Uses of Package
Trees

Packages that use Trees
Ancestors Provides classed to calculate ancestral reconstruction. 
Constraints Provides classes to constrain the state of internal nodes. 
Likelihood Provides classes for calculating the likelihood of a tree given a model and an alignment. 
Optimizers Provides classes for optimising a likelihood. 
Simulations Provides a class to create simulate data. 
Trees Provides classes to define a tree and any constraints on that tree. 
 

Classes in Trees used by Ancestors
Tree
          Represents a phylogenetic tree.
TreeException
          Exception thrown when there is a problem with a tree
 

Classes in Trees used by Constraints
Tree
          Represents a phylogenetic tree.
TreeException
          Exception thrown when there is a problem with a tree
 

Classes in Trees used by Likelihood
Branch
          Represents a branch in a tree
Tree
          Represents a phylogenetic tree.
TreeException
          Exception thrown when there is a problem with a tree
 

Classes in Trees used by Optimizers
TreeException
          Exception thrown when there is a problem with a tree
 

Classes in Trees used by Simulations
Tree
          Represents a phylogenetic tree.
TreeException
          Exception thrown when there is a problem with a tree
 

Classes in Trees used by Trees
Branch
          Represents a branch in a tree
Tree
          Represents a phylogenetic tree.
TreeException
          Exception thrown when there is a problem with a tree