GNU R from Biological Sequences and Simulations to Correlation
Analysis Utilities for computation and analysis of
correlation/covariation in multiple sequence alignments and in
side chain motions during molecular dynamics simulations. Features
include the computation of correlation/covariation scores using a
variety of scoring functions between either sequence positions in
alignments or side chain dihedral angles in molecular dynamics
simulations and utilities to analyze the correlation/covariation
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 covariation analysis are provided in: (1) Pele J, Moreau
M, Abdi H, Rodien P, Castel H, Chabbert M (2014)
<doi:10.1002/prot.24570> and (2) Taddese B, Deniaud M, Garnier A,
Tiss A, Guissouma H, Abdi H, Henrion D, Chabbert M (2018) <doi:
10.1371/journal.pcbi.1006209>. An example of side chain correlated
motion analysis is provided in: Taddese B, Garnier A, Abdi H,
Henrion D, Chabbert M (2020) <doi: 10.1038/s41598-020-72766-
1>. This work was supported by the French National Research
Agency (Grant number: ANR-11-BSV2-026) and by GENCI (Grant
number: 100567).
