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.
|
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) |
Modifier and Type | Class | Description |
---|---|---|
class |
NeutralSelectionRateMatrixGroup |
|
class |
PositiveSelectionRateMatrixGroup |
|
class |
SimpleRateMatrixGroup |