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