| 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 |
| SeqFeatR_GUI | GUI for SeqFeatR |
| 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 |