biology at the University of Washington - http://evolution.genetics.washington.edu/phylip.html

• fasta - From the University of Virginia - http://fasta.bioch.virginia.edu/

• Glimmer - From Center for Bioinformatics and Computational Biology at the University of Maryland - http://www.cbcb.umd.edu/software/glimmer/

• TIGR Assembler - From the J. Craig Venter Institute - http://www.jcvi.org/cms/research/software/

• All the perl utilities mentioned below are from CPAN

• perl-bioperl

• perl-bioperl-ext

• perl-bioperl-run

• perl-bioperl-db

All the packages that appear below are dependencies and are already present in the base and OS Rolls. They are installed automatically during system installation.