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)