Uses of Class
pal.distance.DistanceMatrix

Packages that use DistanceMatrix

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.supgma
pal.tree	Classes for providing the data structure of trees, for constructing and modifying trees, and for parameterizing trees (e.g., clock constraint).

Uses of DistanceMatrix in pal.distance

Subclasses of DistanceMatrix in pal.distance

class	AlignmentDistanceMatrix compute distance matrix (observed and ML) from alignment (SitePattern)
class	JukesCantorDistanceMatrix compute jukes-cantor corrected distance matrix
class	ReadDistanceMatrix reads pairwise distance matrices in PHYLIP format (full matrix)

Methods in pal.distance that return DistanceMatrix

static DistanceMatrix	DistanceTool.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.
DistanceMatrix	DistanceMatrixGenerator.generateNextMatrix(AlgorithmCallback callback)
static DistanceMatrix	DistanceMatrixUtils.minus(DistanceMatrix parent, int taxaToRemove) Returns a distance matrix with the specified taxa removed.
DistanceMatrix	DistanceMatrixAccess.obtainMatrix(AlgorithmCallback callback)

Methods in pal.distance with parameters of type DistanceMatrix

double	DistanceMatrix.absoluteDistance(DistanceMatrix mat) compute absolute distance to second distance matrix
static DistanceMatrixAccess	DistanceMatrixAccess.Utils.createSimple(DistanceMatrix base)
static DistanceMatrix	DistanceMatrixUtils.minus(DistanceMatrix parent, int taxaToRemove) Returns a distance matrix with the specified taxa removed.
double	DistanceMatrix.squaredDistance(DistanceMatrix mat, boolean weighted) compute squared distance to second distance matrix
static double	DistanceMatrixUtils.squaredDistance(DistanceMatrix mat1, DistanceMatrix mat2, boolean weighted) compute squared distance to second distance matrix.

Constructors in pal.distance with parameters of type DistanceMatrix

DistanceMatrix(DistanceMatrix dm)
constructor 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.

JukesCantorDistanceMatrix(DistanceMatrix dist)
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

ChiSquareValue(DistanceMatrix m, boolean w)
initialization

Uses of DistanceMatrix in pal.supgma

Subclasses of DistanceMatrix in pal.supgma

class

SUPGMADistanceMatrix Corrects 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 DistanceMatrix

SUPGMADistanceMatrix(DistanceMatrix raw, TimeOrderCharacterData tocd, DeltaModel deltaModel)
Uses date/time information and a constant rate to correct distance matrices.

SUPGMATree(DistanceMatrix m, TimeOrderCharacterData tocd, DeltaModel deltaModel, boolean allowNegatives, ClusterTree.ClusteringMethod cm)
constructor SUPGMA tree

SUPGMATree(DistanceMatrix m, TimeOrderCharacterData tocd, double rate, ClusterTree.ClusteringMethod cm)
constructor SUPGMA tree

Uses of DistanceMatrix in pal.tree

Subclasses of DistanceMatrix in pal.tree

class

TreeDistanceMatrix computes 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 DistanceMatrix

static Tree	TreeTool.createNeighbourJoiningTree(DistanceMatrix dm) Neighbour-joining tree construction based on a distance matrix
static Tree	TreeTool.createUPGMA(DistanceMatrix dm) UPGMA tree construction based on a distance matrix

Constructors in pal.tree with parameters of type DistanceMatrix

ClusterTree(DistanceMatrix dm, ClusterTree.ClusteringMethod cm)

NeighborJoiningTree(DistanceMatrix m)
construct NJ tree

UPGMATree(DistanceMatrix m)
Deprecated. constructor UPGMA tree