| AlleleNode | A Node with Alleles attached |
| AnnotatableNode | A Tree Node with support for annotation |
| Compatible | Testing compatibility of phylogenetic trees
with nested taxa. |
| DistanceFactory | Construct a tree using distance based methods |
| Node | A Simple Tree Node |
| NodeI | Interface describing a Tree Node |
| NodeNHX | A Simple Tree Node with support for NHX tags |
| RandomFactory | TreeFactory for generating Random Trees |
| Statistics | Calculate certain statistics for a Tree |
| Tree | An implementation of the TreeI interface. |
| TreeFunctionsI | Decorated Interface implementing basic Tree exploration methods |
| TreeI | A Tree object suitable for lots of things, designed
originally for Phylogenetic Trees. |