From Documentation
Revision as of 11:13, 23 April 2013 by Merz (Talk | contribs) (Software Packages: PHYLIP is toast)

Jump to: navigation, search


This page is intended to serve as a community and information hub for our bioinformatics users. It is our hope that interested users and staff share tips and tricks, information about what their groups are doing, and knowledge about the various bioinformatics packages available.

Please edit this page and/or create sub-pages. We ask that information is entered in the wiki (as apposed to linked from a third-party) as much as possible in order to retain the benefits of collective authorship. Remember to tag sub-pages with the category Bioinformatics .

Software Packages

This section is intended to list software that is being used at SHARCNET, as well as other popular packages that users may wish to consider using for their work. Optimally each package listed below will have it's own wiki page including installation, configuration and execution hints and tips, as well as a listing of different groups at SHARCNET that are experienced with the software.

Package Description
BLAST Basic Local Alignment Search Tool
MAFFT multiple sequence alignment program. can employ a range of alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼10,000 sequences), etc.
MrBAYES Bayesian estimation of phylogeny
bioperl toolkit of perl modules useful for scripting bioinformatics


Staff Contacts

The following staff have experience working with bioinformatics applications and may be able to help with domain specific issues. Their contact information can be found in the SHARCNET staff directory.

  • Doug Roberts
  • Mark Hahn
  • Tyson Whitehead
  • Hugh Merz