Uses of Package
pal.tree

Packages that use pal.tree

Package	Description
pal.coalescent	Classes to model population genetic processes using the coalescent.
pal.distance	Classes for reading and generating distance matrices, including computation of pairwise distances for sequence data (maximum-likelihood and observed distances).
pal.eval	Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters.
pal.gui	GUI components for some special objects (e.g., trees).
pal.mep	Classes for the analysis of "measurably evolving populations" (mep).
pal.statistics	Classes with useful for statistics (normal distribution, Gamma distribution, chi-square distribution, exponential distribution, likelihood-ratio test, chi-square test, descriptive statistics, bootstrap estimators etc.)
pal.supgma
pal.tree	Classes for providing the data structure of trees, for constructing and modifying trees, and for parameterizing trees (e.g., clock constraint).
pal.treesearch
pal.xml	Utility classes for converting PAL objects to and from XML documents.

Classes in pal.tree used by pal.coalescent

Class and Description
ClockTree provides parameter interface to a clock tree (parameters are the minimal node height differences at each internal node)
ParameterizedTree abstract base class for a tree with an Parameterized interface
ParameterizedTree.ParameterizedTreeBase For parameterisations that work by adjusting a base tree (that is, they aren't really tree's themselves...)
SimulatedAlignment.Factory A utility class that can be used to generate Simulated alignments based on a tree with predefined sequence length and substitution model
Tree Interface for a phylogenetic or genealogical tree.
TreeOperation Title: TreeOperation

Classes in pal.tree used by pal.distance

Class and Description
Tree Interface for a phylogenetic or genealogical tree.

Classes in pal.tree used by pal.eval

Class and Description
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
Tree Interface for a phylogenetic or genealogical tree.

Classes in pal.tree used by pal.gui

Class and Description
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
SimpleNode data structure for a node (includes branch) in a binary/non-binary rooted/unrooted tree
Tree Interface for a phylogenetic or genealogical tree.

Classes in pal.tree used by pal.mep

Class and Description
Tree Interface for a phylogenetic or genealogical tree.

Classes in pal.tree used by pal.statistics

Class and Description
Tree Interface for a phylogenetic or genealogical tree.

Classes in pal.tree used by pal.supgma

Class and Description
ClusterTree
ClusterTree.ClusteringMethod An interface for describing Clustering methods To be updated to cope with Ward's method and others...
SimpleTree data structure for a binary/non-binary rooted/unrooted trees
SimulatedAlignment.Factory A utility class that can be used to generate Simulated alignments based on a tree with predefined sequence length and substitution model
Tree Interface for a phylogenetic or genealogical tree.

Classes in pal.tree used by pal.tree

Class and Description
AttributeNode interface for a node (includes branch) in a binary/non-binary rooted/unrooted tree.
CladeSystem data structure for a set of splits
ClusterTree.ClusteringMethod An interface for describing Clustering methods To be updated to cope with Ward's method and others...
MutationRateModelTree Provides parameter interface to any clock-like tree with serially sampled tips (parameters are the minimal node height differences at each internal node).
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
ParameterizedTree.ParameterizedTreeBase For parameterisations that work by adjusting a base tree (that is, they aren't really tree's themselves...)
RootedTreeInterface Title: RootedTreeInterface
RootedTreeInterface.Instructee
RootedTreeInterface.RBranch
RootedTreeInterface.RNode
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
Tree Interface for a phylogenetic or genealogical tree.
Tree.TreeBase
TreeGenerator
TreeIterator
TreeManipulator
TreeManipulator.BranchAccess The branch access objects allow specific operations on a particular branch (refered to as connections internally to confuse and bewilder)
TreeManipulator.PALNodeWrapper
TreeOperation Title: TreeOperation
TreeParseException exception thrown by ReadTree
UnconstrainedTree provides parameter interface to an unconstrained tree (parameters are all available branch lengths)
UnrootedTreeInterface Title: UnrootedTreeInterface
UnrootedTreeInterface.BaseBranch
UnrootedTreeInterface.GeneralBranch
UnrootedTreeInterface.Instructee
UnrootedTreeInterface.UBranch
UnrootedTreeInterface.UNode

Classes in pal.tree used by pal.treesearch

Class and Description
Node interface for a node (includes branch) in a binary/non-binary rooted/unrooted tree
Tree Interface for a phylogenetic or genealogical tree.
UnrootedTreeInterface Title: UnrootedTreeInterface
UnrootedTreeInterface.Instructee

Classes in pal.tree used by pal.xml

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