| • Alphabet | Alphabets and genetic codes. | |
| • Sequences | Loading sequences/alignments. | |
| • Tree | Loading trees. | |
| • AlphabetIndex | Setting biochemical properties and distances. | |
| • Process | ||
| • Distribution | Setting of the discrete distributions. | |
| • Estimation | Estimating parameters by maximizing a likelihood function. | |
| • WritingSequences | Writing sequences/alignments to files. | |
| • WritingTrees | Writing trees to files. |