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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 |
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| 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 |
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| 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. |