| Function | Description |
| AAAlignment-class | "AAAlignment" result of pairwise sequence alignment. |
| AAAlphabet-class | Class "AAAlphabet" Amino Acid Alphabet |
| AASequence | AASequence constructor |
| AASequence-class | "AASequence" Object representation of a protein Sequence |
| AASequenceList-class | Class "AASequenceList" - Container |
| EPAM110 | Amino Acid Substitution matrices |
| listdist-methods | Compute distance matrix from a list |
| readFasta-methods | reader for databases in Fasta file format. |
| salign-methods | Optimal pairwise alignment of two protein sequences. |
| sequlist | AASequenceList with 66 entries. |
| Submatrix-class | Class "Submatrix" Substitution Matrix |
| testalign-methods | Scoring of optimal alingments. |