Uses of Class
pal.distance.DistanceMatrix
Packages that use DistanceMatrix
Package
Description
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.
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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Uses of DistanceMatrix in pal.distance
Subclasses of DistanceMatrix in pal.distanceModifier and TypeClassDescriptionclasscompute distance matrix (observed and ML) from alignment (SitePattern)classcompute jukes-cantor corrected distance matrixclassreads pairwise distance matrices in PHYLIP format (full matrix)Methods in pal.distance that return DistanceMatrixModifier and TypeMethodDescriptionstatic final DistanceMatrixDistanceTool.constructEvolutionaryDistances(Alignment a, SubstitutionModel sm) Construct a distance matrix object such that the distance between sequence A, and sequence B, is the evolutionary distance by a given substitution model.DistanceMatrixGenerator.generateNextMatrix(AlgorithmCallback callback) static DistanceMatrixDistanceMatrixUtils.minus(DistanceMatrix parent, int taxaToRemove) Returns a distance matrix with the specified taxa removed.DistanceMatrixAccess.obtainMatrix(AlgorithmCallback callback) Methods in pal.distance with parameters of type DistanceMatrixModifier and TypeMethodDescriptiondoubleDistanceMatrix.absoluteDistance(DistanceMatrix mat) compute absolute distance to second distance matrixstatic DistanceMatrixAccessDistanceMatrixAccess.Utils.createSimple(DistanceMatrix base) static DistanceMatrixDistanceMatrixUtils.minus(DistanceMatrix parent, int taxaToRemove) Returns a distance matrix with the specified taxa removed.doubleDistanceMatrix.squaredDistance(DistanceMatrix mat, boolean weighted) compute squared distance to second distance matrixstatic doubleDistanceMatrixUtils.squaredDistance(DistanceMatrix mat1, DistanceMatrix mat2, boolean weighted) compute squared distance to second distance matrix.Constructors in pal.distance with parameters of type DistanceMatrixModifierConstructorDescriptionconstructor that takes a distance matrix and clones the distances but uses the same idGroup.DistanceMatrix(DistanceMatrix dm, IdGroup subset) constructor that takes a distance matrix and clones the distances, of a the identifiers in idGroup.compute jukes-cantor corrected distances (assumes nucleotides as underlying data)JukesCantorDistanceMatrix(DistanceMatrix dist, int numStates) compute jukes-cantor corrected distances -
Uses of DistanceMatrix in pal.eval
Constructors in pal.eval with parameters of type DistanceMatrix -
Uses of DistanceMatrix in pal.supgma
Subclasses of DistanceMatrix in pal.supgmaModifier and TypeClassDescriptionclassCorrects distances in a distance matrix such that all tips appear contemporaneous, given a time/date and rate information for the taxa.Constructors in pal.supgma with parameters of type DistanceMatrixModifierConstructorDescriptionSUPGMADistanceMatrix(DistanceMatrix raw, TimeOrderCharacterData tocd, DeltaModel deltaModel) Uses date/time information and a constant rate to correct distance matrices.SUPGMATree(DistanceMatrix m, TimeOrderCharacterData tocd, double rate, ClusterTree.ClusteringMethod cm) constructor SUPGMA treeSUPGMATree(DistanceMatrix m, TimeOrderCharacterData tocd, DeltaModel deltaModel, boolean allowNegatives, ClusterTree.ClusteringMethod cm) constructor SUPGMA tree -
Uses of DistanceMatrix in pal.tree
Subclasses of DistanceMatrix in pal.treeModifier and TypeClassDescriptionclasscomputes distance matrix induced by a tree (needs only O(n^2) time, following algorithm DistanceInTree by D.Bryant and P.Methods in pal.tree with parameters of type DistanceMatrixModifier and TypeMethodDescriptionstatic final TreeTreeTool.createNeighbourJoiningTree(DistanceMatrix dm) Neighbour-joining tree construction based on a distance matrixstatic final TreeTreeTool.createUPGMA(DistanceMatrix dm) UPGMA tree construction based on a distance matrixConstructors in pal.tree with parameters of type DistanceMatrixModifierConstructorDescriptionconstruct NJ treeDeprecated.constructor UPGMA tree