Uses of Class
org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix
Packages that use BasicSymmetricalDistanceMatrix
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Uses of BasicSymmetricalDistanceMatrix in org.biojava.nbio.phylo
Methods in org.biojava.nbio.phylo that return BasicSymmetricalDistanceMatrixModifier and TypeMethodDescriptionForesterWrapper.cloneDM
(BasicSymmetricalDistanceMatrix distM) Helper function to clone a forester symmetrical DistanceMatrix.Methods in org.biojava.nbio.phylo with parameters of type BasicSymmetricalDistanceMatrixModifier and TypeMethodDescriptionForesterWrapper.cloneDM
(BasicSymmetricalDistanceMatrix distM) Helper function to clone a forester symmetrical DistanceMatrix.static Phylogeny
TreeConstructor.distanceTree
(BasicSymmetricalDistanceMatrix distM, TreeConstructorType constructor) -
Uses of BasicSymmetricalDistanceMatrix in org.forester.evoinference.distance
Methods in org.forester.evoinference.distance that return BasicSymmetricalDistanceMatrixModifier and TypeMethodDescriptionPairwiseDistanceCalculator.calcFractionalDissimilarities
(Msa msa) PairwiseDistanceCalculator.calcKimuraDistances
(Msa msa) PairwiseDistanceCalculator.calcKimuraDistances
(Msa msa, double value_for_too_large_distance_for_kimura_formula) PairwiseDistanceCalculator.calcPoissonDistances
(Msa msa) Methods in org.forester.evoinference.distance with parameters of type BasicSymmetricalDistanceMatrixModifier and TypeMethodDescriptionfinal Phylogeny
NeighborJoining.execute
(BasicSymmetricalDistanceMatrix distance) final Phylogeny
NeighborJoiningF.execute
(BasicSymmetricalDistanceMatrix distance) final Phylogeny
NeighborJoiningR.execute
(BasicSymmetricalDistanceMatrix distance) final void
Sarray.initialize
(BasicSymmetricalDistanceMatrix d) final void
Method parameters in org.forester.evoinference.distance with type arguments of type BasicSymmetricalDistanceMatrixModifier and TypeMethodDescriptionNeighborJoining.execute
(List<BasicSymmetricalDistanceMatrix> distances_list) NeighborJoiningF.execute
(List<BasicSymmetricalDistanceMatrix> distances_list) NeighborJoiningR.execute
(List<BasicSymmetricalDistanceMatrix> distances_list)