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 DistanceMatrixGenerator
DistanceMatrixGenerator.Utils.createEvolutionary
(Alignment a, SubstitutionModel sm) static DistanceMatrixGenerator
DistanceMatrixGenerator.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 TreeGenerator
TreeGenerator.Utils.createNeighbourJoiningGenerator
(DistanceMatrixGenerator dataGenerator, String[] outgroupNames)