Uses of Class
org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix

Packages that use BasicSymmetricalDistanceMatrix

Package	Description
org.biojava.nbio.phylo
org.forester.evoinference.distance

Uses of BasicSymmetricalDistanceMatrix in org.biojava.nbio.phylo

Methods in org.biojava.nbio.phylo that return BasicSymmetricalDistanceMatrix

Modifier and Type	Method	Description
static BasicSymmetricalDistanceMatrix	ForesterWrapper.cloneDM(BasicSymmetricalDistanceMatrix distM)	Helper function to clone a forester symmetrical DistanceMatrix.

Methods in org.biojava.nbio.phylo with parameters of type BasicSymmetricalDistanceMatrix

Modifier and Type	Method	Description
static BasicSymmetricalDistanceMatrix	ForesterWrapper.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 BasicSymmetricalDistanceMatrix

Modifier and Type	Method	Description
static BasicSymmetricalDistanceMatrix	PairwiseDistanceCalculator.calcFractionalDissimilarities(Msa msa)
static BasicSymmetricalDistanceMatrix	PairwiseDistanceCalculator.calcKimuraDistances(Msa msa)
static BasicSymmetricalDistanceMatrix	PairwiseDistanceCalculator.calcKimuraDistances(Msa msa, double value_for_too_large_distance_for_kimura_formula)
static BasicSymmetricalDistanceMatrix	PairwiseDistanceCalculator.calcPoissonDistances(Msa msa)

Methods in org.forester.evoinference.distance with parameters of type BasicSymmetricalDistanceMatrix

Modifier and Type	Method	Description
Phylogeny	NeighborJoining.execute(BasicSymmetricalDistanceMatrix distance)
Phylogeny	NeighborJoiningF.execute(BasicSymmetricalDistanceMatrix distance)
Phylogeny	NeighborJoiningR.execute(BasicSymmetricalDistanceMatrix distance)
void	Sarray.initialize(BasicSymmetricalDistanceMatrix d)
void	Sset.initialize(BasicSymmetricalDistanceMatrix d)

Method parameters in org.forester.evoinference.distance with type arguments of type BasicSymmetricalDistanceMatrix

Modifier and Type	Method	Description
java.util.List<Phylogeny>	NeighborJoining.execute(java.util.List<BasicSymmetricalDistanceMatrix> distances_list)
java.util.List<Phylogeny>	NeighborJoiningF.execute(java.util.List<BasicSymmetricalDistanceMatrix> distances_list)
java.util.List<Phylogeny>	NeighborJoiningR.execute(java.util.List<BasicSymmetricalDistanceMatrix> distances_list)