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14.2 > Academic > vCAPS_coevolution (2.0_1UN)

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

This requires: bpp1.9-phyl

Maintained by: Petar Petrov
Keywords: caps,vcaps,coevolution,bpp
ChangeLog: vCAPS_coevolution

Homepage:
http://bioinf.gen.tcd.ie/~faresm/software/software.html

Source Downloads:
caps2_src.zip (0914007c32ed22a9cb8a47b55cd18a39)

Download SlackBuild:
vCAPS_coevolution.tar.gz
vCAPS_coevolution.tar.gz.asc (FAQ)

(the SlackBuild does not include the source)

Validated for Slackware 14.2

See our HOWTO for instructions on how to use the contents of this repository.

Access to the repository is available via:
ftp git cgit http rsync

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