CAPS (Coevolution Analysis using Protein Sequences) 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.
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CAPS: coevolution analysis using protein sequences.
Fares MA, McNally D.
Bioinformatics. 2006 Nov 15;22(22):2821-2. Epub 2006 Sep 27.