Uses of Interface
pal.distance.DistanceMatrixGenerator

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).

Uses of DistanceMatrixGenerator in pal.distance

Methods in pal.distance that return DistanceMatrixGenerator

Modifier and Type	Method and Description
static 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 DistanceMatrixGenerator

Modifier and Type	Method and 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 and Description
SUPGMABase(DistanceMatrixAccess distanceAccess, DistanceMatrixGenerator replicateGenerator, TimeOrderCharacterData tocd)

Uses of DistanceMatrixGenerator in pal.tree

Methods in pal.tree with parameters of type DistanceMatrixGenerator

Modifier and Type	Method and Description
static TreeGenerator	TreeGenerator.Utils.createNeighbourJoiningGenerator(DistanceMatrixGenerator dataGenerator, java.lang.String[] outgroupNames)