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.

This is a modified version of "CAPS_coevolution", used in the AutoCoEv
pipeline:
https://github.com/mattilalab/autocoev

It applies two _unofficial_ patches:
- 01_caps_verbose: makes the program output its generated trees, as well
  as the p-value for each correlated amino acid pair
- 02_caps_sort_input: introduce a function to sort input file names

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 libraries, but make sure the current versions of the
bppsuite (and its dependencies) are NOT installed at build time.

Citing CAPS:
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