Here is a list of all class members with links to the classes they belong to:

- n -

• N : bpp::PhyloTreeTools::Moments_, bpp::TreeTools::Moments_
• n_ : bpp::CombineDeltaShifted< T >, bpp::PseudoNewtonOptimizer, bpp::ShiftDelta< T >, bpp::ShiftParameter
• NaiveSubstitutionCount() : bpp::NaiveSubstitutionCount
• name : bpp::Nhx::Property
• name_ : bpp::AbstractFrequencySet, bpp::AbstractSubstitutionRegister, bpp::CodonAdHocSubstitutionModel, bpp::LG10_EX_EHO::EmbeddedModel, bpp::LGL08_CAT::EmbeddedModel, bpp::LLG08_EHO::EmbeddedModel, bpp::LLG08_EX2::EmbeddedModel, bpp::LLG08_EX3::EmbeddedModel, bpp::LLG08_UL2::EmbeddedModel, bpp::LLG08_UL3::EmbeddedModel, bpp::Node, bpp::PhyloDAG, bpp::PhyloNode, bpp::PhyloTree, bpp::Sequence_DF, bpp::TreeTemplate< N >
• names_ : bpp::SitePatterns
• NaNListener() : bpp::NaNListener
• nbAlleles_ : bpp::POMO
• nbBranches_ : bpp::LegacyAbstractMapping
• nbCategories_ : bpp::CategorySubstitutionRegister
• nbClass_ : bpp::ProbabilitiesFromDiscreteDistribution, bpp::ProbabilitiesFromMixedModel
• nbClasses_ : bpp::AbstractHomogeneousTreeLikelihood, bpp::AbstractNonHomogeneousTreeLikelihood, bpp::BranchLikelihood, bpp::DRASDRTreeLikelihoodData, bpp::DRASRTreeLikelihoodData, bpp::LegacyMarginalAncestralStateReconstruction, bpp::MarkovModulatedStateMap, bpp::NonHomogeneousSequenceSimulator, bpp::SimpleSubstitutionProcessSiteSimulator
• nbDependencies() : bpp::Node_DF
• nbDependentNodes() : bpp::Node_DF
• nbDistinctSites_ : bpp::AbstractHomogeneousTreeLikelihood, bpp::AbstractNonHomogeneousTreeLikelihood, bpp::DRASDRTreeLikelihoodData, bpp::DRASRTreeLikelihoodData, bpp::DRTreeParsimonyData, bpp::DRTreeParsimonyScore, bpp::LegacyMarginalAncestralStateReconstruction, bpp::MarginalAncestralReconstruction, bpp::TrivialSitePartition
• nBeta_ : bpp::YNGP_M10, bpp::YNGP_M9
• nbEvalMax : bpp::OptimizationTools::OptimizationOptions
• nbModels_ : bpp::AbstractNonHomogeneousTreeLikelihood::ConstNonHomogeneousSiteModelIterator
• nbNodes_ : bpp::AbstractHomogeneousTreeLikelihood, bpp::AbstractNonHomogeneousTreeLikelihood, bpp::NonHomogeneousSequenceSimulator, bpp::SimpleSubstitutionProcessSiteSimulator
• nbRates_ : bpp::MarkovModulatedSubstitutionModel
• nbrOfAxes_ : bpp::Coala, bpp::CoalaCore, bpp::MvaFrequencySet
• nbSite_ : bpp::BackwardLikelihoodTree
• nbSites_ : bpp::AbstractAlignedPhyloLikelihood, bpp::AbstractHomogeneousTreeLikelihood, bpp::AbstractMapping, bpp::AbstractNonHomogeneousTreeLikelihood, bpp::AbstractTreeLikelihood::ConstNoPartitionBranchModelDescription, bpp::DRASDRTreeLikelihoodData, bpp::DRASRTreeLikelihoodData, bpp::DRTreeParsimonyData, bpp::ForwardLikelihoodTree, bpp::HmmLikelihood_DF, bpp::HmmPhyloAlphabet, bpp::HmmPhyloEmissionProbabilities, bpp::LegacyAbstractMapping, bpp::LegacyMarginalAncestralStateReconstruction, bpp::MarginalAncestralReconstruction
• nbState_ : bpp::BackwardLikelihoodTree, bpp::ForwardLikelihoodTree
• nbStates_ : bpp::AbstractHomogeneousTreeLikelihood, bpp::AbstractNonHomogeneousTreeLikelihood, bpp::AbstractSingleDataPhyloLikelihood, bpp::AbstractTreeParsimonyScore, bpp::BranchLikelihood, bpp::DecompositionMethods, bpp::DRASDRTreeLikelihoodData, bpp::DRASRTreeLikelihoodData, bpp::DRTreeParsimonyData, bpp::HmmLikelihood_DF, bpp::LegacyMarginalAncestralStateReconstruction, bpp::MarginalAncestralReconstruction, bpp::MarkovModulatedSubstitutionModel, bpp::NonHomogeneousSequenceSimulator, bpp::SimpleSubstitutionProcessSiteSimulator, bpp::SubstitutionModelSet, bpp::UniformizationSubstitutionCount
• nbTypes_ : bpp::DecompositionMethods, bpp::RegisterRatesSubstitutionModel
• nCat_ : bpp::CategoryFromDiscreteDistribution, bpp::ProbabilityFromDiscreteDistribution, bpp::ProbabilityFromMixedModel
• ncol_ : bpp::ExtendedFloatCol< R, C, EigenType >
• nCol_ : bpp::UserFrequencySet
• nData_ : bpp::AbstractSingleDataPhyloLikelihood
• nDist_ : bpp::SubstitutionProcessCollectionMember
• NeighborJoining() : bpp::NeighborJoining
• Nested : Eigen::NumTraits< bpp::ExtendedFloat >
• nestedModel() : bpp::gBGC, bpp::MarkovModulatedSubstitutionModel, bpp::RE08, bpp::RE08Codon, bpp::RE08Nucleotide, bpp::RE08Protein, bpp::YpR
• nestedModel_() : bpp::RE08
• nestedPrefix_ : bpp::AbstractFromSubstitutionModelTransitionModel, bpp::gBGC, bpp::MarkovModulatedSubstitutionModel, bpp::RE08
• NestedPrefix_ : bpp::WordFromUniqueFrequencySet
• nestedPrefix_ : bpp::YpR
• nestedRatePrefix_ : bpp::G2001
• neutral_ : bpp::YNGP_M8
• newAlphabet_ : bpp::AbstractWordSubstitutionModel
• Newick() : bpp::Newick
• NEWICK_FORMAT : bpp::IOTreeFactory
• newOutGroup() : bpp::Tree, bpp::TreeTemplate< N >
• next() : bpp::AbstractHomogeneousTreeLikelihood::ConstHomogeneousSiteModelIterator, bpp::AbstractNonHomogeneousTreeLikelihood::ConstNonHomogeneousSiteModelIterator, bpp::AbstractTreeLikelihood::ConstNoPartitionBranchModelIterator, bpp::AbstractTreeLikelihood::SimpleBranchIterator, bpp::AbstractTreeLikelihood::SimpleSiteIterator, bpp::InOrderTreeIterator, bpp::PostOrderTreeIterator, bpp::PreOrderTreeIterator, bpp::TreeIterator, bpp::TreeLikelihoodInterface::BranchIterator, bpp::TreeLikelihoodInterface::ConstBranchModelIterator, bpp::TreeLikelihoodInterface::ConstSiteModelIterator, bpp::TreeLikelihoodInterface::SiteIterator
• NEXUS_FORMAT : bpp::IOTreeFactory
• NexusIOTree() : bpp::NexusIOTree
• nGamma_ : bpp::YNGP_M10, bpp::YNGP_M9
• Nhx() : bpp::Nhx
• NHX_FORMAT : bpp::IOTreeFactory
• nMod_ : bpp::ProcessEdge
• nModel() : bpp::AbstractBiblioMixedTransitionModel, bpp::AbstractMixedTransitionModel, bpp::AbstractWordSubstitutionModel, bpp::MixedTransitionModelInterface
• nModel_() : bpp::AbstractBiblioMixedTransitionModel, bpp::AbstractMixedTransitionModel, bpp::MixedTransitionModelInterface
• nmodel_ : bpp::ProcessComputationEdge
• NNIHomogeneousTreeLikelihood() : bpp::NNIHomogeneousTreeLikelihood
• NNISearchable() : bpp::NNISearchable
• NNITopologyListener() : bpp::NNITopologyListener
• NNITopologyListener2() : bpp::NNITopologyListener2
• NNITopologySearch() : bpp::NNITopologySearch
• noalias() : bpp::ExtendedFloatEigenBase< Derived >
• noChangedStates_ : bpp::OneChangeRegisterTransitionModel
• Node() : bpp::MixedSubstitutionModelSet::HyperNode::Node, bpp::Node
• node_ : bpp::DRASDRTreeLikelihoodNodeData, bpp::DRASRTreeLikelihoodNodeData, bpp::DrawIBranchEvent, bpp::DrawINodeEvent, bpp::DRTreeParsimonyNodeData, bpp::NodePException, bpp::PhyloNodePException
• Node_DF() : bpp::Node_DF
• nodeBitsets_ : bpp::DRTreeParsimonyNodeData
• nodeCache_ : bpp::Context
• nodeD2Likelihoods_ : bpp::DRASDRTreeLikelihoodNodeData, bpp::DRASRTreeLikelihoodNodeData
• nodeData() : bpp::DRTreeParsimonyData, bpp::TreeParsimonyDataInterface
• nodeData_ : bpp::DRASDRTreeLikelihoodData, bpp::DRASRTreeLikelihoodData, bpp::DRTreeParsimonyData
• nodeDepths_ : bpp::PhyloStatistics
• nodeDLikelihoods_ : bpp::DRASDRTreeLikelihoodNodeData, bpp::DRASRTreeLikelihoodNodeData
• NodeEvent() : bpp::NodeEvent
• NodeException() : bpp::NodeException
• nodeHeights_ : bpp::PhyloStatistics
• nodeId_ : bpp::NodeException, bpp::PhyloNodeException
• nodeIds_ : bpp::PhyloStatistics
• NodeIterator : bpp::ProbabilisticRewardMapping, bpp::ProbabilisticSubstitutionMapping
• nodeLikelihoods_ : bpp::DRASDRTreeLikelihoodNodeData, bpp::DRASRTreeLikelihoodNodeData
• NodeNotFoundException() : bpp::NodeNotFoundException
• nodeNumberOfSons_ : bpp::PhyloStatistics
• NodePException() : bpp::NodePException
• nodeProperties_ : bpp::Node
• nodes_ : bpp::AbstractHomogeneousTreeLikelihood, bpp::AbstractNonHomogeneousTreeLikelihood, bpp::LegacyAbstractMapping
• nodeScores_ : bpp::DRTreeParsimonyNodeData
• nodesCounter_ : bpp::StochasticMapping
• nodesId_ : bpp::AbstractTreeLikelihood::ConstNoPartitionSiteModelDescription, bpp::AbstractTreeLikelihood::SimpleBranchIterator
• NodesIdTreeDrawingListener() : bpp::NodesIdTreeDrawingListener
• NodeTemplate() : bpp::NodeTemplate< NodeInfos >
• nodeToLastVisitedSonIndex_ : bpp::TreeIterator
• nodeToModel_ : bpp::NonHomogeneousSubstitutionProcess, bpp::SubstitutionModelSet, bpp::SubstitutionProcessCollectionMember
• nodeToParenthesis() : bpp::Newick, bpp::Nhx, bpp::TreeTemplateTools, bpp::TreeTools
• nodeToSonVisited_ : bpp::TreeIterator
• nodeToVisited_ : bpp::TreeIterator
• NodeType : bpp::NodeEvent
• nodeType_ : bpp::NodeEvent
• NonHomogeneousSequenceSimulator() : bpp::NonHomogeneousSequenceSimulator
• NonHomogeneousSubstitutionProcess() : bpp::NonHomogeneousSubstitutionProcess
• NonInteger : Eigen::NumTraits< bpp::ExtendedFloat >
• normalizations() : bpp::AbstractSinglePhyloSubstitutionMapping, bpp::PhyloSubstitutionMapping
• normalizationsPerformed() : bpp::AbstractSinglePhyloSubstitutionMapping, bpp::PhyloSubstitutionMapping
• normalize() : bpp::AbstractFrequencySet, bpp::AbstractSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, bpp::ExtendedFloat, bpp::ExtendedFloatEigen< R, C, EigenType >, bpp::InMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::SubstitutionModelInterface
• normalize_big() : bpp::ExtendedFloat, bpp::ExtendedFloatEigen< R, C, EigenType >
• normalize_big_factor : bpp::ExtendedFloat
• normalize_small() : bpp::ExtendedFloat, bpp::ExtendedFloatEigen< R, C, EigenType >
• normalize_small_factor : bpp::ExtendedFloat
• normalizeRateChanges_ : bpp::MarkovModulatedSubstitutionModel
• normalizeVRates() : bpp::AbstractBiblioMixedTransitionModel, bpp::AbstractMixedTransitionModel, bpp::MixedTransitionModelInterface
• notifyAllPerformed() : bpp::NNITopologySearch
• notifyAllSuccessful() : bpp::NNITopologySearch
• notifyAllTested() : bpp::NNITopologySearch
• nPath_ : bpp::SubstitutionProcessCollectionMember
• nPhylo_ : bpp::AbstractPhyloLikelihoodSet
• nProc : bpp::ProcPos
• nProc_ : bpp::HmmProcessAlphabet, bpp::MultiProcessSequenceEvolution, bpp::OneProcessSequenceEvolution, bpp::SingleProcessPhyloLikelihood, bpp::SubstitutionProcessCollectionMember
• nRoot_ : bpp::SubstitutionProcessCollectionMember
• nrow_ : bpp::ExtendedFloatRow< R, C, EigenType >
• Ns_ : bpp::AbstractCodonAAFitnessSubstitutionModel
• nSeqEvol_ : bpp::AbstractSequencePhyloLikelihood
• nstep : bpp::OptimizationTools::OptimizationOptions
• nStep_ : bpp::NNITopologyListener
• nTree_ : bpp::SubstitutionProcessCollectionMember
• NUCLEOTIDE : bpp::BppOFrequencySetFormat, bpp::BppOSubstitutionModelFormat
• NullaryExpr() : bpp::ExtendedFloatEigen< R, C, EigenType >
• numberOfAncestors_ : bpp::PhyloStatistics
• numberOfDistinctSites_ : bpp::ProbabilisticRewardMapping, bpp::ProbabilisticSubstitutionMapping
• numberOfLeaves : bpp::ClusterInfos, bpp::PGMAInfos, bpp::TreeTemplateTools::Moments_
• numberOfLeaves_ : bpp::CladogramPlot, bpp::PhylogramPlot, bpp::PhyloStatistics
• numberOfSites_ : bpp::LikelihoodCalculationOnABranch
• numberOfTypes_ : bpp::AbstractSubstitutionMapping
• NumericConstant() : bpp::NumericConstant< T >
• NumericMutable() : bpp::NumericMutable< T >
• numOfMappings_ : bpp::StochasticMapping
• numProc_ : bpp::DistanceEstimation