CAPS (Coevolution Analysis using Protein Sequences) is a PERL based software that identifies co-evolution between amino acid sites. Blosum-corrected amino acid distances are used to identify amino acid co-variation. The phylogenetic sequence relationships are used to remove the phylogenetic and stochastic dependencies between sites. The 3D protein structure is used to identify the nature of the dependencies between co-evolving amino acid sites.
MISTIC is a web server for graphical representation of the information contained within a MSA (multiple sequence alignment) and a complete analysis tool for Mutual Information networks in protein families.
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W8-14. doi: 10.1093/nar/gkt427. Epub 2013 May 28. MISTIC: Mutual information server to infer coevolution.
Simonetti FL1, Teppa E, Chernomoretz A, Nielsen M, Marino Buslje C.
BIS (Blocks In Sequences)is a tool for the analysis of the coevolution of amino-acid fragments in proteins, and for the identification of their networks
(Weighted) Probabilistic substitution mapping – Compute all (weighted) number of substitutions occurring on each branch of a tree, for each site of an alignment.
Co-evolution analysis – Using the substitution mapping, look for significantly groups of sites departing the null hypothesis of independence. Two kind of analyzes are provided: a pairwise analysis, presented in Dutheil et al. (2005), and a clustering analysis in Dutheil and Galtier (2007). In both cases, a parametric bootstrap approach is used to evaluate the significance of groups. Simulation results are written to separate files, a statistics software like R is required to look for the significance.
Coevolution , an integrated online system that enables comparative analyses of residue coevolution with a comprehensive set of commonly used scoring functions, including Statistical Coupling Analysis (SCA), Explicit Likelihood of Subset Variation (ELSC), mutual information and correlation-based methods.
