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• OFrequencySet() : bpp::OFrequencySet
• OMultiPhyloDAG() : bpp::OMultiPhyloDAG
• OMultiPhyloTree() : bpp::OMultiPhyloTree
• OMultiTree() : bpp::OMultiTree
• OnABranchPhyloLikelihood() : bpp::OnABranchPhyloLikelihood
• OneChangeRegisterTransitionModel() : bpp::OneChangeRegisterTransitionModel
• OneChangeTransitionModel() : bpp::OneChangeTransitionModel
• OneJumpSubstitutionCount() : bpp::OneJumpSubstitutionCount
• OneProcessSequenceEvolution() : bpp::OneProcessSequenceEvolution
• OneProcessSequencePhyloLikelihood() : bpp::OneProcessSequencePhyloLikelihood
• OneProcessSequenceSubstitutionMapping() : bpp::OneProcessSequenceSubstitutionMapping
• Ones() : bpp::ExtendedFloatEigen< R, C, EigenType >
• operator double() : bpp::ExtendedFloat
• operator!=() : bpp::AbstractStateMap, bpp::ExtendedFloat, bpp::ExtendedFloatEigen< R, C, EigenType >, bpp::StateMapInterface
• operator()() : bpp::AbstractPhyloLikelihood::StringPairHash, bpp::ConstantTransitionFunction, bpp::Context::CachedNodeRefHash, bpp::CWiseCompound< R, ReductionOf< T > >::compound_functor, bpp::CWiseMatching< R, ReductionOf< T > >::matching_functor, bpp::CWisePattern< R >::pattern_functor, bpp::ExtendedFloatEigen< R, C, EigenType >, bpp::HmmEmissionProbabilities_Eigen, bpp::HmmPhyloEmissionProbabilities, bpp::LegacyProbabilisticRewardMapping, bpp::LegacyProbabilisticSubstitutionMapping, bpp::LegacyRewardMappingInterface, bpp::LegacySubstitutionMappingInterface, bpp::PhyloBranchMapping, bpp::PhyloBranchReward, bpp::ProbabilisticRewardMapping, bpp::ProbabilisticSubstitutionMapping, bpp::RewardMappingInterface, bpp::SubstitutionMapping, bpp::SubstitutionProcessCollectionMember::Deleter
• operator*() : bpp::ExtendedFloat, bpp::ExtendedFloatArrayWrapper< R, C >, bpp::ExtendedFloatEigen< R, C, EigenType >
• operator*=() : bpp::ExtendedFloat, bpp::ExtendedFloatArrayWrapper< R, C >, bpp::ExtendedFloatEigen< R, C, EigenType >, bpp::PhyloDAG, bpp::PhyloTree
• operator+() : bpp::ExtendedFloat, bpp::ExtendedFloatEigen< R, C, EigenType >
• operator++() : bpp::TreeIterator
• operator+=() : bpp::ExtendedFloat, bpp::ExtendedFloatArrayWrapper< R, C >, bpp::ExtendedFloatEigen< R, C, EigenType >, bpp::ExtendedFloatNoAlias< DerivedEF >, bpp::MixedSubstitutionModelSet::HyperNode::Node, bpp::MixedSubstitutionModelSet::HyperNode, bpp::ModelPath, bpp::ModelPath::PathNode, bpp::PhyloDAG, bpp::PhyloTree
• operator-() : bpp::ExtendedFloat, bpp::ExtendedFloatEigen< R, C, EigenType >
• operator-=() : bpp::ExtendedFloat, bpp::ExtendedFloatEigen< R, C, EigenType >, bpp::ExtendedFloatNoAlias< DerivedEF >, bpp::ModelPath, bpp::ModelPath::PathNode, bpp::PhyloDAG, bpp::PhyloTree
• operator/() : bpp::ExtendedFloat, bpp::ExtendedFloatEigen< R, C, EigenType >
• operator/=() : bpp::ExtendedFloat, bpp::ExtendedFloatEigen< R, C, EigenType >, bpp::PhyloDAG, bpp::PhyloTree
• operator<() : bpp::ExtendedFloat, bpp::Nhx::Property, bpp::SitePatterns::SortableSite
• operator<=() : bpp::ExtendedFloat, bpp::MixedSubstitutionModelSet::HyperNode::Node, bpp::MixedSubstitutionModelSet::HyperNode, bpp::ModelPath, bpp::ModelPath::PathNode
• operator=() : bpp::AAExteriorSubstitutionRegister, bpp::AAInteriorSubstitutionRegister, bpp::AbstractAgglomerativeDistanceMethod, bpp::AbstractAlignedPhyloLikelihood, bpp::AbstractAlignedPhyloLikelihoodSet, bpp::AbstractAutonomousSubstitutionProcess, bpp::AbstractBiblioMixedTransitionModel, bpp::AbstractBiblioSubstitutionModel, bpp::AbstractBiblioTransitionModel, bpp::AbstractCodonAAFitnessSubstitutionModel, bpp::AbstractCodonAARateSubstitutionModel, bpp::AbstractCodonBGCSubstitutionModel, bpp::AbstractCodonClusterAASubstitutionModel, bpp::AbstractCodonCpGSubstitutionModel, bpp::AbstractCodonDistanceSubstitutionModel, bpp::AbstractCodonFitnessSubstitutionModel, bpp::AbstractCodonFrequenciesSubstitutionModel, bpp::AbstractCodonPhaseFrequenciesSubstitutionModel, bpp::AbstractCodonSubstitutionModel, bpp::AbstractDFPSubstitutionModel, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood, bpp::AbstractFrequencySet, bpp::AbstractFromSubstitutionModelTransitionModel, bpp::AbstractHomogeneousTreeLikelihood, bpp::AbstractKroneckerCodonSubstitutionModel, bpp::AbstractKroneckerWordSubstitutionModel, bpp::AbstractMapping, bpp::AbstractMixedTransitionModel, bpp::AbstractNonHomogeneousTreeLikelihood, bpp::AbstractParametrizableSequencePhyloLikelihood, bpp::AbstractPhyloLikelihood, bpp::AbstractPhyloLikelihoodSet, bpp::AbstractReward, bpp::AbstractRewardMapping, bpp::AbstractSequencePhyloLikelihood, bpp::AbstractSingleDataPhyloLikelihood, bpp::AbstractSinglePhyloSubstitutionMapping, bpp::AbstractStateMap, bpp::AbstractSubstitutionDistance, bpp::AbstractSubstitutionMapping, bpp::AbstractSubstitutionModel, bpp::AbstractSubstitutionRegister, bpp::AbstractTransitionModel, bpp::AbstractTreeDrawing, bpp::AbstractTreeLikelihood::ConstNoPartitionBranchModelDescription, bpp::AbstractTreeLikelihood::ConstNoPartitionSiteModelDescription, bpp::AbstractTreeLikelihood, bpp::AbstractTreeLikelihoodData, bpp::AbstractTreeParsimonyData, bpp::AbstractWeightedSubstitutionCount, bpp::AbstractWordFrequencySet, bpp::AbstractWordSubstitutionModel, bpp::AlignedPhyloLikelihoodAutoCorrelation, bpp::AlignedPhyloLikelihoodHmm, bpp::AlignedPhyloLikelihoodMixture, bpp::AlignedPhyloLikelihoodProduct, bpp::AutoCorrelationProcessPhyloLikelihood, bpp::AutoCorrelationSequenceEvolution, bpp::AwareNode, bpp::BasicTreeDrawingDisplayControler, bpp::BipartitionList, bpp::BootstrapValuesTreeDrawingListener, bpp::BppOBranchModelFormat, bpp::BppOFrequencySetFormat, bpp::BppOSubstitutionModelFormat, bpp::BppOTransitionModelFormat, bpp::BranchLengthsTreeDrawingListener, bpp::BranchLikelihood, bpp::CodonAdHocSubstitutionModel, bpp::CodonFromIndependentFrequencySet, bpp::CodonFromUniqueFrequencySet, bpp::CodonSameAARateSubstitutionModel, bpp::CompleteSubstitutionRegister, bpp::D1WalkSubstitutionModel, bpp::DecompositionMethods, bpp::DecompositionReward, bpp::DecompositionSubstitutionCount, bpp::DFP07, bpp::DistanceEstimation, bpp::DnDsSubstitutionRegister, bpp::DRASDRTreeLikelihoodData, bpp::DRASDRTreeLikelihoodLeafData, bpp::DRASDRTreeLikelihoodNodeData, bpp::DRASRTreeLikelihoodData, bpp::DRASRTreeLikelihoodNodeData, bpp::DrawBranchEvent, bpp::DrawIBranchEvent, bpp::DrawINodeEvent, bpp::DrawNodeEvent, bpp::DrawTreeEvent, bpp::DRHomogeneousMixedTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::DRTreeParsimonyData, bpp::DRTreeParsimonyLeafData, bpp::DRTreeParsimonyNodeData, bpp::DRTreeParsimonyScore, bpp::DSO78, bpp::EquiprobableSubstitutionModel, bpp::EvolutionSequenceSimulator, bpp::ExtendedFloat, bpp::ExtendedFloatArrayWrapper< R, C >, bpp::ExtendedFloatCol< R, C, EigenType >, bpp::ExtendedFloatEigen< R, C, EigenType >, bpp::ExtendedFloatNoAlias< DerivedEF >, bpp::ExtendedFloatRow< R, C, EigenType >, bpp::ExtendedFloatVectorwiseOp< DerivedEF, MatType, Direction >, bpp::FixedCodonFrequencySet, bpp::FromMixtureSubstitutionModel, bpp::FromModelFrequencySet, bpp::FullCodonFrequencySet, bpp::FullPerAACodonFrequencySet, bpp::G2001, bpp::gBGC, bpp::GCPositionSubstitutionRegister, bpp::GCSynonymousSubstitutionRegister, bpp::GeneralSubstitutionRegister, bpp::GivenDataSubstitutionProcessSiteSimulator, bpp::GlobalClockTreeLikelihoodFunctionWrapper, bpp::GY94, bpp::HmmProcessAlphabet, bpp::HmmSequenceEvolution, bpp::InMixedSubstitutionModel, bpp::JCprot, bpp::JTT92, bpp::KCM, bpp::KrKcSubstitutionRegister, bpp::LaplaceSubstitutionCount, bpp::LeafNamesTreeDrawingListener, bpp::LegacyAbstractMapping, bpp::LegacyAbstractRewardMapping, bpp::LegacyAbstractSubstitutionMapping, bpp::LegacyMarginalAncestralStateReconstruction, bpp::LegacyOptimizationTools::ScaleFunction, bpp::LegacyProbabilisticRewardMapping, bpp::LegacyProbabilisticSubstitutionMapping, bpp::LG08, bpp::LGL08_CAT, bpp::MarginalAncestralReconstruction, bpp::MarkovModulatedFrequencySet, bpp::MarkovModulatedSubstitutionModel, bpp::MG94, bpp::MixedSubstitutionModelSet::HyperNode::Node, bpp::MixedSubstitutionModelSet::HyperNode, bpp::MixedSubstitutionModelSet, bpp::MixtureOfASubstitutionModel, bpp::MixtureOfATransitionModel, bpp::MixtureOfSubstitutionModels, bpp::MixtureOfTransitionModels, bpp::MixtureProcessPhyloLikelihood, bpp::MixtureSequenceEvolution, bpp::ModelList, bpp::ModelPath, bpp::ModelPath::PathNode, bpp::ModelScenario, bpp::MultinomialFromTransitionModel, bpp::MultiProcessSequenceEvolution, bpp::MultiProcessSequencePhyloLikelihood, bpp::MutationPath, bpp::NaNListener, bpp::NNIHomogeneousTreeLikelihood, bpp::NNITopologyListener2, bpp::NNITopologyListener, bpp::NNITopologySearch, bpp::Node, bpp::Node_DF, bpp::NodePException, bpp::NodesIdTreeDrawingListener, bpp::NodeTemplate< NodeInfos >, bpp::NonHomogeneousSequenceSimulator, bpp::NonHomogeneousSubstitutionProcess, bpp::OneChangeRegisterTransitionModel, bpp::OneChangeTransitionModel, bpp::OneJumpSubstitutionCount, bpp::OneProcessSequenceEvolution, bpp::OneProcessSequencePhyloLikelihood, bpp::OneProcessSequenceSubstitutionMapping, bpp::ParametrizablePhyloTree, bpp::PartitionProcessPhyloLikelihood, bpp::PartitionSequenceEvolution, bpp::PhyloBranch, bpp::PhyloBranchMapping, bpp::PhyloBranchParam, bpp::PhyloBranchPException, bpp::PhyloBranchReward, bpp::PhyloLikelihoodFormula, bpp::PhyloNode, bpp::PhyloNodePException, bpp::PhyloTreeException, bpp::POMO, bpp::ProbabilisticRewardMapping, bpp::ProbabilisticSubstitutionMapping, bpp::ProcessTree, bpp::RateAcrossSitesSubstitutionProcess, bpp::RE08, bpp::RegisterRatesSubstitutionModel, bpp::RHomogeneousMixedTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousMixedTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, bpp::SimData, bpp::SimpleSubstitutionProcess, bpp::SimpleSubstitutionProcessSiteSimulator, bpp::SingleProcessSubstitutionMapping, bpp::SitePatterns::SortableSite, bpp::SiteSimulationResult, bpp::SubstitutionModelSet, bpp::SubstitutionProcessCollection, bpp::SubstitutionProcessCollectionMember, bpp::SubstitutionProcessSequenceSimulator, bpp::SWSubstitutionRegister, bpp::TransitionFromTransitionModel, bpp::TreeDrawingDisplayControler, bpp::TreeException, bpp::TreeIterator, bpp::TreeTemplate< N >, bpp::TsTvSubstitutionRegister, bpp::UniformizationSubstitutionCount, bpp::UserCodonFrequencySet, bpp::UserFrequencySet, bpp::UserProteinSubstitutionModel, bpp::WAG01, bpp::WordFromIndependentFrequencySet, bpp::WordFromUniqueFrequencySet, bpp::YN98, bpp::YNGP_M10, bpp::YNGP_M7, bpp::YNGP_M8, bpp::YNGP_M9, bpp::YNGP_M, bpp::YpR
• operator==() : bpp::AbstractStateMap, bpp::Context::CachedNodeRef, bpp::ExtendedFloat, bpp::ExtendedFloatEigen< R, C, EigenType >, bpp::Node, bpp::StateMapInterface
• operator>() : bpp::ExtendedFloat
• operator>=() : bpp::ExtendedFloat, bpp::MixedSubstitutionModelSet::HyperNode::Node, bpp::MixedSubstitutionModelSet::HyperNode, bpp::ModelPath, bpp::ModelPath::PathNode
• operator[]() : bpp::AwareNode, bpp::ExtendedFloatEigen< R, C, EigenType >, bpp::LegacyProbabilisticRewardMapping, bpp::LegacyProbabilisticSubstitutionMapping, bpp::MixedSubstitutionModelSet::HyperNode::Node, bpp::Node, bpp::NodeTemplate< NodeInfos >, bpp::PhyloLikelihoodContainer
• OPhyloDAG() : bpp::OPhyloDAG
• OPhyloTree() : bpp::OPhyloTree
• optimizationInitializationPerformed() : bpp::NaNListener
• OptimizationOptions() : bpp::OptimizationTools::OptimizationOptions
• optimizationStepPerformed() : bpp::NaNListener
• OptimizationTools() : bpp::OptimizationTools
• optimizeBranchLengthsParameters() : bpp::LegacyOptimizationTools
• optimizeNumericalParameters() : bpp::LegacyOptimizationTools, bpp::OptimizationTools
• optimizeNumericalParameters2() : bpp::LegacyOptimizationTools, bpp::OptimizationTools
• optimizeParameters() : bpp::LegacyPhylogeneticsApplicationTools, bpp::PhylogeneticsApplicationTools
• optimizer() : bpp::DistanceEstimation
• optimizeTreeNNI() : bpp::LegacyOptimizationTools
• optimizeTreeNNI2() : bpp::LegacyOptimizationTools
• optimizeTreeScale() : bpp::LegacyOptimizationTools
• orderTree() : bpp::TreeTemplateTools
• orderTree_() : bpp::TreeTemplateTools
• OrderTreeData_() : bpp::TreeTemplateTools::OrderTreeData_
• OSubstitutionModel() : bpp::OSubstitutionModel
• OTree() : bpp::OTree
• output() : bpp::PhyloLikelihoodFormula
• outputInternalSequences() : bpp::GivenDataSubstitutionProcessSequenceSimulator, bpp::NonHomogeneousSequenceSimulator, bpp::SequenceSimulatorInterface, bpp::SimpleSubstitutionProcessSequenceSimulator, bpp::SubstitutionProcessSequenceSimulator
• outputInternalSites() : bpp::NonHomogeneousSequenceSimulator, bpp::SimpleSubstitutionProcessSiteSimulator, bpp::SiteSimulatorInterface
• outputPerSitePerBranch() : bpp::LegacySubstitutionMappingTools, bpp::SubstitutionMappingTools
• outputPerSitePerBranchPerType() : bpp::LegacySubstitutionMappingTools, bpp::SubstitutionMappingTools
• outputPerSitePerType() : bpp::LegacySubstitutionMappingTools, bpp::SubstitutionMappingTools
• outputPerType() : bpp::SubstitutionMappingTools
• outputPositiveLengths() : bpp::NeighborJoining
• OwnedExtendedFloat() : bpp::ExtendedFloatEigen< R, C, EigenType >::OwnedExtendedFloat