CAPS: coevolution analysis using protein sequences

Coevolution Analysis using Protein Sequences (CAPS) is a PERL based software that identifies co-evolution between amino acid sites. Blosum-corrected amino acid distances are used to identify amino acid co-variation. The phylogenetic sequence relationships are used to remove the phylogenetic and stochastic dependencies between sites. The 3D protein structure is used to identify the nature of the dependencies between co-evolving amino acid sites. Friendly interpretable output files are generated. Availability: CAPS version 1 is available at http://bioinf.gen.tcd.ie/similar to faresm/software/caps/.Distribution versions for Linux/Unix, Mac OS X and Windows operating systems are available, including manual and example files. Contact: faresm@tcd.ie.