CorMut-package          Detect the correlated mutations based on
                        selection pressure
JI-class                Class "JI"
MI-class                Class "MI"
biCkaksCodon-class      Class "biCkaksCodon", "biCkaksAA", "biMICodon"
                        and "biMIAA"
biCompare-class         Class "biCompare"
biCompare-methods       biCompare implement biCompare methods for
                        comparison of the correlated mutations between
                        two conditions by the means of correlated
                        mutation network
ckaks-class             Class "ckaks"
ckaksAA                 Compute the conditional kaks(conditional
                        selection pressure) among amino mutations
ckaksCodon              Compute the conditional kaks(conditional
                        selection pressure) among codons
filterSites-methods     filterSites methods
jiAA                    Compute the Jaccard index among individual
                        amino mutations
kaksAA                  Compute kaks for individual amino mutation
kaksAA-class            Class "kaksAA"
kaksCodon               Compute kaks for individual codon
kaksCodon-class         Class "kaksCodon"
miAA                    Compute the mutual information among individual
                        amino mutations
miCodon                 Compute the mutual information among codons
plot                    Plot methods for CorMut package
seqFormat-methods       Process the multiple sequence alignment files
