Uses of Package
pal.tree
Packages that use pal.tree
Package
Description
Classes to model population genetic processes using the coalescent.
Classes for reading and generating distance matrices, including computation
of pairwise distances for sequence data (maximum-likelihood and observed
distances).
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
GUI components for some special objects (e.g., trees).
Classes for the analysis of "measurably evolving populations" (mep).
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.)
Classes for providing the data structure of
trees, for constructing and modifying trees, and for parameterizing
trees (e.g., clock constraint).
Utility classes for converting PAL objects to and from XML documents.
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Classes in pal.tree used by pal.coalescentClassDescriptionprovides parameter interface to a clock tree (parameters are the minimal node height differences at each internal node)abstract base class for a tree with an Parameterized interfaceFor parameterisations that work by adjusting a base tree (that is, they aren't really tree's themselves...)A utility class that can be used to generate Simulated alignments based on a tree with predefined sequence length and substitution modelInterface for a phylogenetic or genealogical tree.Title: TreeOperation
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Classes in pal.tree used by pal.distance
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ClassDescriptioninterface for a node (includes branch) in a binary/non-binary rooted/unrooted treeabstract base class for a tree with an Parameterized interfaceInterface for a phylogenetic or genealogical tree.
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ClassDescriptioninterface for a node (includes branch) in a binary/non-binary rooted/unrooted tree.interface for a node (includes branch) in a binary/non-binary rooted/unrooted treedata structure for a node (includes branch) in a binary/non-binary rooted/unrooted treeInterface for a phylogenetic or genealogical tree.
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Classes in pal.tree used by pal.statistics
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Classes in pal.tree used by pal.supgmaClassDescriptionAn interface for describing Clustering methods To be updated to cope with Ward's method and others...data structure for a binary/non-binary rooted/unrooted treesA utility class that can be used to generate Simulated alignments based on a tree with predefined sequence length and substitution modelInterface for a phylogenetic or genealogical tree.
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ClassDescriptioninterface for a node (includes branch) in a binary/non-binary rooted/unrooted tree.data structure for a set of splitsAn interface for describing Clustering methods To be updated to cope with Ward's method and others...Provides parameter interface to any clock-like tree with serially sampled tips (parameters are the minimal node height differences at each internal node).interface for a node (includes branch) in a binary/non-binary rooted/unrooted treeabstract base class for a tree with an Parameterized interfaceFactory interfaceFor parameterisations that work by adjusting a base tree (that is, they aren't really tree's themselves...)Title: RootedTreeInterfacedata structure for a binary/non-binary rooted/unrooted treesgenerates an artificial data setdata structure for a set of splitsInterface for a phylogenetic or genealogical tree.The branch access objects allow specific operations on a particular branch (refered to as connections internally to confuse and bewilder)Title: TreeOperationexception thrown by ReadTreeprovides parameter interface to an unconstrained tree (parameters are all available branch lengths)Title: UnrootedTreeInterface
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Classes in pal.tree used by pal.treesearchClassDescriptioninterface for a node (includes branch) in a binary/non-binary rooted/unrooted treeInterface for a phylogenetic or genealogical tree.Title: UnrootedTreeInterface
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