Here is a list of all class members with links to the classes they belong to:
- n -
- N
: bpp::TreeTools::Moments_
- n_
: bpp::PseudoNewtonOptimizer
- NaiveSubstitutionCount()
: bpp::NaiveSubstitutionCount
- name
: bpp::Nhx::Property
- name_
: bpp::LLG08_EX2::EmbeddedModel
, bpp::LLG08_EX3::EmbeddedModel
, bpp::AbstractFrequenciesSet
, bpp::LLG08_UL2::EmbeddedModel
, bpp::LLG08_UL3::EmbeddedModel
, bpp::LGL08_CAT::EmbeddedModel
, bpp::Node
, bpp::TreeTemplate< N >
, bpp::LLG08_EHO::EmbeddedModel
- names_
: bpp::SitePatterns
- NaNListener()
: bpp::NaNListener
- nbBranches_
: bpp::AbstractSubstitutionMapping
- nbCategories_
: bpp::CategorySubstitutionRegister
- nbClasses_
: bpp::TwoTreeLikelihood
, bpp::AbstractHomogeneousTreeLikelihood
, bpp::AbstractNonHomogeneousTreeLikelihood
, bpp::DRASDRTreeLikelihoodData
, bpp::DRASRTreeLikelihoodData
, bpp::MarginalAncestralStateReconstruction
, bpp::BranchLikelihood
, bpp::RateDistributionFactory
, bpp::NonHomogeneousSequenceSimulator
- nbDistinctSites_
: bpp::DRASRTreeLikelihoodData
, bpp::MarginalAncestralStateReconstruction
, bpp::DRTreeParsimonyData
, bpp::DRTreeParsimonyScore
, bpp::TwoTreeLikelihood
, bpp::AbstractHomogeneousTreeLikelihood
, bpp::AbstractNonHomogeneousTreeLikelihood
, bpp::DRASDRTreeLikelihoodData
- nbModels_
: bpp::AbstractNonHomogeneousTreeLikelihood::ConstNonHomogeneousSiteModelIterator
- nbNodes_
: bpp::AbstractHomogeneousTreeLikelihood
, bpp::AbstractNonHomogeneousTreeLikelihood
, bpp::NonHomogeneousSequenceSimulator
- nbRates_
: bpp::MarkovModulatedSubstitutionModel
- nbrOfAxes_
: bpp::MvaFrequenciesSet
, bpp::Coala
, bpp::CoalaCore
- nbSites_
: bpp::TwoTreeLikelihood
, bpp::AbstractHomogeneousTreeLikelihood
, bpp::AbstractNonHomogeneousTreeLikelihood
, bpp::AbstractTreeLikelihood::ConstNoPartitionBranchModelDescription
, bpp::DRASDRTreeLikelihoodData
, bpp::DRASRTreeLikelihoodData
, bpp::MarginalAncestralStateReconstruction
, bpp::AbstractSubstitutionMapping
, bpp::DRTreeParsimonyData
- nbStates_
: bpp::AbstractTreeParsimonyScore
, bpp::DRTreeParsimonyData
, bpp::NonHomogeneousSequenceSimulator
, bpp::TwoTreeLikelihood
, bpp::AbstractHomogeneousTreeLikelihood
, bpp::AbstractNonHomogeneousTreeLikelihood
, bpp::DRASDRTreeLikelihoodData
, bpp::DRASRTreeLikelihoodData
, bpp::MarginalAncestralStateReconstruction
, bpp::BranchLikelihood
, bpp::DecompositionSubstitutionCount
, bpp::UniformizationSubstitutionCount
, bpp::MarkovModulatedSubstitutionModel
, bpp::SubstitutionModelSet
- NeighborJoining()
: bpp::NeighborJoining
- nestedPrefix_
: bpp::MarkovModulatedSubstitutionModel
, bpp::gBGC
, bpp::RE08
- NestedPrefix_
: bpp::WordFromUniqueFrequenciesSet
- nestedRatePrefix_
: bpp::G2001
- new_alphabet_
: bpp::AbstractWordSubstitutionModel
- Newick()
: bpp::Newick
- NEWICK_FORMAT
: bpp::IOTreeFactory
- newOutGroup()
: bpp::Tree
, bpp::TreeTemplate< N >
- next()
: bpp::AbstractHomogeneousTreeLikelihood::ConstHomogeneousSiteModelIterator
, bpp::AbstractNonHomogeneousTreeLikelihood::ConstNonHomogeneousSiteModelIterator
, bpp::AbstractTreeLikelihood::SimpleBranchIterator
, bpp::AbstractTreeLikelihood::SimpleSiteIterator
, bpp::AbstractTreeLikelihood::ConstNoPartitionBranchModelIterator
, bpp::TreeLikelihood::BranchIterator
, bpp::TreeLikelihood::SiteIterator
, bpp::TreeLikelihood::ConstBranchModelIterator
, bpp::TreeLikelihood::ConstSiteModelIterator
- NEXUS_FORMAT
: bpp::IOTreeFactory
- NexusIOTree()
: bpp::NexusIOTree
- Nhx()
: bpp::Nhx
- NHX_FORMAT
: bpp::IOTreeFactory
- NNIHomogeneousTreeLikelihood()
: bpp::NNIHomogeneousTreeLikelihood
- NNISearchable()
: bpp::NNISearchable
- NNITopologyListener()
: bpp::NNITopologyListener
- NNITopologyListener2()
: bpp::NNITopologyListener2
- NNITopologySearch()
: bpp::NNITopologySearch
- Node()
: bpp::Node
, bpp::MixedSubstitutionModelSet::HyperNode::Node
, bpp::Node
- node_
: bpp::DrawIBranchEvent
, bpp::DrawINodeEvent
, bpp::DRASDRTreeLikelihoodNodeData
, bpp::DRASRTreeLikelihoodNodeData
, bpp::DRTreeParsimonyNodeData
, bpp::NodePException
- nodeBitsets_
: bpp::DRTreeParsimonyNodeData
- nodeD2Likelihoods_
: bpp::DRASDRTreeLikelihoodNodeData
, bpp::DRASRTreeLikelihoodNodeData
- nodeData_
: bpp::DRASDRTreeLikelihoodData
, bpp::DRTreeParsimonyData
, bpp::DRASRTreeLikelihoodData
- nodeDepths_
: bpp::PhyloStatistics
- nodeDLikelihoods_
: bpp::DRASDRTreeLikelihoodNodeData
, bpp::DRASRTreeLikelihoodNodeData
- NodeException()
: bpp::NodeException
- nodeHeights_
: bpp::PhyloStatistics
- nodeId_
: bpp::NodeException
- nodeIds_
: bpp::PhyloStatistics
- nodeLikelihoods_
: bpp::DRASDRTreeLikelihoodNodeData
, bpp::DRASRTreeLikelihoodNodeData
- NodeNotFoundException()
: bpp::NodeNotFoundException
- nodeNumberOfSons_
: bpp::PhyloStatistics
- NodePException()
: bpp::NodePException
- nodeProperties_
: bpp::Node
- nodes_
: bpp::AbstractHomogeneousTreeLikelihood
, bpp::AbstractSubstitutionMapping
, bpp::AbstractNonHomogeneousTreeLikelihood
- nodeScores_
: bpp::DRTreeParsimonyNodeData
- nodesId_
: bpp::AbstractTreeLikelihood::SimpleBranchIterator
, bpp::AbstractTreeLikelihood::ConstNoPartitionSiteModelDescription
- NodesIdTreeDrawingListener()
: bpp::NodesIdTreeDrawingListener
- NodeTemplate()
: bpp::NodeTemplate< NodeInfos >
- nodeToModel_
: bpp::SubstitutionModelSet
- nodeToParenthesis()
: bpp::TreeTools
, bpp::Nhx
, bpp::TreeTemplateTools
- NonHomogeneousSequenceSimulator()
: bpp::NonHomogeneousSequenceSimulator
- normalizeRateChanges_
: bpp::MarkovModulatedSubstitutionModel
- normalizeVRates()
: bpp::AbstractBiblioMixedSubstitutionModel
, bpp::AbstractMixedSubstitutionModel
, bpp::MixedSubstitutionModel
- notifyAllPerformed()
: bpp::NNITopologySearch
- notifyAllSuccessful()
: bpp::NNITopologySearch
- notifyAllTested()
: bpp::NNITopologySearch
- nStep_
: bpp::NNITopologyListener
- NUCLEOTIDE
: bpp::BppOFrequenciesSetFormat
, bpp::BppOSubstitutionModelFormat
- numberOfAncestors_
: bpp::PhyloStatistics
- numberOfLeaves
: bpp::PGMAInfos
, bpp::ClusterInfos
, bpp::TreeTemplateTools::Moments_
- numberOfLeaves_
: bpp::CladogramPlot
, bpp::PhylogramPlot
, bpp::PhyloStatistics