Uses of Class
pal.tree.SimulatedAlignment.Factory

Packages that use SimulatedAlignment.Factory

pal.coalescent	Classes to model population genetic processes using the coalescent.
pal.supgma

Uses of SimulatedAlignment.Factory in pal.coalescent

Constructors in pal.coalescent with parameters of type SimulatedAlignment.Factory

SerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, int numberOfTreesToGenerate, TreeOperation treeFinisher, SimulatedAlignment.Factory alignmentFactory)

SerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, TreeOperation treeFinisher, SimulatedAlignment.Factory alignmentFactory)

Uses of SimulatedAlignment.Factory in pal.supgma

Methods in pal.supgma with parameters of type SimulatedAlignment.Factory

SUPGMABase.CISummary

SUPGMABase.PopulationParameters.inferCI(AlgorithmCallback callback, int numberOfReplicates, SimulatedAlignment.Factory alignmentFactory, SubstitutionModel evolutionaryModel, LMSSolver solver)