| Package | Description |
|---|---|
| pal.coalescent |
Classes to model population genetic processes using the coalescent.
|
| pal.supgma |
| Constructor | Description |
|---|---|
SerialCoalescentGenerator(TimeOrderCharacterData tocd,
DemographicModel demographicModel,
int numberOfTreesToGenerate,
TreeOperation treeFinisher,
SimulatedAlignment.Factory alignmentFactory) |
|
SerialCoalescentGenerator(TimeOrderCharacterData tocd,
DemographicModel demographicModel,
TreeOperation treeFinisher,
SimulatedAlignment.Factory alignmentFactory) |
| Modifier and Type | Method | Description |
|---|---|---|
SUPGMABase.CISummary |
SUPGMABase.PopulationParameters.inferCI(AlgorithmCallback callback,
int numberOfReplicates,
SimulatedAlignment.Factory alignmentFactory,
SubstitutionModel evolutionaryModel,
LMSSolver solver) |