| Package | Description |
|---|---|
| pal.tree |
Classes for providing the data structure of
trees, for constructing and modifying trees, and for parameterizing
trees (e.g., clock constraint).
|
| Modifier and Type | Method | Description |
|---|---|---|
static CladeSystem |
CladeSystem.getClades(IdGroup idGroup,
Tree tree) |
creates a clade system from a tree
(using a pre-specified order of sequences)
|
static CladeSystem |
CladeSystem.getClades(Tree tree) |
creates a clade system from a tree
(using tree-induced order of sequences)
|
static CladeSystem[] |
CladeSystem.getCladeSystems(Tree[] trees) |
| Modifier and Type | Method | Description |
|---|---|---|
static void |
CladeSystem.calculateCladeProbabilities(Tree tree,
CladeSystem[] cladeSystems) |