Here is a list of all class members with links to the classes they belong to:
- u -
- unaliasParameters() : bpp::SubstitutionProcessCollection
- UniformizationSubstitutionCount() : bpp::UniformizationSubstitutionCount
- uniqueToSharedMap() : bpp::PhylogeneticsApplicationTools
- unparsedArguments_ : bpp::BppOFrequencySetFormat, bpp::BppOMultiTreeReaderFormat, bpp::BppOMultiTreeWriterFormat, bpp::BppOSubstitutionModelFormat, bpp::BppOTreeReaderFormat, bpp::BppOTreeWriterFormat
- unregisterNode() : bpp::Node_DF
- UNRESOLVED_AVERAGE : bpp::SubstitutionMappingTools
- UNRESOLVED_ONE : bpp::SubstitutionMappingTools
- UNRESOLVED_ZERO : bpp::SubstitutionMappingTools
- 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
- upperNode_ : bpp::RNonHomogeneousMixedTreeLikelihood
- useBootstrap_ : bpp::Newick
- useCG_ : bpp::PseudoNewtonOptimizer
- useClock : bpp::OptimizationTools::OptimizationOptions
- usePatterns() : bpp::ProbabilisticRewardMapping, bpp::ProbabilisticSubstitutionMapping
- usePatterns_ : bpp::DRASRTreeLikelihoodData, bpp::ProbabilisticRewardMapping, bpp::ProbabilisticSubstitutionMapping
- useProb() : bpp::ProcessComputationEdge
- useProb_ : bpp::ProcessComputationEdge
- UserCodonFrequencySet() : bpp::UserCodonFrequencySet
- UserFrequencySet() : bpp::UserFrequencySet
- UserNucleotideFrequencySet() : bpp::UserNucleotideFrequencySet
- UserProteinFrequencySet() : bpp::UserProteinFrequencySet
- UserProteinSubstitutionModel() : bpp::UserProteinSubstitutionModel
- useTagsAsPropertyNames() : bpp::Nhx
- useTagsAsPropertyNames_ : bpp::Nhx