Uses of Class
pal.distance.DistanceMatrix
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Packages that use DistanceMatrix Package Description 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). -
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Uses of DistanceMatrix in pal.distance
Subclasses of DistanceMatrix in pal.distance Modifier and Type Class Description class
AlignmentDistanceMatrix
compute distance matrix (observed and ML) from alignment (SitePattern)class
JukesCantorDistanceMatrix
compute jukes-cantor corrected distance matrixclass
ReadDistanceMatrix
reads pairwise distance matrices in PHYLIP format (full matrix)Methods in pal.distance that return DistanceMatrix Modifier and Type Method Description 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 Modifier and Type Method Description double
DistanceMatrix. absoluteDistance(DistanceMatrix mat)
compute absolute distance to second distance matrixstatic 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 matrixstatic 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 Constructor Description 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 Constructor Description ChiSquareValue(DistanceMatrix m, boolean w)
initialization -
Uses of DistanceMatrix in pal.supgma
Subclasses of DistanceMatrix in pal.supgma Modifier and Type Class Description 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 Constructor Description SUPGMADistanceMatrix(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.tree Modifier and Type Class Description 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 Modifier and Type Method Description static Tree
TreeTool. createNeighbourJoiningTree(DistanceMatrix dm)
Neighbour-joining tree construction based on a distance matrixstatic Tree
TreeTool. createUPGMA(DistanceMatrix dm)
UPGMA tree construction based on a distance matrixConstructors in pal.tree with parameters of type DistanceMatrix Constructor Description ClusterTree(DistanceMatrix dm, ClusterTree.ClusteringMethod cm)
NeighborJoiningTree(DistanceMatrix m)
construct NJ treeUPGMATree(DistanceMatrix m)
Deprecated.constructor UPGMA tree
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