Package pal.tree
Classes for providing the data structure of
trees, for constructing and modifying trees, and for parameterizing
trees (e.g., clock constraint).
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Interface Summary Interface Description AttributeNode interface for a node (includes branch) in a binary/non-binary rooted/unrooted tree.ClusterTree.ClusteringMethod An interface for describing Clustering methods To be updated to cope with Ward's method and others...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 interfaceRootedTreeInterface Title: RootedTreeInterfaceRootedTreeInterface.Instructee RootedTreeInterface.RBranch RootedTreeInterface.RNode Tree Interface for a phylogenetic or genealogical tree.TreeGenerator TreeIterator TreeManipulator.BranchAccess The branch access objects allow specific operations on a particular branch (refered to as connections internally to confuse and bewilder)TreeOperation Title: TreeOperationUnrootedTreeInterface Title: UnrootedTreeInterfaceUnrootedTreeInterface.BaseBranch UnrootedTreeInterface.GeneralBranch UnrootedTreeInterface.Instructee UnrootedTreeInterface.UBranch UnrootedTreeInterface.UNode -
Class Summary Class Description CladeSystem data structure for a set of splitsClockTree provides parameter interface to a clock tree (parameters are the minimal node height differences at each internal node)ClusterTree Local Implements LOCAL (Larget and Simon, 1999) and stochastic NNI moves for unrooted trees.LogParameterizedTree This class logarithmically transforms tree parameters.MutationRateModelTree Provides parameter interface to any clock-like tree with serially sampled tips (parameters are the minimal node height differences at each internal node).NeighborJoiningTree constructs a neighbor-joining tree from pairwise distances
Saitou, N., and Nei, M., (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees.NodeFactory NodeUtils Helper routines for dealing with nodes.ParameterizedTree.ParameterizedTreeBase For parameterisations that work by adjusting a base tree (that is, they aren't really tree's themselves...)ReadTree constructs a tree reading in a New Hampshire treefile, taking care for internal labels and branch lengths and binary/nonbinary and rooted/unrooted treesRootedTreeInterface.Utils RootedTreeUtils This class contains utility methods.SimpleNode data structure for a node (includes branch) in a binary/non-binary rooted/unrooted treeSimpleTree data structure for a binary/non-binary rooted/unrooted treesSimulatedAlignment generates an artificial data setSimulatedAlignment.Factory A utility class that can be used to generate Simulated alignments based on a tree with predefined sequence length and substitution modelSplitSystem data structure for a set of splitsSplitUtils utilities for split systemsTree.TreeBase TreeDistanceMatrix computes distance matrix induced by a tree (needs only O(n^2) time, following algorithm DistanceInTree by D.Bryant and P.TreeGenerator.Utils TreeManipulator TreeManipulator.PALBranchWrapper TreeManipulator.PALNodeWrapper TreeOperation.Utils Utility classTreeRestricter TreeTool TreeUtils various utility functions on trees.UnconstrainedTree provides parameter interface to an unconstrained tree (parameters are all available branch lengths)UnrootedTreeInterface.Utils UPGMATree Deprecated. Use ClusterTree -
Exception Summary Exception Description TreeParseException exception thrown by ReadTree