| Package | Description |
|---|---|
| pal.mep |
Classes for the analysis of "measurably evolving populations" (mep).
|
| pal.treesearch |
| Modifier and Type | Method | Description |
|---|---|---|
ConstraintModel |
DeltaModel.buildConstraintModel(SampleInformation si,
MolecularClockLikelihoodModel.Instance likelihoodModel) |
|
ConstraintModel |
MutationRateModel.Factory.buildConstraintModel(SampleInformation si,
MolecularClockLikelihoodModel.Instance likelihoodModel) |
| Modifier and Type | Class | Description |
|---|---|---|
class |
FixedBSRDTGlobalClockModel |
|
class |
FixedSRDTGlobalClockModel |
|
class |
GlobalClockModel |
|
class |
MRDTGlobalClockModel |
|
class |
SRDTGlobalClockModel |
|
class |
UnconstrainedModel |
| Modifier and Type | Method | Description |
|---|---|---|
GeneralConstraintGroupManager |
GeneralConstraintGroupManager.Store.getConstraintGroupManager(java.lang.String[] leafLabelSet,
ConstraintModel constraints) |
| Constructor | Description |
|---|---|
GeneralConstructionTool(ConstraintModel constraints,
Alignment alignment) |
The constructor
|
GeneralLikelihoodSearcher(Node baseTopology,
Alignment baseAlignment,
ConstraintModel constraintModel) |