Uses of Class
pal.tree.SimulatedAlignment.Factory
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Packages that use SimulatedAlignment.Factory Package Description pal.coalescent Classes to model population genetic processes using the coalescent.pal.supgma -
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Uses of SimulatedAlignment.Factory in pal.coalescent
Constructors in pal.coalescent with parameters of type SimulatedAlignment.Factory Constructor Description 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 Modifier and Type Method Description SUPGMABase.CISummarySUPGMABase.PopulationParameters. inferCI(AlgorithmCallback callback, int numberOfReplicates, SimulatedAlignment.Factory alignmentFactory, SubstitutionModel evolutionaryModel, LMSSolver solver)
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