Uses of Interface
pal.eval.MolecularClockLikelihoodModel.Instance

Packages that use MolecularClockLikelihoodModel.Instance

pal.eval	Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters.
pal.mep	Classes for the analysis of "measurably evolving populations" (mep).
pal.treesearch

Uses of MolecularClockLikelihoodModel.Instance in pal.eval

Methods in pal.eval that return MolecularClockLikelihoodModel.Instance

static MolecularClockLikelihoodModel.Instance	SimpleMolecularClockLikelihoodModel.createInstance(LHCalculator.Factory baseFactory, SubstitutionModel model)
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)
static MolecularClockLikelihoodModel.Instance	SimpleMolecularClockLikelihoodModel.createInstance(SubstitutionModel model)

Uses of MolecularClockLikelihoodModel.Instance in pal.mep

Methods in pal.mep with parameters of type MolecularClockLikelihoodModel.Instance

ConstraintModel	DeltaModel.buildConstraintModel(SampleInformation si, MolecularClockLikelihoodModel.Instance likelihoodModel)
ConstraintModel	MutationRateModel.Factory.buildConstraintModel(SampleInformation si, MolecularClockLikelihoodModel.Instance likelihoodModel)

Uses of MolecularClockLikelihoodModel.Instance in pal.treesearch

Constructors in pal.treesearch with parameters of type MolecularClockLikelihoodModel.Instance

FixedBSRDTGlobalClockModel(SampleInformation sampleInformation, MolecularClockLikelihoodModel.Instance likelihoodModel, double rate)

FixedSRDTGlobalClockModel(SampleInformation sampleInformation, MolecularClockLikelihoodModel.Instance likelihoodModel, double rate)

GlobalClockModel(MolecularClockLikelihoodModel.Instance likelihoodModel)

MRDTGlobalClockModel(SampleInformation sampleInformation, MolecularClockLikelihoodModel.Instance likelihoodModel)

MRDTGlobalClockModel(SampleInformation sampleInformation, MolecularClockLikelihoodModel.Instance likelihoodModel, double[] rateChangeTimes)

SRDTGlobalClockModel(SampleInformation sampleInformation, MolecularClockLikelihoodModel.Instance likelihoodModel)

SRDTGlobalClockModel(SampleInformation sampleInformation, MolecularClockLikelihoodModel.Instance likelihoodModel, boolean allowMetaRate)