- n -

• N : bpp::PhyloTreeTools::Moments_ , bpp::TreeTools::Moments_
• n_ : bpp::CombineDeltaShifted< T > , bpp::PseudoNewtonOptimizer , bpp::ShiftDelta< T > , bpp::ShiftParameter
• 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::PhyloNode , bpp::PhyloTree , bpp::Sequence_DF , bpp::TreeTemplate< N >
• names_ : bpp::SitePatterns
• 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
• 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
• 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_FORMAT : bpp::IOTreeFactory
• NEXUS_FORMAT : bpp::IOTreeFactory
• nGamma_ : bpp::YNGP_M10 , bpp::YNGP_M9
• NHX_FORMAT : bpp::IOTreeFactory
• nMod_ : bpp::ProcessEdge
• nmodel_ : bpp::ProcessComputationEdge
• noChangedStates_ : bpp::OneChangeRegisterTransitionModel
• node_ : bpp::DRASDRTreeLikelihoodNodeData , bpp::DRASRTreeLikelihoodNodeData , bpp::DrawIBranchEvent , bpp::DrawINodeEvent , bpp::DRTreeParsimonyNodeData , bpp::NodePException , bpp::PhyloNodePException
• nodeBitsets_ : bpp::DRTreeParsimonyNodeData
• nodeCache_ : bpp::Context
• nodeD2Likelihoods_ : bpp::DRASDRTreeLikelihoodNodeData , bpp::DRASRTreeLikelihoodNodeData
• nodeData_ : bpp::DRASDRTreeLikelihoodData , bpp::DRASRTreeLikelihoodData , bpp::DRTreeParsimonyData
• nodeDepths_ : bpp::PhyloStatistics
• nodeDLikelihoods_ : bpp::DRASDRTreeLikelihoodNodeData , bpp::DRASRTreeLikelihoodNodeData
• nodeHeights_ : bpp::PhyloStatistics
• nodeId_ : bpp::NodeException , bpp::PhyloNodeException
• nodeIds_ : bpp::PhyloStatistics
• nodeLikelihoods_ : bpp::DRASDRTreeLikelihoodNodeData , bpp::DRASRTreeLikelihoodNodeData
• nodeNumberOfSons_ : bpp::PhyloStatistics
• nodeProperties_ : bpp::Node
• nodes_ : bpp::AbstractHomogeneousTreeLikelihood , bpp::AbstractNonHomogeneousTreeLikelihood , bpp::LegacyAbstractMapping
• nodeScores_ : bpp::DRTreeParsimonyNodeData
• nodesCounter_ : bpp::StochasticMapping
• nodesId_ : bpp::AbstractTreeLikelihood::ConstNoPartitionSiteModelDescription , bpp::AbstractTreeLikelihood::SimpleBranchIterator
• nodeToLastVisitedSonIndex_ : bpp::TreeIterator
• nodeToModel_ : bpp::NonHomogeneousSubstitutionProcess , bpp::SubstitutionModelSet , bpp::SubstitutionProcessCollectionMember
• nodeToSonVisited_ : bpp::TreeIterator
• nodeToVisited_ : bpp::TreeIterator
• nodeType_ : bpp::NodeEvent
• normalize_big_factor : bpp::ExtendedFloat
• normalize_small_factor : bpp::ExtendedFloat
• normalizeRateChanges_ : bpp::MarkovModulatedSubstitutionModel
• 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
• 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
• numOfMappings_ : bpp::StochasticMapping
• numProc_ : bpp::DistanceEstimation