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)