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