|
||||||||||
| PREV PACKAGE NEXT PACKAGE | FRAMES NO FRAMES | |||||||||
See:
Description
| Interface Summary | |
|---|---|
| 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 Summary | |
|---|---|
| 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 Summary | |
|---|---|
| TreeParseException | exception thrown by ReadTree |
Classes for providing the data structure of trees, for constructing and modifying trees, and for parameterizing trees (e.g., clock constraint).
|
||||||||||
| PREV PACKAGE NEXT PACKAGE | FRAMES NO FRAMES | |||||||||