Package jebl.evolution.trees

Interface Summary

IntervalGenerator
RootedTree	A tree with a root (node with maximum height).
Tree	An unrooted tree.
TreeBuilder<T extends Tree>

Class Summary

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>	Build a consensus tree for a set of trees.
FilteredRootedTree
GreedyRootedConsensusTreeBuilder	Date: 5/03/2006 Time: 09:40:18
GreedyUnrootedConsensusTreeBuilder	Builds greedy consensus tree given a set of unrooted trees.
MRCACConsensusTreeBuilder	Construct a consensus tree for a set of rooted trees.
MutableRootedTree	A simple rooted tree providing some ability to manipulate the tree.
NeighborJoiningTreeBuilder	Constructs an unrooted tree by neighbor-joining using pairwise distances.
RootedFromUnrooted	Root an unrooted tree.
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.
TreeBuilderFactory	A meeting point for tree building from sequence data.
TreeSimulator	This class provides the framework for (backwards-through-time) tree simulation.
Utils	A collection of utility functions for trees.

Enum Summary

ConsensusTreeBuilder.Method	Supported consesus methods.
SortedRootedTree.BranchOrdering
TransformedRootedTree.Transform
TreeBuilderFactory.ConsensusMethod	Supported consensus methods.
TreeBuilderFactory.DistanceModel	Supported pairwise distance methods
TreeBuilderFactory.Method	Supported methods for tree building