Package jebl.evolution.trees

Interface Summary
RootedTree A tree with a root (node with maximum height).
Tree A rooted or unrooted tree.
TreeBuilder<T extends Tree>  
 

Class Summary
AttributedCladeSystem Stores a set of unique clades for a tree
BaseEdge Common implementation of Attributable interface used by Nodes.
BaseNode Common implementation of Attributable interface used by Nodes.
CalculateSplitRates Created by IntelliJ IDEA.
CladeSystem Stores a set of unique clades for a tree
ClusteringTreeBuilder<T extends Tree> An abstract base class for clustering algorithms from pairwise distances
CompactRootedTree A memory efficient rooted tree.
ConsensusTreeBuilder<T extends Tree> A TreeBuilder that builds a consensus tree for a set of trees on identical leaf sets.
FilteredRootedTree  
MostProbableTopology Given a set of trees determine the most probable trees, i.e.
MutableRootedTree A simple rooted tree providing some ability to manipulate the tree.
NeighborJoiningTreeBuilder Constructs an unrooted tree by neighbor-joining using pairwise distances.
ReRootedTree  
RootedFromUnrooted Root an unrooted tree.
RootedSubtree A simple, immutable rooted tree implementation that is a subtree of an existing tree subtending a specified set of taxa..
RootedTreeUtils Static utility functions for rooted trees.
SimpleRootedTree A simple, and initially immutable rooted tree implementation.
SimpleTree A basic implementation on an unrooted tree.
SortedRootedTree  
SplitSystem data structure for a set of splits
SplitUtils utilities for split systems
TransformedRootedTree This RootedTree class wraps another RootedTree and transforms the branch lengths and node heights using various functions.
TreeBiPartitionInfo Work in progress
TreeBuilderFactory A meeting point for tree building from sequence data.
TreeChangeEvent Represents a change to a tree.
TreeChangeListener A listener for notifying about changes to a tree or to the selected nodes in a tree.
TreeSelectionChangeEvent Represents a change to the selected nodes in a tree.
Utils A collection of utility functions for trees.
 

Enum Summary
ConsensusTreeBuilder.Method Supported consensus methods.
ReRootedTree.RootingType  
SortedRootedTree.BranchOrdering  
TransformedRootedTree.Transform  
TreeBiPartitionInfo.DistanceNorm  
TreeBuilderFactory.ConsensusMethod Supported consensus methods.
TreeBuilderFactory.DistanceModel Supported pairwise distance methods
TreeBuilderFactory.Method Supported methods for tree building
 



http://code.google.com/p/jebl2/