Bios2cor: 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).

Version: 2.2.1
Depends: R (≥ 3.5), bio3d, circular, bigmemory, parallel
Imports: igraph
Published: 2022-07-08
Author: Bruck Taddese [aut], Antoine Garnier [aut], Madeline Deniaud [aut], Julien Pele [ctb], Lea Bellenger [ctb], Jean-Michel Becu [ctb], Marie Chabbert [aut,cre]
Maintainer: Marie Chabbert <marie.chabbert at>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: no
CRAN checks: Bios2cor results


Reference manual: Bios2cor.pdf


Package source: Bios2cor_2.2.1.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): Bios2cor_2.2.1.tgz, r-oldrel (arm64): Bios2cor_2.2.1.tgz, r-release (x86_64): Bios2cor_2.2.1.tgz
Old sources: Bios2cor archive


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