Uses of Interface
pal.distance.DistanceMatrixGenerator

Packages that use DistanceMatrixGenerator
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
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
 Tree SUPGMABase.PopulationParameters.generateSUPGMATree(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, DistanceMatrixGenerator replicateSource, int numberOfAlignmentBootstrapReplicates, LMSSolver solver)
           
 

Constructors in pal.supgma with parameters of type DistanceMatrixGenerator
SUPGMABase(DistanceMatrixAccess distanceAccess, DistanceMatrixGenerator replicateGenerator, TimeOrderCharacterData tocd)
           
 

Uses of DistanceMatrixGenerator in pal.tree
 

Methods in pal.tree with parameters of type DistanceMatrixGenerator
static TreeGenerator TreeGenerator.Utils.createNeighbourJoiningGenerator(DistanceMatrixGenerator dataGenerator, java.lang.String[] outgroupNames)