Uses of Interface
pal.eval.UnconstrainedLikelihoodModel.External
Packages that use UnconstrainedLikelihoodModel.External
Package
Description
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
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Uses of UnconstrainedLikelihoodModel.External in pal.eval
Methods in pal.eval that return UnconstrainedLikelihoodModel.External -
Uses of UnconstrainedLikelihoodModel.External in pal.treesearch
Methods in pal.treesearch that return UnconstrainedLikelihoodModel.ExternalModifier and TypeMethodDescriptionConstraintModel.createNewFreeExternal()FixedBSRDTGlobalClockModel.createNewFreeExternal()FixedSRDTGlobalClockModel.createNewFreeExternal()GlobalClockModel.createNewFreeExternal()MRDTGlobalClockModel.createNewFreeExternal()SRDTGlobalClockModel.createNewFreeExternal()UnconstrainedModel.createNewFreeExternal()GeneralConstructionTool.obtainFreeExternalCalculator()Methods in pal.treesearch with parameters of type UnconstrainedLikelihoodModel.ExternalModifier and TypeMethodDescriptionFreeBranch.calculateSiteDetails(UnconstrainedLikelihoodModel.External calculator, GeneralConstructionTool tool) FreeBranch.getExtendedConditionalProbabilities(FreeNode caller, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore extendedStore, GeneralConstructionTool tool) FreeInternalNode.getExtendedConditionalProbabilities(double distance, FreeBranch callerConnection, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) FreeLeafNode.getExtendedConditionalProbabilities(double distance, FreeBranch callingBranch, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) FreeNode.getExtendedConditionalProbabilities(double distance, FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) PivotNode.getExtendedConditionalProbabilities(double distance, FreeBranch caller, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) FreeInternalNode.getFlatConditionalProbabilities(FreeBranch callerConnection, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) FreeLeafNode.getFlatConditionalProbabilities(FreeBranch callingBranch, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) FreeInternalNode.getLeftExtendedConditionalProbabilities(FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) FreeLeafNode.getLeftExtendedConditionalProbabilities(FreeBranch caller, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore) FreeInternalNode.getRightExtendedConditionalProbabilities(FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) FreeLeafNode.getRightExtendedConditionalProbabilities(FreeBranch caller, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore)