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