ang_evo_graph           Angle evolution graphs
angle_conversion        Conversion of dihedral angles to rotamers
bios2cor-package        Correlation Analysis in Biological Sequences
                        and Simulations
centered_pca            Principal component analysis of a
                        correlation/covariation matrix
corr_contact            Calculates the number of contacts for each
                        element of the top pairs
create_boxplot          Creates boxplot file
create_corrfile         Creates a correlation file
create_entropyfile      Stores entropy values
create_network          Creates network structure of top elements
create_pcafile          Creates a file of coordinates in PCA space
create_screeplot        Creates PCA screeplot
cyto_entropy            Creation of a entropy file in Cytoscape format
cyto_zscore             Creation of a Z-score file in Cytoscape format
delta_weighting         Creation of a Delta weighting filter for each
                        element
dynamic_struct          Creates the data structure for the analysis of
                        side chain dihedral angles
elsc                    ELSC(Explicit Likelihood of Subset Covariation)
                        function
entropy                 Entropy score
entropy_graph           Entropy graph
gauss_weighting         Creation of a gaussian weighting filter for
                        each element
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
mip                     MIp(Mutual Information product) function
omes                    OMES(Observed minus Expected Squared) function
pca_2d                  PCA projection on two dimensions
random.msa              Random Alignment
rotamer_circular        Circular correlation
rotamer_entropy         Entropy score
rotamer_mip             MIP(Mutual Information Product) function
                        applied to rotamers in molecular dynamics
                        simulations
rotamer_omes            OMES(Observed minus Expected Squared) function
                        applied to rotamers in molecular dynamics
                        simulations
shuffle_all             Amino acids shuffle
shuffle_positions       Amino acids shuffle
sigmoid_weighting       Sigmoid weighting for each position
write_pdb               PDB and PML file creation for 3D representation
                        of PCA analysis
xyz2torsion             Convert Cartesian Coordinates to Torsion Angles
