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Packages that use DistanceMatrix | |
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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 |
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Subclasses of DistanceMatrix in pal.distance | |
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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 | |
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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)
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static DistanceMatrix |
DistanceMatrixUtils.minus(DistanceMatrix parent,
int taxaToRemove)
Returns a distance matrix with the specified taxa removed. |
DistanceMatrix |
DistanceMatrixAccess.obtainMatrix(AlgorithmCallback callback)
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Methods in pal.distance with parameters of type DistanceMatrix | |
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double |
DistanceMatrix.absoluteDistance(DistanceMatrix mat)
compute absolute distance to second distance matrix |
static DistanceMatrixAccess |
DistanceMatrixAccess.Utils.createSimple(DistanceMatrix base)
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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 | |
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DistanceMatrix(DistanceMatrix dm)
constructor that takes a distance matrix and clones the distances but uses the same idGroup. |
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DistanceMatrix(DistanceMatrix dm,
IdGroup subset)
constructor that takes a distance matrix and clones the distances, of a the identifiers in idGroup. |
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JukesCantorDistanceMatrix(DistanceMatrix dist)
compute jukes-cantor corrected distances (assumes nucleotides as underlying data) |
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JukesCantorDistanceMatrix(DistanceMatrix dist,
int numStates)
compute jukes-cantor corrected distances |
Uses of DistanceMatrix in pal.eval |
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Constructors in pal.eval with parameters of type DistanceMatrix | |
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ChiSquareValue(DistanceMatrix m,
boolean w)
initialization |
Uses of DistanceMatrix in pal.supgma |
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Subclasses of DistanceMatrix in pal.supgma | |
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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 | |
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SUPGMADistanceMatrix(DistanceMatrix raw,
TimeOrderCharacterData tocd,
DeltaModel deltaModel)
Uses date/time information and a constant rate to correct distance matrices. |
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SUPGMATree(DistanceMatrix m,
TimeOrderCharacterData tocd,
DeltaModel deltaModel,
boolean allowNegatives,
ClusterTree.ClusteringMethod cm)
constructor SUPGMA tree |
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SUPGMATree(DistanceMatrix m,
TimeOrderCharacterData tocd,
double rate,
ClusterTree.ClusteringMethod cm)
constructor SUPGMA tree |
Uses of DistanceMatrix in pal.tree |
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Subclasses of DistanceMatrix in pal.tree | |
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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 | |
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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 | |
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ClusterTree(DistanceMatrix dm,
ClusterTree.ClusteringMethod cm)
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NeighborJoiningTree(DistanceMatrix m)
construct NJ tree |
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UPGMATree(DistanceMatrix m)
Deprecated. constructor UPGMA tree |
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