| AlignI | An interface for describing sequence alignments. |
| DNAStatistics | Calculate some statistics for a DNA alignment |
| PairwiseStatistics | Base statistic object for Pairwise Alignments |
| ProteinStatistics | Calculate Protein Alignment statistics (mostly distances) |
| StatisticsI | Calculate some statistics for an alignment |
| Utilities | A collection of utilities regarding converting and manipulating alignment objects |