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authorPetar Petrov <slackalaxy@gmail.com>2020-10-09 09:40:49 +0100
committerWilly Sudiarto Raharjo <willysr@slackbuilds.org>2020-10-10 10:18:48 +0700
commit2c2f50823f08c9c6cf9219e6a50dfdb1449d8769 (patch)
tree5c5f2ba272216181c92ed78bba9dd028247feb3c /academic/vCAPS_coevolution/README
parente4fea76d0129fd05e7138772f4714dca3994f853 (diff)
academic/vCAPS_coevolution: Added (Coevolution Analysis)
Signed-off-by: Dave Woodfall <dave@slackbuilds.org> Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
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+vCAPS: (verbose) 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:
+This applies an _unofficial_ patch by Petrov et al 2020, to enable more
+verbose output of the program, including CAPS generated phylogenetic
+trees and p-values of the pairwise results. The produced executable is
+called "vCAPS" and can be installed along "caps" from CAPS_coevolution.
+Building CAPS from source requires the Bio++ 1.9 suite.
+
+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