Uses of Class
Trees.Branch

Packages that use Branch
Likelihood Provides classes for calculating the likelihood of a tree given a model and an alignment. 
Trees Provides classes to define a tree and any constraints on that tree. 
 

Uses of Branch in Likelihood
 

Methods in Likelihood with parameters of type Branch
 double Probabilities.getP(RateCategory r, Branch b, java.lang.String startState, java.lang.String endState)
          Gets a specific probability for a change from one state to another along a specific branch under a specific RateClass
 

Uses of Branch in Trees
 

Methods in Trees that return Branch
 Branch Tree.getBranchByChild(java.lang.String child)
          Gets the branch which has the given node as the child node
 

Methods in Trees that return types with arguments of type Branch
 java.util.List<Branch> Tree.getBranches()
          Gets a list of branches.
 java.util.Set<Branch> Tree.getBranchesByParent(java.lang.String parent)
          Gets the set of branches which have the passed node as a parent
 java.util.List<Branch> Tree.getBranchesReversed()
          Gets the branches in the reverse order to that returned by Tree.getBranches().
 java.util.Iterator<Branch> Tree.iterator()
           
 

Methods in Trees with parameters of type Branch
 boolean Tree.isExternal(Branch b)
          Tests whether the given branch is an external branch (i.e.
 

Constructor parameters in Trees with type arguments of type Branch
Tree(java.util.List<Branch> branches)
          Creates a tree from a list of branches