Sequence analysis and bioinformatics using Debian GNU/Linux

Libre Software Meeting, Nantes, 9. July 2009


The Debian Med project intends to support all fields of medical care and it turned out that the field of microbiology is currently the strongest part of the Debian Med project.

The Lenny release saw the arrival in Debian of EMBOSS, a very comprehensive suite of software for sequence analysis, with one of its web interfaces, EMBOSS Explorer, that you can use locally, on your intranet or on the Internet after an installation as simple as typing "aptitude install emboss-explorer".

Debian Med now distributes all the major free programs for multiple sequence alignment. One of them, T-Coffee, can function as a meta-aligner ("M-Coffee"), that runs multiple programs and combines their outputs in a higher-quality alignment. Its author kindly developed a version that only depends on free software, "DM-Coffee", in which Clustal W is substituted by Kalign.