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