| Package | Description |
|---|---|
| jebl.evolution.align |
Provides classes and interfaces for pairwise alignment of two sequences.
|
| jebl.evolution.coalescent | |
| jebl.evolution.io | |
| jebl.evolution.parsimony | |
| jebl.evolution.treemetrics | |
| jebl.evolution.trees | |
| jebl.evolution.treesimulation |
| Class | Description |
|---|---|
| RootedTree |
A tree with a root (node with maximum height).
|
| Tree |
A rooted or unrooted tree.
|
| TreeBuilderFactory.DistanceModel |
Supported pairwise distance methods
|
| TreeBuilderFactory.Method |
Supported methods for tree building
|
| Class | Description |
|---|---|
| RootedTree |
A tree with a root (node with maximum height).
|
| Class | Description |
|---|---|
| Tree |
A rooted or unrooted tree.
|
| Class | Description |
|---|---|
| Tree |
A rooted or unrooted tree.
|
| Class | Description |
|---|---|
| RootedTree |
A tree with a root (node with maximum height).
|
| Class | Description |
|---|---|
| CladeSystem |
Stores a set of unique clades for a tree
|
| ClusteringTreeBuilder |
An abstract base class for clustering algorithms from pairwise distances
|
| ConsensusTreeBuilder |
A
TreeBuilder that builds a consensus tree for a set of trees on identical leaf sets. |
| ConsensusTreeBuilder.Method |
Supported consensus methods.
|
| FilteredRootedTree | |
| ReRootedTree.RootingType | |
| RootedTree |
A tree with a root (node with maximum height).
|
| SortedRootedTree.BranchOrdering | |
| SplitSystem |
data structure for a set of splits
|
| TransformedRootedTree.Transform | |
| Tree |
A rooted or unrooted tree.
|
| TreeBiPartitionInfo |
Work in progress
|
| TreeBiPartitionInfo.DistanceNorm | |
| TreeBuilder | |
| 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.
|
| TreeSelectionChangeEvent |
Represents a change to the selected nodes in a tree.
|
| Class | Description |
|---|---|
| RootedTree |
A tree with a root (node with maximum height).
|
http://code.google.com/p/jebl2/