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)
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Uses of SimulatedAlignment.Factory in pal.supgma
Methods in pal.supgma with parameters of type SimulatedAlignment.Factory Modifier and Type Method Description SUPGMABase.CISummary
SUPGMABase.PopulationParameters. inferCI(AlgorithmCallback callback, int numberOfReplicates, SimulatedAlignment.Factory alignmentFactory, SubstitutionModel evolutionaryModel, LMSSolver solver)
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