Methods in pal.supgma with parameters of type LMSSolver |
Tree |
SUPGMABase.generateAlignmentBootstrappedSUPGMATree(AlgorithmCallback callback,
ClusterTree.ClusteringMethod cm,
SUPGMABase.PopulationParameters pp,
int numberOfReplicates,
LMSSolver solver)
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Tree |
SUPGMABase.PopulationParameters.generateSUPGMATree(AlgorithmCallback callback,
ClusterTree.ClusteringMethod cm,
DistanceMatrixGenerator replicateSource,
int numberOfAlignmentBootstrapReplicates,
LMSSolver solver)
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SUPGMABase.CISummary |
SUPGMABase.PopulationParameters.inferCI(AlgorithmCallback callback,
int numberOfReplicates,
SimulatedAlignment.Factory alignmentFactory,
SubstitutionModel evolutionaryModel,
LMSSolver solver)
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SUPGMABase.PopulationParameters |
SUPGMABase.process(AlgorithmCallback callback,
LMSSolver solver)
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SUPGMABase.PopulationParameters |
SUPGMABase.process(DistanceMatrixAccess alternativeSource,
AlgorithmCallback callback,
LMSSolver solver)
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Tree[] |
SUPGMABase.PopulationParameters.simulateTrees(int numberOfTreesToSimulate,
AlgorithmCallback callback,
LMSSolver solver)
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Tree |
SUPGMABase.solve(AlgorithmCallback callback,
ClusterTree.ClusteringMethod cm,
LMSSolver solver)
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