Package pal.tree

Classes for providing the data structure of trees, for constructing and modifying trees, and for parameterizing trees (e.g., clock constraint).

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
 

Package pal.tree Description

Classes for providing the data structure of trees, for constructing and modifying trees, and for parameterizing trees (e.g., clock constraint).