Uses of Class
pal.tree.CladeSystem

Packages that use CladeSystem

pal.tree

Classes for providing the data structure of trees, for constructing and modifying trees, and for parameterizing trees (e.g., clock constraint).

Uses of CladeSystem in pal.tree

Methods in pal.tree that return CladeSystem

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)

Methods in pal.tree with parameters of type CladeSystem

static void

CladeSystem.calculateCladeProbabilities(Tree tree, CladeSystem[] cladeSystems)