Interface | Description |
---|---|
RootedTree |
A tree with a root (node with maximum height).
|
Tree |
A rooted or unrooted tree.
|
TreeBuilder<T extends Tree> |
Class | Description |
---|---|
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 | Description |
---|---|
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/