CoMap

Description

comap website

CoMap performs the following tasks: * Compute probabilistic substitution maps * Test for pairs/groups of sites that do not evolve independently This module includes 'mica'.

Environment Modules

Run module spider comap to find out what environment modules are available for this application.

Environment Variables

• HPC_COMAP_DIR - installation directory
• HPC_COMAP_BIN - executable directory

Citation

If you publish research that uses comap you have to cite it as follows:

Cite the following article if you use the pairwise method

Dutheil J, Pupko T, Jean-Marie A, Galtier N.

A model-based approach for detecting coevolving positions in a molecule.

Mol Biol Evol. 2005 Sep;22(9):1919-28.

Cite the following article if you use the clustering method

Dutheil J, Galtier N.

Detecting groups of co-evolving positions in a molecule: a clustering approach.

BMC Evol Biol. 2007 Nov 30;7(1):242

Cite the following article if you use the candidate approach method

Dutheil JY, Jossinet F, Westhof E.

Base pairing constraints drive structural epistasis in ribosomal RNA sequences.

Mol Biol Evol. 2010 Aug;27(8):1868-76

MICA and the new p-value computation algorithm are described in:

Dutheil JY. Detecting coevolving positions in a molecule: why and how to account for phylogeny. Brief Bioinform. 2011 Sep 24.

Categories

biology, genomics