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)