Uses of Interface
pal.distance.DistanceMatrixGenerator
Packages that use DistanceMatrixGenerator
Package
Description
Classes for reading and generating distance matrices, including computation
of pairwise distances for sequence data (maximum-likelihood and observed
distances).
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 DistanceMatrixGenerator in pal.distance
Methods in pal.distance that return DistanceMatrixGeneratorModifier and TypeMethodDescriptionstatic DistanceMatrixGeneratorDistanceMatrixGenerator.Utils.createEvolutionary(Alignment a, SubstitutionModel sm) static DistanceMatrixGeneratorDistanceMatrixGenerator.Utils.createParametric(Tree baseTree, SubstitutionModel sm, int numberOfSites) Silly idea stuff -
Uses of DistanceMatrixGenerator in pal.supgma
Methods in pal.supgma with parameters of type DistanceMatrixGeneratorModifier and TypeMethodDescriptionSUPGMABase.PopulationParameters.generateSUPGMATree(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, DistanceMatrixGenerator replicateSource, int numberOfAlignmentBootstrapReplicates, LMSSolver solver) Constructors in pal.supgma with parameters of type DistanceMatrixGeneratorModifierConstructorDescriptionSUPGMABase(DistanceMatrixAccess distanceAccess, DistanceMatrixGenerator replicateGenerator, TimeOrderCharacterData tocd) -
Uses of DistanceMatrixGenerator in pal.tree
Methods in pal.tree with parameters of type DistanceMatrixGeneratorModifier and TypeMethodDescriptionstatic final TreeGeneratorTreeGenerator.Utils.createNeighbourJoiningGenerator(DistanceMatrixGenerator dataGenerator, String[] outgroupNames)