- f -

• F81() : bpp::F81
• F84() : bpp::F84
• factorial() : bpp::MultinomialFromTransitionModel
• fill() : bpp::ExtendedFloatEigen< R, C, EigenType >
• fillBasicGenerator_() : bpp::AbstractKroneckerWordSubstitutionModel , bpp::AbstractWordSubstitutionModel
• fillBMatrice_() : bpp::DecompositionReward
• fillBMatrices_() : bpp::DecompositionSubstitutionCount , bpp::UniformizationSubstitutionCount
• fillMappingVectorForSite() : bpp::ProbabilisticSubstitutionMapping
• finalStep() : bpp::AbstractAgglomerativeDistanceMethod , bpp::HierarchicalClustering , bpp::NeighborJoining , bpp::PGMA
• fireAfterBranchEvent_() : bpp::AbstractTreeDrawing
• fireAfterNodeEvent_() : bpp::AbstractTreeDrawing
• fireAfterTreeEvent_() : bpp::AbstractTreeDrawing
• fireBeforeBranchEvent_() : bpp::AbstractTreeDrawing
• fireBeforeNodeEvent_() : bpp::AbstractTreeDrawing
• fireBeforeTreeEvent_() : bpp::AbstractTreeDrawing
• fireParameterChanged() : bpp::AbstractAutonomousSubstitutionProcess , bpp::AbstractBiblioTransitionModel , bpp::AbstractCodonAAFitnessSubstitutionModel , bpp::AbstractCodonAARateSubstitutionModel , bpp::AbstractCodonBGCSubstitutionModel , bpp::AbstractCodonClusterAASubstitutionModel , bpp::AbstractCodonCpGSubstitutionModel , bpp::AbstractCodonDistanceSubstitutionModel , bpp::AbstractCodonFitnessSubstitutionModel , bpp::AbstractCodonFrequenciesSubstitutionModel , bpp::AbstractCodonPhaseFrequenciesSubstitutionModel , bpp::AbstractDFPSubstitutionModel , bpp::AbstractFromSubstitutionModelTransitionModel , bpp::AbstractParametrizableSequencePhyloLikelihood , bpp::AbstractPhyloLikelihoodSet , bpp::AbstractTransitionModel , bpp::AlignedPhyloLikelihoodAutoCorrelation , bpp::AlignedPhyloLikelihoodHmm , bpp::AlignedPhyloLikelihoodMixture , bpp::AutoCorrelationProcessPhyloLikelihood , bpp::AutoCorrelationSequenceEvolution , bpp::BranchLikelihood , bpp::CodonAdHocSubstitutionModel , bpp::CodonDistanceFrequenciesSubstitutionModel , bpp::CodonDistancePhaseFrequenciesSubstitutionModel , bpp::CodonDistanceSubstitutionModel , bpp::CodonSameAARateSubstitutionModel , bpp::D1WalkSubstitutionModel , bpp::DFPDistanceFrequenciesSubstitutionModel , bpp::DRHomogeneousMixedTreeLikelihood , bpp::DRHomogeneousTreeLikelihood , bpp::DRNonHomogeneousTreeLikelihood , bpp::DSO78 , bpp::EquiprobableSubstitutionModel , bpp::FixedCodonFrequencySet , bpp::FromMixtureSubstitutionModel , bpp::FromModelFrequencySet , bpp::FullCodonFrequencySet , bpp::FullFrequencySet , bpp::FullNucleotideFrequencySet , bpp::FullPerAACodonFrequencySet , bpp::G2001 , bpp::gBGC , bpp::GCFrequencySet , bpp::GlobalClockTreeLikelihoodFunctionWrapper , bpp::HmmProcessPhyloLikelihood , bpp::HmmSequenceEvolution , bpp::InMixedSubstitutionModel , bpp::JCprot , bpp::JTT92 , bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel , bpp::KroneckerCodonDistanceSubstitutionModel , bpp::LG08 , bpp::MarkovModulatedFrequencySet , bpp::MarkovModulatedSubstitutionModel , bpp::MixedSubstitutionModelSet , bpp::MixtureSequenceEvolution , bpp::MultinomialFromTransitionModel , bpp::MultiProcessSequenceEvolution , bpp::MvaFrequencySet , bpp::NonHomogeneousSubstitutionProcess , bpp::OneChangeRegisterTransitionModel , bpp::OneProcessSequenceEvolution , bpp::ParametrizablePhyloTree , bpp::POMO , bpp::RateAcrossSitesSubstitutionProcess , bpp::RE08 , bpp::RegisterRatesSubstitutionModel , bpp::RHomogeneousMixedTreeLikelihood , bpp::RHomogeneousTreeLikelihood , bpp::RNonHomogeneousMixedTreeLikelihood , bpp::RNonHomogeneousTreeLikelihood , bpp::SENCA , bpp::SimpleSubstitutionProcess , bpp::SubstitutionModelSet , bpp::SubstitutionProcessCollection , bpp::TransitionFromTransitionModel , bpp::UserCodonFrequencySet , bpp::UserProteinSubstitutionModel , bpp::WAG01 , bpp::WordFromIndependentFrequencySet , bpp::WordFromUniqueFrequencySet , bpp::YpR
• firstOrderDerivativeNode() : bpp::AbstractPhyloLikelihood
• firstOrderDerivativeVector() : bpp::OnABranchPhyloLikelihood , bpp::OneProcessSequencePhyloLikelihood , bpp::SingleProcessPhyloLikelihood
• fitness() : bpp::AbstractCodonFitnessSubstitutionModel , bpp::POMO
• FixedCodonFrequencySet() : bpp::FixedCodonFrequencySet
• FixedFrequencySet() : bpp::FixedFrequencySet
• FixedNucleotideFrequencySet() : bpp::FixedNucleotideFrequencySet
• FixedProteinFrequencySet() : bpp::FixedProteinFrequencySet
• fixLikelihood() : bpp::BppPhylogeneticsApplication
• flip() : bpp::BipartitionList
• float_part() : bpp::ExtendedFloat , bpp::ExtendedFloatArrayWrapper< R, C > , bpp::ExtendedFloatCol< R, C, EigenType > , bpp::ExtendedFloatEigen< R, C, EigenType > , bpp::ExtendedFloatRow< R, C, EigenType >
• ForwardHmmD2Likelihood_DF() : bpp::ForwardHmmD2Likelihood_DF
• ForwardHmmDLikelihood_DF() : bpp::ForwardHmmDLikelihood_DF
• ForwardHmmLikelihood_DF() : bpp::ForwardHmmLikelihood_DF
• ForwardLikelihoodTree() : bpp::ForwardLikelihoodTree
• freq() : bpp::AbstractTotallyWrappedTransitionModel , bpp::AbstractTransitionModel , bpp::InMixedSubstitutionModel , bpp::MarkovModulatedSubstitutionModel , bpp::OneChangeRegisterTransitionModel , bpp::OneChangeTransitionModel , bpp::TransitionModelInterface
• FrequenciesFromFrequencySet() : bpp::FrequenciesFromFrequencySet
• FrequenciesFromSimplex() : bpp::FrequenciesFromSimplex
• frequencySet() : bpp::AbstractBiblioMixedTransitionModel , bpp::AbstractCodonFrequenciesSubstitutionModel , bpp::AbstractCodonPhaseFrequenciesSubstitutionModel , bpp::AbstractTransitionModel , bpp::AbstractWrappedModel , bpp::AbstractWrappedTransitionModel , bpp::BranchModelInterface , bpp::CodonDistanceFrequenciesSubstitutionModel , bpp::CodonDistancePhaseFrequenciesSubstitutionModel , bpp::D1WalkSubstitutionModel , bpp::DSO78 , bpp::EquiprobableSubstitutionModel , bpp::JCprot , bpp::JTT92 , bpp::LG08 , bpp::MarkovModulatedSubstitutionModel , bpp::OneChangeRegisterTransitionModel , bpp::OneChangeTransitionModel , bpp::RegisterRatesSubstitutionModel , bpp::SubstitutionProcessCollection , bpp::UserProteinSubstitutionModel , bpp::WAG01 , bpp::YN98
• frequencySetForLetter() : bpp::WordFrequencySetInterface , bpp::WordFromIndependentFrequencySet , bpp::WordFromUniqueFrequencySet
• from() : bpp::MixtureOfATransitionModel
• FromMixtureSubstitutionModel() : bpp::FromMixtureSubstitutionModel
• FromModelFrequencySet() : bpp::FromModelFrequencySet
• FullCodonFrequencySet() : bpp::FullCodonFrequencySet
• FullFrequencySet() : bpp::FullFrequencySet
• FullNucleotideFrequencySet() : bpp::FullNucleotideFrequencySet
• FullPerAACodonFrequencySet() : bpp::FullPerAACodonFrequencySet
• FullProteinFrequencySet() : bpp::FullProteinFrequencySet
• fullyResolvedConsensus() : bpp::TreeTools