SeqFeatR_GUI            GUI for SeqFeatR
assocpair               Finding pairs of alignment positions that
                        jointly mutate
assocpairfeat           Finding pairs of sequence alignment positions
                        associated with sequence feature.
assocpoint              Searches for associations of single alignment
                        positions with feature(s)
assocpointhierarchical
                        Searches for associations of single alignment
                        positions with feature(s) with a simple
                        hierarchical model
assocpointpair          Compare results of SeqFeatRs assocpoint with
                        SeqFeatRs assocpair, assocpairfeat
assoctuple              Searches for associations of a tuple of
                        alignment positions with feature(s)
comparewithancestral    Compares ancestral sequence with sequence
                        alignment
foundereffectfinder     Tries to identify a founder effect in results
                        from SeqFeatRs assocpair
getfreqs                Get frequencies for amino acids/nucleotides in
                        alignment window (epitope)
orPlot                  Visualize odds ratios and p-values from
                        SeqFeatRs assocpoint
qvalues                 Calculate q-values from p-values
rewritetuple            Rewrite result from SeqFeatRs assoctuple
smallmanhattan          A small version of manhattan plot
tartan                  Visualize association of mutation pairs and
                        features from two (comparable) analyses.
visualizepair           Visualize pairs of alignment positions that
                        jointly mutate
visualizepairfeat       Visualize pairs of sequence alignment positions
                        associated with sequence feature.
volcanoplot             Create volcano plot
