Uses of Interface
pal.math.LMSSolver
Packages that use LMSSolver
Package
Description
Classes for math stuff such as optimisation, numerical derivatives, matrix exponentials,
random numbers, special function etc.
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Uses of LMSSolver in pal.math
Modifier and TypeMethodDescriptionstatic final LMSSolverLMSSolver.Utils.getSimpleSolver()Obtain a simple LMSSolver that uses the "traditional" method for LMS stuff (IE, using row reduction to find the inverse, with poor numerical accuracy) -
Uses of LMSSolver in pal.supgma
Methods in pal.supgma with parameters of type LMSSolverModifier and TypeMethodDescriptionSUPGMABase.generateAlignmentBootstrappedSUPGMATree(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, SUPGMABase.PopulationParameters pp, int numberOfReplicates, LMSSolver solver) SUPGMABase.PopulationParameters.generateSUPGMATree(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, DistanceMatrixGenerator replicateSource, int numberOfAlignmentBootstrapReplicates, LMSSolver solver) SUPGMABase.PopulationParameters.inferCI(AlgorithmCallback callback, int numberOfReplicates, SimulatedAlignment.Factory alignmentFactory, SubstitutionModel evolutionaryModel, LMSSolver solver) SUPGMABase.process(DistanceMatrixAccess alternativeSource, AlgorithmCallback callback, LMSSolver solver) SUPGMABase.process(AlgorithmCallback callback, LMSSolver solver) Tree[]SUPGMABase.PopulationParameters.simulateTrees(int numberOfTreesToSimulate, AlgorithmCallback callback, LMSSolver solver) SUPGMABase.solve(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, LMSSolver solver)