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Packages that use pal.tree | |
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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 | |
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ClockTree
provides parameter interface to a clock tree (parameters are the minimal node height differences at each internal node) |
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ParameterizedTree
abstract base class for a tree with an Parameterized interface |
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ParameterizedTree.ParameterizedTreeBase
For parameterisations that work by adjusting a base tree (that is, they aren't really tree's themselves...) |
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SimulatedAlignment.Factory
A utility class that can be used to generate Simulated alignments based on a tree with predefined sequence length and substitution model |
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Tree
Interface for a phylogenetic or genealogical tree. |
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TreeOperation
Title: TreeOperation |
Classes in pal.tree used by pal.distance | |
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Tree
Interface for a phylogenetic or genealogical tree. |
Classes in pal.tree used by pal.eval | |
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Node
interface for a node (includes branch) in a binary/non-binary rooted/unrooted tree |
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ParameterizedTree
abstract base class for a tree with an Parameterized interface |
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Tree
Interface for a phylogenetic or genealogical tree. |
Classes in pal.tree used by pal.gui | |
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AttributeNode
interface for a node (includes branch) in a binary/non-binary rooted/unrooted tree. |
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Node
interface for a node (includes branch) in a binary/non-binary rooted/unrooted tree |
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SimpleNode
data structure for a node (includes branch) in a binary/non-binary rooted/unrooted tree |
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Tree
Interface for a phylogenetic or genealogical tree. |
Classes in pal.tree used by pal.mep | |
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Tree
Interface for a phylogenetic or genealogical tree. |
Classes in pal.tree used by pal.statistics | |
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Tree
Interface for a phylogenetic or genealogical tree. |
Classes in pal.tree used by pal.supgma | |
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ClusterTree
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ClusterTree.ClusteringMethod
An interface for describing Clustering methods To be updated to cope with Ward's method and others... |
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SimpleTree
data structure for a binary/non-binary rooted/unrooted trees |
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SimulatedAlignment.Factory
A utility class that can be used to generate Simulated alignments based on a tree with predefined sequence length and substitution model |
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Tree
Interface for a phylogenetic or genealogical tree. |
Classes in pal.tree used by pal.tree | |
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AttributeNode
interface for a node (includes branch) in a binary/non-binary rooted/unrooted tree. |
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CladeSystem
data structure for a set of splits |
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ClusterTree.ClusteringMethod
An interface for describing Clustering methods To be updated to cope with Ward's method and others... |
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MutationRateModelTree
Provides parameter interface to any clock-like tree with serially sampled tips (parameters are the minimal node height differences at each internal node). |
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Node
interface for a node (includes branch) in a binary/non-binary rooted/unrooted tree |
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ParameterizedTree
abstract base class for a tree with an Parameterized interface |
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ParameterizedTree.Factory
Factory interface |
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ParameterizedTree.ParameterizedTreeBase
For parameterisations that work by adjusting a base tree (that is, they aren't really tree's themselves...) |
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RootedTreeInterface
Title: RootedTreeInterface |
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RootedTreeInterface.Instructee
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RootedTreeInterface.RBranch
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RootedTreeInterface.RNode
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SimpleTree
data structure for a binary/non-binary rooted/unrooted trees |
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SimulatedAlignment
generates an artificial data set |
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SplitSystem
data structure for a set of splits |
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Tree
Interface for a phylogenetic or genealogical tree. |
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Tree.TreeBase
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TreeGenerator
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TreeIterator
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TreeManipulator
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TreeManipulator.BranchAccess
The branch access objects allow specific operations on a particular branch (refered to as connections internally to confuse and bewilder) |
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TreeManipulator.PALNodeWrapper
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TreeOperation
Title: TreeOperation |
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TreeParseException
exception thrown by ReadTree |
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UnconstrainedTree
provides parameter interface to an unconstrained tree (parameters are all available branch lengths) |
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UnrootedTreeInterface
Title: UnrootedTreeInterface |
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UnrootedTreeInterface.BaseBranch
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UnrootedTreeInterface.GeneralBranch
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UnrootedTreeInterface.Instructee
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UnrootedTreeInterface.UBranch
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UnrootedTreeInterface.UNode
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Classes in pal.tree used by pal.treesearch | |
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Node
interface for a node (includes branch) in a binary/non-binary rooted/unrooted tree |
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Tree
Interface for a phylogenetic or genealogical tree. |
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UnrootedTreeInterface
Title: UnrootedTreeInterface |
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UnrootedTreeInterface.Instructee
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Classes in pal.tree used by pal.xml | |
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Node
interface for a node (includes branch) in a binary/non-binary rooted/unrooted tree |
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Tree
Interface for a phylogenetic or genealogical tree. |
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