See: Description
| Interface | Description |
|---|---|
| AttributeNode |
interface for a node (includes branch) in a binary/non-binary
rooted/unrooted tree.
|
| ClusterTree.ClusteringMethod |
An interface for describing Clustering methods
To be updated to cope with Ward's method and others...
|
| Node |
interface for a node (includes branch) in a binary/non-binary
rooted/unrooted tree
|
| ParameterizedTree |
abstract base class for a tree with an Parameterized interface
|
| ParameterizedTree.Factory |
Factory interface
|
| RootedTreeInterface |
Title: RootedTreeInterface
|
| RootedTreeInterface.Instructee | |
| RootedTreeInterface.RBranch | |
| RootedTreeInterface.RNode | |
| Tree |
Interface for a phylogenetic or genealogical tree.
|
| TreeGenerator | |
| TreeIterator | |
| TreeManipulator.BranchAccess |
The branch access objects allow specific operations on a particular branch (refered to as connections
internally to confuse and bewilder)
|
| TreeOperation |
Title: TreeOperation
|
| UnrootedTreeInterface |
Title: UnrootedTreeInterface
|
| UnrootedTreeInterface.BaseBranch | |
| UnrootedTreeInterface.GeneralBranch | |
| UnrootedTreeInterface.Instructee | |
| UnrootedTreeInterface.UBranch | |
| UnrootedTreeInterface.UNode |
| Class | Description |
|---|---|
| CladeSystem |
data structure for a set of splits
|
| ClockTree |
provides parameter interface to a clock tree
(parameters are the minimal node height differences
at each internal node)
|
| ClusterTree | |
| Local |
Implements LOCAL (Larget and Simon, 1999) and stochastic NNI moves for unrooted trees.
|
| LogParameterizedTree |
This class logarithmically transforms tree parameters.
|
| MutationRateModelTree |
Provides parameter interface to any clock-like tree with
serially sampled tips (parameters are the minimal node height differences
at each internal node).
|
| NeighborJoiningTree |
constructs a neighbor-joining tree from pairwise distances
Saitou, N., and Nei, M., (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. |
| NodeFactory | |
| NodeUtils |
Helper routines for dealing with nodes.
|
| ParameterizedTree.ParameterizedTreeBase |
For parameterisations that work by adjusting a base tree (that is, they aren't really
tree's themselves...)
|
| ReadTree |
constructs a tree reading in a New Hampshire treefile, taking care
for internal labels and branch lengths and binary/nonbinary and
rooted/unrooted trees
|
| RootedTreeInterface.Utils | |
| RootedTreeUtils |
This class contains utility methods.
|
| SimpleNode |
data structure for a node (includes branch) in a binary/non-binary
rooted/unrooted tree
|
| SimpleTree |
data structure for a binary/non-binary rooted/unrooted trees
|
| SimulatedAlignment |
generates an artificial data set
|
| SimulatedAlignment.Factory |
A utility class that can be used to generate Simulated alignments based on
a tree with predefined sequence length and substitution model
|
| SplitSystem |
data structure for a set of splits
|
| SplitUtils |
utilities for split systems
|
| Tree.TreeBase | |
| TreeDistanceMatrix |
computes distance matrix induced by a tree
(needs only O(n^2) time, following algorithm DistanceInTree by
D.Bryant and P.
|
| TreeGenerator.Utils | |
| TreeManipulator | |
| TreeManipulator.PALBranchWrapper | |
| TreeManipulator.PALNodeWrapper | |
| TreeOperation.Utils |
Utility class
|
| TreeRestricter | |
| TreeTool | |
| TreeUtils |
various utility functions on trees.
|
| UnconstrainedTree |
provides parameter interface to an unconstrained tree
(parameters are all available branch lengths)
|
| UnrootedTreeInterface.Utils | |
| UPGMATree | Deprecated
Use ClusterTree
|
| Exception | Description |
|---|---|
| TreeParseException |
exception thrown by ReadTree
|