- 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