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 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, also available at SBo, which can be safely
installed along the current version. Fore details of the patch see pre-
print at bioRxiv by Petrov et al.:
https://doi.org/10.1101/2020.09.29.315374

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