CoMap
A package for the evolution-based detection of co-evolving positions in a molecule

News

06/03/12
New 1.4.1 version, using Bio++ 2.0.3. Make new alignment file formats and substitution models from Bio++ 2.0.3 available to CoMap and MICA. CoMap packages are now distributed on the Bio++ forge at http://biopp.univ-montp2.fr/repos/. Please note that example files for CoMap and MICA are now distributed along the source code.

29/03/11
New 1.4.0 version, using Bio++ 2.0.1. This version includes a brand new program (MICA - Mutual Information Coevolution Analysis), reimplementing several published MI-based methods. The CoMap software now offers a fast built-in p-value computation for pairwise and candidate groups analyses.

21/01/08
New 1.3.0 version, using Bio++ 1.5. This version includes support for the gamma+invariant rate distribution and for non-homogeneous models of substitutions.

30/11/07
The clutering method has been published in the BMC Evolutionary Biology journal, read the full article at Biomed Central

27/07/07
Update download section with new example files corresponding to cvs version of CoMap (include a bug fix in compensaiton analysis).

19/07/07
New CoMap version 1.2.0, compatibility update with Bio++ 1.4. Rpm file can now also be downloaded (Bio++ rpm files need to be installed too).

19/03/07
New CoMap version, including a new test for compensatory changes. CoMap can now read files from the AAIndex 1 and 2 database.

22/11/06
New CoMap website.

Description

CoMap performs the following tasks:

Download

CoMap may be downloaded from http://biopp.univ-montp2.fr/repos/. Older versions are available at http://download.gna.org/comap. The source code is available as a .tar.gz archive, and requires the Bio++ libraries (bpp-core, bpp-seq and bpp-phyl) to be installed (see http://biopp.univ-montp2.fr). Static executables are also available for the Linux and Win32 platforms.

Supplementary material:

Example data sets (supplementary material of the 2007 paper) are frequently updated as the program options change. These files are distributed along with the source code, in the "example" subdirectory.

Documentation

The documentation of the program is available here [HTML][PDF]. It is distributed along with the program source code.

Citation

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.