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33 lines
1.6 KiB
Text
33 lines
1.6 KiB
Text
vCAPS: (verbose) Coevolution Analysis using Protein Sequences
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CAPS is aimed at measuring the coevolution between amino acid sites
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belonging to the same protein (intra-molecular coevolution) or to two
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functionally or physically interacting proteins (inter-molecular
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coevolution). The Software implements an improved method to detect
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intra-molecular coevolution as published in Genetics (Fares and Travers,
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2006) and also inter-protein coevolution analysis. The improved scoring
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of amino acid sites is obtained by maximum likelihood ancestral state
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reconstruction along with simulations to assess significance.
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This is a modified version of "CAPS_coevolution", used in the AutoCoEv
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pipeline:
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https://github.com/mattilalab/autocoev
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It applies two _unofficial_ patches:
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- 01_caps_verbose: makes the program output its generated trees, as well
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as the p-value for each correlated amino acid pair
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- 02_caps_sort_input: introduce a function to sort input file names
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The produced executable is called "vCAPS" and can be installed along
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"caps" from CAPS_coevolution. Building CAPS from source requires the
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Bio++ 1.9 suite libraries, but make sure the current versions of the
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bppsuite (and its dependencies) are NOT installed at build time.
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Citing CAPS:
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CAPS: coevolution analysis using protein sequences. Fares MA, McNally D.
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Bioinformatics. 2006 Nov 15;22(22):2821-2. PMID: 17005535
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The mathematical model has been described separately:
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A novel method for detecting intramolecular coevolution: adding a
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further dimension to selective constraints analyses. Fares MA, Travers
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SA. Genetics. 2006 May;173(1):9-23. PMID: 16547113
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