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
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
