Uses of Interface
pal.substmodel.RateMatrixGroup

Packages that use RateMatrixGroup
pal.eval Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters. 
pal.substmodel Classes describing substitution models, i.e. 
 

Uses of RateMatrixGroup in pal.eval
 

Methods in pal.eval with parameters of type RateMatrixGroup
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)
           
 

Uses of RateMatrixGroup in pal.substmodel
 

Classes in pal.substmodel that implement RateMatrixGroup
 class NeutralSelectionRateMatrixGroup
           
 class PositiveSelectionRateMatrixGroup
           
 class SimpleRateMatrixGroup