- u -

• unaliasParameters() : bpp::SubstitutionProcessCollection
• UniformizationSubstitutionCount() : bpp::UniformizationSubstitutionCount
• uniqueToSharedMap() : bpp::PhylogeneticsApplicationTools
• unregisterNode() : bpp::Node_DF
• unresolveUncertainNodes() : bpp::TreeTemplateTools
• unroot() : bpp::Tree , bpp::TreeTemplate< N >
• UnrootedPhyloTreeException() : bpp::UnrootedPhyloTreeException
• UnrootedTreeException() : bpp::UnrootedTreeException
• updateBranchByDwellingTimes() : bpp::StochasticMapping
• updateBranchMapping() : bpp::StochasticMapping
• updateFreq_() : bpp::FullCodonFrequencySet , bpp::FullFrequencySet
• updateFrequencies() : bpp::CodonFromIndependentFrequencySet , bpp::CodonFromUniqueFrequencySet , bpp::MvaFrequencySet , bpp::WordFromIndependentFrequencySet , bpp::WordFromUniqueFrequencySet
• updateFrequencies_() : bpp::FullPerAACodonFrequencySet
• updateMatrices_() : bpp::AbstractBiblioSubstitutionModel , bpp::AbstractBiblioTransitionModel , bpp::AbstractCodonSubstitutionModel , bpp::AbstractDFPSubstitutionModel , bpp::AbstractReversibleSubstitutionModel , bpp::AbstractSubstitutionModel , bpp::AbstractTransitionModel , bpp::AbstractWordSubstitutionModel , bpp::BinarySubstitutionModel , bpp::Coala , bpp::D1WalkSubstitutionModel , bpp::DFP07 , bpp::EquiprobableSubstitutionModel , bpp::F81 , bpp::F84 , bpp::gBGC , bpp::GTR , bpp::HKY85 , bpp::JCnuc , bpp::JCprot , bpp::K80 , bpp::L95 , bpp::MarkovModulatedSubstitutionModel , bpp::MixtureOfASubstitutionModel , bpp::MixtureOfATransitionModel , bpp::MixtureOfTransitionModels , bpp::OneChangeRegisterTransitionModel , bpp::POMO , bpp::RE08 , bpp::RegisterRatesSubstitutionModel , bpp::RELAX , bpp::RN95 , bpp::RN95s , bpp::SSR , bpp::T92 , bpp::TN93 , bpp::TwoParameterBinarySubstitutionModel , bpp::WordSubstitutionModel , bpp::YNGP_M10 , bpp::YNGP_M1 , bpp::YNGP_M2 , bpp::YNGP_M3 , bpp::YNGP_M7 , bpp::YNGP_M8 , bpp::YNGP_M9 , bpp::YpR , bpp::YpR_Gen , bpp::YpR_Sym
• updateMatrix_() : bpp::AAExteriorSubstitutionRegister , bpp::AAInteriorSubstitutionRegister
• updateParameters() : bpp::SubstitutionProcessCollectionMember
• updateParameters_() : bpp::BppOSubstitutionModelFormat
• updateRatesModel_() : bpp::G2001 , bpp::MarkovModulatedSubstitutionModel , bpp::TS98
• updateRootFrequencies() : bpp::SubstitutionModelSet
• updateTree() : bpp::AwareNode
• updateTypes_() : bpp::GeneralSubstitutionRegister
• usePatterns() : bpp::ProbabilisticRewardMapping , bpp::ProbabilisticSubstitutionMapping
• useProb() : bpp::ProcessComputationEdge
• UserCodonFrequencySet() : bpp::UserCodonFrequencySet
• UserFrequencySet() : bpp::UserFrequencySet
• UserNucleotideFrequencySet() : bpp::UserNucleotideFrequencySet
• UserProteinFrequencySet() : bpp::UserProteinFrequencySet
• UserProteinSubstitutionModel() : bpp::UserProteinSubstitutionModel
• useTagsAsPropertyNames() : bpp::Nhx