Uses of Interface
pal.substmodel.RateMatrixGroup
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Packages that use RateMatrixGroup Package Description pal.eval Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters.pal.substmodel Classes describing substitution models, i.e. -
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Uses of RateMatrixGroup in pal.eval
Methods in pal.eval with parameters of type RateMatrixGroup Modifier and Type Method Description static MolecularClockLikelihoodModel.Instance
SingleSplitMolecularClockLikelihoodModel. createInstance(RateMatrixGroup beforeSplitMatrices, RateMatrixGroup afterSplitMatrics, NeoParameterized acrossSplitParameters, double splitTime)
static MolecularClockLikelihoodModel.Instance
SingleSplitMolecularClockLikelihoodModel. createInstance(RateMatrixGroup beforeSplitMatrices, RateMatrixGroup afterSplitMatrics, NeoParameterized acrossSplitParameters, double[] classProbabilities, double splitTime)
static MolecularClockLikelihoodModel.Instance
SingleSplitMolecularClockLikelihoodModel. createInstance(RateMatrixGroup beforeSplitMatrices, RateMatrixGroup afterSplitMatrics, NeoParameterized acrossSplitParameters, SingleSplitDistribution probabilityModel, double splitTime)
static MolecularClockLikelihoodModel.Instance
SingleSplitMolecularClockLikelihoodModel. createInstance(RateMatrixGroup beforeSplitMatrices, RateMatrixGroup afterSplitMatrics, NeoParameterized acrossSplitParameters, SingleSplitDistribution probabilityModel, LHCalculator.Factory baseFactory, double splitTime)
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Uses of RateMatrixGroup in pal.substmodel
Classes in pal.substmodel that implement RateMatrixGroup Modifier and Type Class Description class
NeutralSelectionRateMatrixGroup
class
PositiveSelectionRateMatrixGroup
class
SimpleRateMatrixGroup
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