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