- f -

• F84() : bpp::F84
• fillBMatrices_() : bpp::DecompositionSubstitutionCount , bpp::UniformizationSubstitutionCount
• 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::DRHomogeneousTreeLikelihood , bpp::CodonDistanceFrequenciesSubstitutionModel , bpp::CodonDistancePhaseFrequenciesSubstitutionModel , bpp::DRNonHomogeneousTreeLikelihood , bpp::CodonDistanceSubstitutionModel , bpp::CodonRateFrequenciesSubstitutionModel , bpp::GlobalClockTreeLikelihoodFunctionWrapper , bpp::CodonRateSubstitutionModel , bpp::FullCodonFrequenciesSet , bpp::BranchLikelihood , bpp::FixedCodonFrequenciesSet , bpp::FullPerAACodonFrequenciesSet , bpp::RHomogeneousClockTreeLikelihood , bpp::FullFrequenciesSet , bpp::SubstitutionModelSet , bpp::RE08 , bpp::WAG01 , bpp::UserProteinSubstitutionModel , bpp::MarkovModulatedFrequenciesSet , bpp::JTT92 , bpp::JCprot , bpp::DSO78 , bpp::RHomogeneousMixedTreeLikelihood , bpp::gBGC , bpp::MixedSubstitutionModelSet , bpp::FixedFrequenciesSet , bpp::MvaFrequenciesSet , bpp::WordFromUniqueFrequenciesSet , bpp::WordFromIndependentFrequenciesSet , bpp::RHomogeneousTreeLikelihood , bpp::GCFrequenciesSet , bpp::FullNucleotideFrequenciesSet , bpp::RNonHomogeneousMixedTreeLikelihood , bpp::RNonHomogeneousTreeLikelihood , bpp::G2001 , bpp::MarkovModulatedSubstitutionModel , bpp::AbstractBiblioSubstitutionModel , bpp::AbstractSubstitutionModel , bpp::YpR , bpp::AbstractCodonDistanceSubstitutionModel , bpp::TwoTreeLikelihood , bpp::AbstractCodonFitnessSubstitutionModel , bpp::LG08 , bpp::CodonDistanceFitnessPhaseFrequenciesSubstitutionModel , bpp::AbstractCodonFrequenciesSubstitutionModel , bpp::DRHomogeneousMixedTreeLikelihood , bpp::AbstractCodonPhaseFrequenciesSubstitutionModel
• FixedCodonFrequenciesSet() : bpp::FixedCodonFrequenciesSet
• FixedFrequenciesSet() : bpp::FixedFrequenciesSet
• FixedNucleotideFrequenciesSet() : bpp::FixedNucleotideFrequenciesSet
• FixedProteinFrequenciesSet() : bpp::FixedProteinFrequenciesSet
• flip() : bpp::BipartitionList
• freq() : bpp::MarkovModulatedSubstitutionModel , bpp::AbstractBiblioSubstitutionModel , bpp::SubstitutionModel , bpp::AbstractSubstitutionModel
• from() : bpp::MixtureOfASubstitutionModel
• FullCodonFrequenciesSet() : bpp::FullCodonFrequenciesSet
• FullFrequenciesSet() : bpp::FullFrequenciesSet
• FullNucleotideFrequenciesSet() : bpp::FullNucleotideFrequenciesSet
• FullPerAACodonFrequenciesSet() : bpp::FullPerAACodonFrequenciesSet
• FullProteinFrequenciesSet() : bpp::FullProteinFrequenciesSet
• fullyResolvedConsensus() : bpp::TreeTools