# From Biological Sequences and Simulations to Correlation Analysis

## Documentation for package ‘Bios2cor’ version 2.2.1

- DESCRIPTION file.

## Help Pages

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