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- CAPS: Coevolution Analysis using Protein Sequences
- CAPS is aimed at measuring the coevolution between amino acid sites
- belonging to the same protein (intra-molecular coevolution) or to two
- functionally or physically interacting proteins (inter-molecular
- coevolution). The Software implements an improved method to detect
- intra-molecular coevolution as published in Genetics (Fares and Travers,
- 2006) and also inter-protein coevolution analysis. The improved scoring
- of amino acid sites is obtained by maximum likelihood ancestral state
- reconstruction along with simulations to assess significance.
- In addition, a test which assesses whether two proteins are interacting
- is implemented.
- NOTE:
- The script just repackages the binaries provided from upstream. If you
- want to compile the program from source check "vCAPS_coevolution", which
- also comes with an unofficial patch that extends the verbosity of the
- results.
- CITING:
- CAPS: coevolution analysis using protein sequences. Fares MA, McNally D.
- Bioinformatics. 2006 Nov 15;22(22):2821-2. PMID: 17005535
- The mathematical model has been described separately:
- A novel method for detecting intramolecular coevolution: adding a
- further dimension to selective constraints analyses. Fares MA, Travers
- SA. Genetics. 2006 May;173(1):9-23. PMID: 16547113
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