Package | Description |
---|---|
pal.eval |
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
|
pal.treesearch |
Modifier and Type | Method | Description |
---|---|---|
static LHCalculator.Factory |
FastFourStateLHCalculator.getFactory() |
|
static LHCalculator.Factory |
FastFourStateLHCalculator.getFactory(LHCalculator.Factory fallbackFactory) |
|
static LHCalculator.Factory |
SimpleLHCalculator.getFactory() |
|
static LHCalculator.Factory |
SimpleModelFastFourStateLHCalculator.getFactory() |
|
static LHCalculator.Factory |
SimpleModelFastFourStateLHCalculator.getFactory(LHCalculator.Factory fallbackFactory) |
Modifier and Type | Method | Description |
---|---|---|
static MolecularClockLikelihoodModel.Instance |
SimpleMolecularClockLikelihoodModel.createInstance(LHCalculator.Factory baseFactory,
SubstitutionModel model) |
|
static UnconstrainedLikelihoodModel.Instance |
SimpleUnconstrainedLikelihoodModel.createInstance(LHCalculator.Factory base,
SubstitutionModel model) |
Create a SimpleUnconstrainedLikelihoodModel instance
|
static MolecularClockLikelihoodModel.Instance |
SingleSplitMolecularClockLikelihoodModel.createInstance(RateMatrixGroup beforeSplitMatrices,
RateMatrixGroup afterSplitMatrics,
NeoParameterized acrossSplitParameters,
SingleSplitDistribution probabilityModel,
LHCalculator.Factory baseFactory,
double splitTime) |
|
static LHCalculator.Factory |
FastFourStateLHCalculator.getFactory(LHCalculator.Factory fallbackFactory) |
|
static LHCalculator.Factory |
SimpleModelFastFourStateLHCalculator.getFactory(LHCalculator.Factory fallbackFactory) |
Constructor | Description |
---|---|
UnrootedMLSearcher(Alignment alignment,
SubstitutionModel model,
LHCalculator.Factory calcFactory) |
|
UnrootedMLSearcher(Node root,
Alignment alignment,
SubstitutionModel model,
LHCalculator.Factory calcFactory) |