# Package jebl.evolution.trees

package jebl.evolution.trees

Class
Description
AbstractRootedTree
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.
ConsensusTreeBuilder.Method
Supported consensus methods.
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
A rooted tree concrete class that wraps another tree and provides a differently rooted view of that tree.
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..
RootedTree
A tree with a root (node with maximum height).
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
SortedRootedTree.BranchOrdering
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.
TransformedRootedTree.Transform
Tree
A rooted or unrooted tree.
TreeBiPartitionInfo
Work in progress
TreeBiPartitionInfo.DistanceNorm
TreeBuilder<T extends Tree>
TreeBuilderFactory
A meeting point for tree building from sequence data.
TreeBuilderFactory.ConsensusMethod
Supported consensus methods.
TreeBuilderFactory.DistanceModel
Supported pairwise distance methods
TreeBuilderFactory.Method
Supported methods for tree building
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.