- 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