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