Utilities for computation and analysis of correlation/co-variation in multiple sequence alignments and in side chain motions during molecular dynamics simulations. Features include the computation of correlation/co-variation scores using a variety of scoring functions between either sequence positions in alignments or side chain dihedral angles in molecular dynamics simulations and to analyze the correlation/co-variation matrix through a variety of tools including network representation and principal components analysis. In addition, several utility functions are based on the R graphical environment to provide friendly tools for help in data interpretation. Examples of sequence co-variation analysis and utility tools are provided in: Pele J, Moreau M, Abdi H, Rodien P, Castel H, Chabbert M. (2014) <doi:10.1002/prot.24570>. This work was supported by the French National Research Agency (Grant number: ANR-11-BSV2-026).
