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.
Node interface for a node (includes branch) in a binary/non-binary rooted/unrooted tree
Tree Interface for a phylogenetic or genealogical tree.
 

Class Summary
ClockTree provides parameter interface to a clock tree (parameters are the minimal node height differences at each internal node)
DatedTipsClockTree provides parameter interface to a clock tree with dated tips, following A.
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
NodeFactory Creates nodes The purpose of this class is to decouple the creation of a class of type "Node" from its actual implementation.
NodeUtils Helper routines for dealing with nodes.
ParameterizedTree abstract base class for a tree with an Parameterized interface
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
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
SplitSystem data structure for a set of splits
SplitUtils utilities for split systems
SUPGMATree constructs an SUPGMA tree from pairwise distances.
TreeDistanceMatrix computes distance matrix induced by a tree (needs only O(n^2) time, following algorithm DistanceInTree by D.Bryant and P.
TreeUtils various utility functions on trees.
UnconstrainedTree provides parameter interface to an unconstrained tree (parameters are all available branch lengths)
UPGMATree constructs a UPGMA tree from pairwise distances
 

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).