Uses of Interface
pal.distance.DistanceMatrixGenerator
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Packages that use DistanceMatrixGenerator 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.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 DistanceMatrixGenerator in pal.distance
Methods in pal.distance that return DistanceMatrixGenerator Modifier and Type Method Description static DistanceMatrixGenerator
DistanceMatrixGenerator.Utils. createEvolutionary(Alignment a, SubstitutionModel sm)
static DistanceMatrixGenerator
DistanceMatrixGenerator.Utils. createParametric(Tree baseTree, SubstitutionModel sm, int numberOfSites)
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Uses of DistanceMatrixGenerator in pal.supgma
Methods in pal.supgma with parameters of type DistanceMatrixGenerator Modifier and Type Method Description Tree
SUPGMABase.PopulationParameters. generateSUPGMATree(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, DistanceMatrixGenerator replicateSource, int numberOfAlignmentBootstrapReplicates, LMSSolver solver)
Constructors in pal.supgma with parameters of type DistanceMatrixGenerator Constructor Description SUPGMABase(DistanceMatrixAccess distanceAccess, DistanceMatrixGenerator replicateGenerator, TimeOrderCharacterData tocd)
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Uses of DistanceMatrixGenerator in pal.tree
Methods in pal.tree with parameters of type DistanceMatrixGenerator Modifier and Type Method Description static TreeGenerator
TreeGenerator.Utils. createNeighbourJoiningGenerator(DistanceMatrixGenerator dataGenerator, java.lang.String[] outgroupNames)
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