Uses of Package
pal.tree
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Packages that use pal.tree 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. -
Classes in pal.tree used by pal.coalescent 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 interfaceParameterizedTree.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 modelTree Interface for a phylogenetic or genealogical tree.TreeOperation Title: TreeOperation -
Classes in pal.tree used by pal.distance Class Description Tree Interface for a phylogenetic or genealogical tree. -
Classes in pal.tree used by pal.eval Class Description Node interface for a node (includes branch) in a binary/non-binary rooted/unrooted treeParameterizedTree abstract base class for a tree with an Parameterized interfaceTree Interface for a phylogenetic or genealogical tree. -
Classes in pal.tree used by pal.gui 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 treeSimpleNode data structure for a node (includes branch) in a binary/non-binary rooted/unrooted treeTree Interface for a phylogenetic or genealogical tree. -
Classes in pal.tree used by pal.mep Class Description Tree Interface for a phylogenetic or genealogical tree. -
Classes in pal.tree used by pal.statistics Class Description Tree Interface for a phylogenetic or genealogical tree. -
Classes in pal.tree used by pal.supgma 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 treesSimulatedAlignment.Factory A utility class that can be used to generate Simulated alignments based on a tree with predefined sequence length and substitution modelTree Interface for a phylogenetic or genealogical tree. -
Classes in pal.tree used by pal.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 splitsClusterTree.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 treeParameterizedTree abstract base class for a tree with an Parameterized interfaceParameterizedTree.Factory Factory interfaceParameterizedTree.ParameterizedTreeBase For parameterisations that work by adjusting a base tree (that is, they aren't really tree's themselves...)RootedTreeInterface Title: RootedTreeInterfaceRootedTreeInterface.Instructee RootedTreeInterface.RBranch RootedTreeInterface.RNode SimpleTree data structure for a binary/non-binary rooted/unrooted treesSimulatedAlignment generates an artificial data setSplitSystem data structure for a set of splitsTree 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: TreeOperationTreeParseException exception thrown by ReadTreeUnconstrainedTree provides parameter interface to an unconstrained tree (parameters are all available branch lengths)UnrootedTreeInterface Title: UnrootedTreeInterfaceUnrootedTreeInterface.BaseBranch UnrootedTreeInterface.GeneralBranch UnrootedTreeInterface.Instructee UnrootedTreeInterface.UBranch UnrootedTreeInterface.UNode -
Classes in pal.tree used by pal.treesearch Class Description Node interface for a node (includes branch) in a binary/non-binary rooted/unrooted treeTree Interface for a phylogenetic or genealogical tree.UnrootedTreeInterface Title: UnrootedTreeInterfaceUnrootedTreeInterface.Instructee -
Classes in pal.tree used by pal.xml Class Description Node interface for a node (includes branch) in a binary/non-binary rooted/unrooted treeTree Interface for a phylogenetic or genealogical tree.