Package | Description |
---|---|
pal.eval |
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
|
pal.misc |
Classes that don't fit elsewhere ;^)
|
pal.substmodel |
Classes describing substitution models, i.e.
|
pal.treesearch |
Modifier and Type | Method | Description |
---|---|---|
NeoParameterized |
MolecularClockLikelihoodModel.Instance.getParameterAccess() |
|
NeoParameterized |
UnconstrainedLikelihoodModel.Instance.getParameterAccess() |
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 |
ParameterizedDoubleBundle |
Title: ParameterizedDoubleBundle
|
class |
ParameterizedNeoWrapper |
Title: ParameterizedNeoWrapper
|
Modifier and Type | Interface | Description |
---|---|---|
interface |
SingleSplitDistribution |
Modifier and Type | Class | Description |
---|---|---|
class |
ConstantIndependentSingleSplitDistribution |
Title: ConstantIndependentSingleSplitDistribution
|
class |
MultiRateMatrixHandler |
|
class |
SaturatedSingleSplitDistribution |
Title: SaturatedSingleSplitDistribution
|
class |
VariableIndependentSingleSplitDistribution |
Title: VariableIndependentSingleSplitDistribution
|
Modifier and Type | Class | Description |
---|---|---|
class |
FixedBSRDTGlobalClockModel |
|
class |
GlobalClockModel |
|
class |
MRDTGlobalClockModel |
|
class |
SRDTGlobalClockModel |