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.


BACKGROUND
CAPS version 1 is available at http://bioinf.gen.tcd.ie/~faresm/software/caps/. Distribution versions for Linux/Unix, Mac OS X and Windows operating systems are available, including manual and example files.
Fares
Mario A
MA
Evolutionary Genetics and Bioinformatics Laboratory, Department of Genetics Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Dublin, Ireland. faresm@tcd.ie
McNally
David
D
D000465:Algorithms; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D019143:Evolution, Molecular; D020407:Internet; D010802:Phylogeny; D011381:Programming Languages; D011506:Proteins / Q000737:chemistry*; D040901:Proteomics / Q000379:methods; D020539:Sequence Analysis, Protein; D012984:Software; D014584:User-Computer Interface
D011506:Proteins