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
|