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