CoMap¶

Description¶

CoMap performs the following tasks:

Compute probabilistic substitution maps * Test for pairs/groups of sites that do not evolve independently

This module includes 'mica'.

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

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. (2005). A model-based approach for detecting coevolving positions in a molecule. Molecular Biology and Evolution, 22(9), 1919–1928. https://doi.org/10.1093/molbev/msi185

Cite the following article if you use the clustering method

Dutheil, J., & Galtier, N. (2007). Detecting groups of co-evolving positions in a molecule: A clustering approach. BMC Evolutionary Biology, 7, 242. https://doi.org/10.1186/1471-2148-7-242

Cite the following article if you use the candidate approach method

Dutheil, J. Y., Jossinet, F., & Westhof, E. (2010). Base pairing constraints drive structural epistasis in ribosomal RNA sequences. Molecular Biology and Evolution, 27(8), 1868–1876. https://doi.org/10.1093/molbev/msq079

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

Dutheil, J. Y. (2012). Detecting coevolving positions in a molecule: Why and how to account for phylogeny. Briefings in Bioinformatics, 13(2), 228–243. https://doi.org/10.1093/bib/bbr048

biology, genomics