- s -

• S_ : bpp::AbstractCodonBGCSubstitutionModel
• s_ : bpp::UniformizationSubstitutionCount
• sChangingPos_ : bpp::AbstractKroneckerWordSubstitutionModel
• searchableTree_ : bpp::NNITopologySearch
• secondOrderDerivativeNodes_ : bpp::AbstractPhyloLikelihood
• secondOrderDerivativeVectors_ : bpp::OnABranchPhyloLikelihood , bpp::OneProcessSequencePhyloLikelihood , bpp::SingleProcessPhyloLikelihood
• seqEvol_ : bpp::AbstractSequencePhyloLikelihood , bpp::EvolutionSequenceSimulator
• seqIndexes_ : bpp::SimpleSubstitutionProcessSiteSimulator
• seqNames_ : bpp::NonHomogeneousSequenceSimulator , bpp::SimpleSubstitutionProcessSiteSimulator , bpp::SubstitutionProcessSequenceSimulator
• settings_ : bpp::AbstractTreeDrawing , bpp::BasicTreeDrawingDisplayControler , bpp::BootstrapValuesTreeDrawingListener , bpp::BranchLengthsTreeDrawingListener , bpp::LeafNamesTreeDrawingListener , bpp::NodesIdTreeDrawingListener
• sFreq_ : bpp::FullCodonFrequencySet , bpp::FullFrequencySet
• shrunkData_ : bpp::DRASDRTreeLikelihoodData , bpp::DRASRTreeLikelihoodData , bpp::DRTreeParsimonyData , bpp::LikelihoodCalculationSingleProcess
• sigma_ : bpp::RN95
• simpleExchangeabilities_ : bpp::RE08
• simpleGenerator_ : bpp::RE08
• simpleModel_ : bpp::RE08
• simplex_ : bpp::AlignedPhyloLikelihoodMixture , bpp::ConfiguredSimplex , bpp::MixtureProcessPhyloLikelihood , bpp::MixtureSequenceEvolution
• SINGLE : bpp::HierarchicalClustering
• siteLik_ : bpp::LikelihoodCalculationOnABranch::RateCategoryEdge
• siteLikelihoods_ : bpp::AlignedLikelihoodCalculation
• siteModelDescription_ : bpp::AbstractHomogeneousTreeLikelihood::ConstHomogeneousSiteModelIterator
• siteModelDescriptions_ : bpp::AbstractNonHomogeneousTreeLikelihood::ConstNonHomogeneousSiteModelIterator
• siteP : bpp::SitePatterns::SortableSite
• siteS : bpp::SitePatterns::SortableSite
• sites_ : bpp::DistanceEstimation , bpp::SitePatterns
• siteSim_ : bpp::SimpleSubstitutionProcessSequenceSimulator
• sitesPositions_ : bpp::AbstractMapping , bpp::LegacyAbstractMapping
• size : bpp::TreeTemplateTools::OrderTreeData_
• size_ : bpp::AbstractFromSubstitutionModelTransitionModel , bpp::AbstractMutationProcess , bpp::AbstractTransitionModel , bpp::GeneralSubstitutionRegister , bpp::MultinomialFromTransitionModel , bpp::TransitionFromTransitionModel
• smallest_normalized_radix_power : bpp::ExtendedFloat
• smallest_normalized_value : bpp::ExtendedFloat
• smallest_repr_radix_power : bpp::ExtendedFloat
• sons_ : bpp::AwareNode , bpp::Node , bpp::SimProcessNode
• sorted_ : bpp::BipartitionList
• speciationEvent : bpp::NodeEvent
• speciesIndex_ : bpp::ProcessComputationEdge , bpp::ProcessComputationNode , bpp::ProcessEdge
• speciesLt : bpp::LikelihoodCalculationSingleProcess::RateCategoryTrees
• speciesNodes_ : bpp::SimpleSubstitutionProcessSiteSimulator
• squaredSum : bpp::PhyloTreeTools::Moments_ , bpp::TreeTools::Moments_
• squaresSum : bpp::TreeTemplateTools::Moments_
• state : bpp::SimData
• state_ : bpp::SimProcessNode
• stateMap_ : bpp::AbstractCodonAAFitnessSubstitutionModel , bpp::AbstractCodonAARateSubstitutionModel , bpp::AbstractCodonBGCSubstitutionModel , bpp::AbstractCodonClusterAASubstitutionModel , bpp::AbstractCodonCpGSubstitutionModel , bpp::AbstractCodonDistanceSubstitutionModel , bpp::AbstractFrequencySet , bpp::AbstractSubstitutionRegister , bpp::AbstractTransitionModel
• statemap_ : bpp::BackwardLikelihoodTree , bpp::ForwardLikelihoodTree
• stateMap_ : bpp::MarkovModulatedSubstitutionModel
• statemap_ : bpp::SiteSimulationResult
• states : bpp::SimData
• states_ : bpp::AbstractStateMap , bpp::MutationPath
• statesMap_ : bpp::AbstractTreeParsimonyScore
• stationarity_ : bpp::CategorySubstitutionRegister , bpp::SubstitutionModelSet
• str : StringAndInt
• subModel_ : bpp::AbstractFromSubstitutionModelTransitionModel , bpp::FromMixtureSubstitutionModel , bpp::MultinomialFromTransitionModel , bpp::TransitionFromTransitionModel
• subModelNumber_ : bpp::InMixedSubstitutionModel
• subsProc_ : bpp::OneProcessSequenceEvolution
• substitutionCount_ : bpp::LegacyProbabilisticSubstitutionMapping
• sum : bpp::PhyloTreeTools::Moments_ , bpp::TreeTemplateTools::Moments_ , bpp::TreeTools::Moments_
• sumDist_ : bpp::NeighborJoining
• supportedChars_ : bpp::LabelSubstitutionCount , bpp::NaiveSubstitutionCount
• supportedProperties_ : bpp::Nhx
• supportedStates_ : bpp::NonHomogeneousSequenceSimulator
• synfrom_ : bpp::DFP07 , bpp::YNGP_M
• synto_ : bpp::DFP07 , bpp::YNGP_M