- 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