| Package | Description |
|---|---|
| pal.mep |
Classes for the analysis of "measurably evolving populations" (mep).
|
| pal.misc |
Classes that don't fit elsewhere ;^)
|
| 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 |
TOCDSampleInformation |
Title: TOCDSampleInformation
|
| Modifier and Type | Method | Description |
|---|---|---|
SampleInformation |
SampleInformation.Factory.createSampleInformation(java.lang.String[] allLeafIDs) |
| Constructor | Description |
|---|---|
FixedBSRDTGlobalClockModel(SampleInformation sampleInformation,
MolecularClockLikelihoodModel.Instance likelihoodModel,
double rate) |
|
FixedSRDTGlobalClockModel(SampleInformation sampleInformation,
MolecularClockLikelihoodModel.Instance likelihoodModel,
double rate) |
|
MRDTGlobalClockModel(SampleInformation sampleInformation,
MolecularClockLikelihoodModel.Instance likelihoodModel) |
|
MRDTGlobalClockModel(SampleInformation sampleInformation,
MolecularClockLikelihoodModel.Instance likelihoodModel,
double[] rateChangeTimes) |
|
SRDTGlobalClockModel(SampleInformation sampleInformation,
MolecularClockLikelihoodModel.Instance likelihoodModel) |
|
SRDTGlobalClockModel(SampleInformation sampleInformation,
MolecularClockLikelihoodModel.Instance likelihoodModel,
boolean allowMetaRate) |