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See:
Description
Interface Summary | |
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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 | |
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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 | |
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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).
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