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.