Package pal.tree
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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ClassDescriptioninterface for a node (includes branch) in a binary/non-binary rooted/unrooted tree.data structure for a set of splitsprovides parameter interface to a clock tree (parameters are the minimal node height differences at each internal node)An interface for describing Clustering methods To be updated to cope with Ward's method and others...Implements LOCAL (Larget and Simon, 1999) and stochastic NNI moves for unrooted trees.This class logarithmically transforms tree parameters.Provides parameter interface to any clock-like tree with serially sampled tips (parameters are the minimal node height differences at each internal node).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.interface for a node (includes branch) in a binary/non-binary rooted/unrooted treeHelper routines for dealing with nodes.abstract 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...)constructs a tree reading in a New Hampshire treefile, taking care for internal labels and branch lengths and binary/nonbinary and rooted/unrooted treesTitle: RootedTreeInterfaceThis class contains utility methods.data structure for a node (includes branch) in a binary/non-binary rooted/unrooted treedata structure for a binary/non-binary rooted/unrooted treesgenerates an artificial data setA utility class that can be used to generate Simulated alignments based on a tree with predefined sequence length and substitution modeldata structure for a set of splitsutilities for split systemsInterface for a phylogenetic or genealogical tree.computes distance matrix induced by a tree (needs only O(n^2) time, following algorithm DistanceInTree by D.Bryant and P.The branch access objects allow specific operations on a particular branch (refered to as connections internally to confuse and bewilder)Title: TreeOperationUtility classexception thrown by ReadTreevarious utility functions on trees.provides parameter interface to an unconstrained tree (parameters are all available branch lengths)Title: UnrootedTreeInterfaceDeprecated.Use ClusterTree