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 and Description |
---|---|
NeoParameterized |
MolecularClockLikelihoodModel.Instance.getParameterAccess() |
NeoParameterized |
UnconstrainedLikelihoodModel.Instance.getParameterAccess() |
Modifier and Type | Method and 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 and Description |
---|---|
class |
ParameterizedDoubleBundle
Title: ParameterizedDoubleBundle
|
class |
ParameterizedNeoWrapper
Title: ParameterizedNeoWrapper
|
Modifier and Type | Interface and Description |
---|---|
interface |
SingleSplitDistribution |
Modifier and Type | Class and Description |
---|---|
class |
ConstantIndependentSingleSplitDistribution
Title: ConstantIndependentSingleSplitDistribution
|
class |
MultiRateMatrixHandler |
class |
SaturatedSingleSplitDistribution
Title: SaturatedSingleSplitDistribution
|
class |
VariableIndependentSingleSplitDistribution
Title: VariableIndependentSingleSplitDistribution
|
Modifier and Type | Class and Description |
---|---|
class |
FixedBSRDTGlobalClockModel |
class |
GlobalClockModel |
class |
MRDTGlobalClockModel |
class |
SRDTGlobalClockModel |