Uses of Package
pal.tree

Packages that use pal.tree

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

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

Tree
Interface for a phylogenetic or genealogical tree.

Classes in pal.tree used by pal.eval

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

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

Tree
Interface for a phylogenetic or genealogical tree.

Classes in pal.tree used by pal.statistics

Tree
Interface for a phylogenetic or genealogical tree.

Classes in pal.tree used by pal.supgma

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

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

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

Node
interface for a node (includes branch) in a binary/non-binary rooted/unrooted tree

Tree
Interface for a phylogenetic or genealogical tree.