From Biological Sequences and Simulations to Correlation Analysis

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Documentation for package ‘Bios2cor’ version 2.2

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bios2cor-package Correlation/covariation Analysis in Biological Sequences and Simulations
angle2rotamer Converts dihedral angles to rotamers
angles.plot plots the time evolution of the dihedral angles in top pairs
Bios2cor Correlation/covariation Analysis in Biological Sequences and Simulations
bios2cor Correlation/covariation Analysis in Biological Sequences and Simulations
centered_pca Performs principal component analysis of a correlation/covariation matrix
delta_filter Creation of an entropy/dynamic score delta filter for each element
dynamic_circular Circular correlation
dynamic_entropy Variability score
dynamic_mi Mutual Information (MI) function applied to rotamers in molecular dynamics simulations
dynamic_mip Mutual Information Product (MIP) function applied to rotamers in molecular dynamics simulations
dynamic_omes OMES (Observed minus Expected Squared) function applied to rotamers in molecular dynamics simulations
dynamic_structure Creates the data structure for the analysis of side chain dihedral angles
elsc Explicit Likelihood of Subset Covariation (ELSC) function
entropy Entropy score
import.fasta Reads a file in FASTA format
import.msf Reads a multiple sequence alignment file in MSF format
mcbasc McBASC (McLachlan Based Substitution Correlation) function
mi Mutual Information (MI) function
mip Mutual Information product (MIP) function
network.plot Creates network structure of top elements
omes OMES (Observed minus Expected Squared) function
pca_2d PCA projection on two dimensions
pca_screeplot Creates PCA screeplot
random.msa Random Alignment
scores.boxplot Creates boxplots of correlation/covariation scores
scores_entropy.plot Scores versus entropy graph
top_pairs_analysis Calculates the number of contacts for each element of the top pairs
write.entropy Writes and displays entropy values
write.pca Creates a file of coordinates in PCA space
write.pca.pdb PDB and PML file creation for 3D representation of PCA analysis
write.scores Creates a correlation/covariation ouput file
xyz2torsion Convert Cartesian Coordinates to Torsion Angles