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

- s -

• S_ : bpp::AbstractCodonBGCSubstitutionModel
• s_ : bpp::UniformizationSubstitutionCount
• sampleAncestrals() : bpp::StochasticMapping
• sampleMutationsGivenAncestrals() : bpp::StochasticMapping
• sampleMutationsGivenAncestralsPerBranch() : bpp::StochasticMapping
• sampleState() : bpp::StochasticMapping
• sampleSubtree() : bpp::TreeTemplateTools
• Scalar : bpp::ExtendedFloatEigenBase< Derived >
• ScalarProduct() : bpp::ScalarProduct< R, T0, T1 >
• scaleDAG() : bpp::PhyloDAG
• ScaleFunction() : bpp::LegacyOptimizationTools::ScaleFunction
• scaleTree() : bpp::PhyloTree, bpp::Tree, bpp::TreeTemplate< N >, bpp::TreeTemplateTools, bpp::TreeTools
• sChangingPos_ : bpp::AbstractKroneckerWordSubstitutionModel
• search() : bpp::NNITopologySearch, bpp::TopologySearch
• searchableTree_ : bpp::NNITopologySearch
• searchBetter() : bpp::NNITopologySearch
• searchFast() : bpp::NNITopologySearch
• searchFirstNodeWithId() : bpp::TreeTemplateTools
• searchLeaf() : bpp::TreeTemplateTools, bpp::TreeTools
• searchNodeWithId() : bpp::TreeTemplateTools
• searchNodeWithName() : bpp::TreeTemplateTools
• searchPhyML() : bpp::NNITopologySearch
• secondOrderDerivableFunction() : bpp::PseudoNewtonOptimizer
• secondOrderDerivativeNode() : bpp::AbstractPhyloLikelihood
• secondOrderDerivativeNodes_ : bpp::AbstractPhyloLikelihood
• secondOrderDerivativeVector() : bpp::OnABranchPhyloLikelihood, bpp::OneProcessSequencePhyloLikelihood, bpp::SingleProcessPhyloLikelihood
• secondOrderDerivativeVectors_ : bpp::OnABranchPhyloLikelihood, bpp::OneProcessSequencePhyloLikelihood, bpp::SingleProcessPhyloLikelihood
• SelectedSubstitutionRegister() : bpp::SelectedSubstitutionRegister
• Self : bpp::BackwardHmmLikelihood_DF, bpp::CategoryFromDiscreteDistribution, bpp::CombineDeltaShifted< T >, bpp::ConfiguredDistribution, bpp::ConfiguredFrequencySet, bpp::ConfiguredModel, bpp::ConfiguredParameter, bpp::ConfiguredSimplex, bpp::ConfiguredTransitionMatrix, bpp::ConstantOne< T >, bpp::ConstantZero< T >, bpp::Convert< R, F >, bpp::CWiseAdd< R, T >, bpp::CWiseAdd< R, ReductionOf< T > >, bpp::CWiseAdd< R, std::tuple< T0, T1 > >, bpp::CWiseApply< R, T, F >, bpp::CWiseCompound< R, ReductionOf< T > >, bpp::CWiseConstantPow< T >, bpp::CWiseDiv< R, std::tuple< T0, T1 > >, bpp::CWiseExp< T >, bpp::CWiseFill< R, T >, bpp::CWiseInverse< T >, bpp::CWiseLog< T >, bpp::CWiseMatching< R, ReductionOf< T > >, bpp::CWiseMean< R, ReductionOf< T >, P >, bpp::CWiseMean< R, ReductionOf< T >, ReductionOf< P > >, bpp::CWiseMul< R, ReductionOf< T > >, bpp::CWiseMul< R, std::tuple< T0, T1 > >, bpp::CWiseNegate< T >, bpp::CWisePattern< R >, bpp::CWiseSub< R, std::tuple< T0, T1 > >, bpp::EquilibriumFrequenciesFromModel, bpp::EquilibriumFrequenciesFromTransitionMatrix, bpp::ExtendedFloatArrayWrapper< R, C >, bpp::ExtendedFloatEigen< R, C, EigenType >, bpp::ForwardHmmD2Likelihood_DF, bpp::ForwardHmmDLikelihood_DF, bpp::ForwardHmmLikelihood_DF, bpp::FrequenciesFromFrequencySet, bpp::FrequenciesFromSimplex, bpp::Identity< R >, bpp::LogSumExp< R, T0, T1 >, bpp::MatrixProduct< R, T0, T1 >, bpp::NumericConstant< T >, bpp::NumericMutable< T >, bpp::ProbabilitiesFromDiscreteDistribution, bpp::ProbabilitiesFromMixedModel, bpp::ProbabilityFromDiscreteDistribution, bpp::ProbabilityFromMixedModel, bpp::ScalarProduct< R, T0, T1 >, bpp::Sequence_DF, bpp::ShiftDelta< T >, bpp::ShiftParameter, bpp::SumOfLogarithms< F >, bpp::TransitionFunctionFromModel, bpp::TransitionMatrixFromModel, bpp::TransitionMatrixFromTransitionMatrix, bpp::ValueFromConfiguredParameter
• SelfMutationProcess() : bpp::SelfMutationProcess
• SENCA() : bpp::SENCA
• seqEvol_ : bpp::AbstractSequencePhyloLikelihood, bpp::EvolutionSequenceSimulator
• seqIndexes_ : bpp::SimpleSubstitutionProcessSiteSimulator
• seqNames_ : bpp::NonHomogeneousSequenceSimulator, bpp::SimpleSubstitutionProcessSiteSimulator, bpp::SubstitutionProcessSequenceSimulator
• Sequence_DF() : bpp::Sequence_DF
• sequenceEvolution() : bpp::AbstractSequencePhyloLikelihood, bpp::SequencePhyloLikelihoodInterface
• SequenceSimulationTools() : bpp::SequenceSimulationTools
• SequenceSimulatorInterface() : bpp::SequenceSimulatorInterface
• set_exponent_part() : bpp::ExtendedFloatEigen< R, C, EigenType >::OwnedExtendedFloat
• set_float_part() : bpp::ExtendedFloatEigen< R, C, EigenType >::OwnedExtendedFloat
• setAAModel() : bpp::AbstractCodonAARateSubstitutionModel
• setAdditionalParameters() : bpp::DistanceEstimation
• setAlphabetCategories() : bpp::CategorySubstitutionRegister
• setAlphabetIndex() : bpp::AbstractReward, bpp::Reward
• setBranchedModelSet_() : bpp::OneProcessSequenceSubstitutionMapping, bpp::SingleProcessSubstitutionMapping
• setBranchLengths() : bpp::PhyloDAG, bpp::PhyloTree, bpp::Tree, bpp::TreeTemplate< N >, bpp::TreeTemplateTools, bpp::TreeTools
• setBranchProperty() : bpp::Node, bpp::Tree, bpp::TreeTemplate< N >
• setBrLen() : bpp::ProcessEdge
• setChangingPositions() : bpp::AbstractKroneckerWordSubstitutionModel
• setClockLike() : bpp::LikelihoodCalculationSingleProcess
• setData() : bpp::AbstractParametrizableSequencePhyloLikelihood, bpp::AbstractSingleDataPhyloLikelihood, bpp::DistanceEstimation, bpp::DRHomogeneousMixedTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::LikelihoodCalculationSingleProcess, bpp::MultiProcessSequencePhyloLikelihood, bpp::NNIHomogeneousTreeLikelihood, bpp::OneProcessSequencePhyloLikelihood, bpp::PartitionProcessPhyloLikelihood, bpp::PhyloLikelihoodContainer, bpp::RHomogeneousMixedTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousMixedTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, bpp::SingleDataPhyloLikelihoodInterface, bpp::SingleProcessPhyloLikelihood, bpp::TreeLikelihoodInterface
• setDiagonal() : bpp::AbstractSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::SubstitutionModelInterface
• setDisplaySettings() : bpp::AbstractTreeDrawing, bpp::TreeDrawing
• setDistanceBMatrices_() : bpp::DecompositionSubstitutionCount, bpp::UniformizationSubstitutionCount
• setDistanceMatrix() : bpp::AbstractAgglomerativeDistanceMethod, bpp::BioNJ, bpp::DistanceMethodInterface, bpp::NeighborJoining, bpp::PGMA
• setDistances() : bpp::AbstractSinglePhyloSubstitutionMapping, bpp::AbstractSubstitutionDistance, bpp::PhyloSubstitutionMapping, bpp::SubstitutionDistance
• setDistanceToFather() : bpp::AwareNode, bpp::Node, bpp::Tree, bpp::TreeTemplate< N >
• setExpectedAncestrals() : bpp::StochasticMapping
• setFather() : bpp::AwareNode, bpp::Node
• setFreq() : bpp::AbstractBiblioTransitionModel, bpp::AbstractCodonAAFitnessSubstitutionModel, bpp::AbstractCodonAARateSubstitutionModel, bpp::AbstractCodonBGCSubstitutionModel, bpp::AbstractCodonClusterAASubstitutionModel, bpp::AbstractCodonCpGSubstitutionModel, bpp::AbstractCodonDistanceSubstitutionModel, bpp::AbstractCodonFitnessSubstitutionModel, bpp::AbstractCodonFrequenciesSubstitutionModel, bpp::AbstractCodonPhaseFrequenciesSubstitutionModel, bpp::AbstractMixedTransitionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractTransitionModel, bpp::AbstractWordSubstitutionModel, bpp::BinarySubstitutionModel, bpp::CodonAdHocSubstitutionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonSameAARateSubstitutionModel, bpp::CoreCodonSubstitutionModelInterface, bpp::D1WalkSubstitutionModel, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::EquiprobableSubstitutionModel, bpp::F81, bpp::F84, bpp::GTR, bpp::HKY85, bpp::InMixedSubstitutionModel, bpp::KCM, bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::L95, bpp::MarkovModulatedSubstitutionModel, bpp::MG94, bpp::MixtureOfATransitionModel, bpp::MixtureOfTransitionModels, bpp::MultinomialFromTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::OneChangeTransitionModel, bpp::POMO, bpp::RE08, bpp::RE08Codon, bpp::RN95, bpp::RN95s, bpp::SENCA, bpp::SSR, bpp::T92, bpp::TN93, bpp::TransitionFromTransitionModel, bpp::TransitionModelInterface, bpp::YN98
• setFreqFromData() : bpp::AbstractBiblioTransitionModel, bpp::AbstractMixedTransitionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractTransitionModel, bpp::Coala, bpp::DSO78, bpp::InMixedSubstitutionModel, bpp::JCnuc, bpp::JCprot, bpp::JTT92, bpp::K80, bpp::LG08, bpp::MarkovModulatedSubstitutionModel, bpp::MultinomialFromTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::OneChangeTransitionModel, bpp::RE08, bpp::TransitionFromTransitionModel, bpp::TransitionModelInterface, bpp::UserProteinSubstitutionModel, bpp::WAG01
• setFrequencies() : bpp::FixedCodonFrequencySet, bpp::FixedFrequencySet, bpp::FrequencySetInterface, bpp::FromModelFrequencySet, bpp::FullCodonFrequencySet, bpp::FullFrequencySet, bpp::FullNucleotideFrequencySet, bpp::FullPerAACodonFrequencySet, bpp::GCFrequencySet, bpp::MarkovModulatedFrequencySet, bpp::MvaFrequencySet, bpp::UserCodonFrequencySet, bpp::UserFrequencySet, bpp::WordFromIndependentFrequencySet, bpp::WordFromUniqueFrequencySet
• setFrequencies_() : bpp::AbstractFrequencySet
• setFrequenciesFromAlphabetStatesFrequencies() : bpp::AbstractFrequencySet, bpp::FrequencySetInterface
• setFrequencySet() : bpp::DSO78, bpp::EquiprobableSubstitutionModel, bpp::JCprot, bpp::JTT92, bpp::LG08, bpp::UserProteinSubstitutionModel, bpp::WAG01
• setGenerator() : bpp::AnonymousSubstitutionModel
• setGeneticCode() : bpp::BppOFrequencySetFormat, bpp::BppOSubstitutionModelFormat
• setHmmStateAlphabet() : bpp::HmmEmissionProbabilities_Eigen, bpp::HmmPhyloEmissionProbabilities
• setHorizontalOrientation() : bpp::AbstractDendrogramPlot
• setId() : bpp::AwareNode, bpp::Node
• setInfos() : bpp::NodeTemplate< NodeInfos >
• setLeadModel() : bpp::ModelPath
• setLeafsStates() : bpp::StochasticMapping
• setLength() : bpp::PhyloBranch, bpp::PhyloBranchParam
• setLikelihoodNode() : bpp::LikelihoodCalculation
• setMap() : bpp::SubstitutionProcessSequenceSimulator
• setMatrixOfRowCoords() : bpp::MvaFrequencySet
• setMaximumBranchLength() : bpp::AbstractHomogeneousTreeLikelihood, bpp::AbstractNonHomogeneousTreeLikelihood, bpp::ParametrizablePhyloTree
• setMaximumNumberOfCorrections() : bpp::PseudoNewtonOptimizer
• setMinimumBranchLength() : bpp::AbstractHomogeneousTreeLikelihood, bpp::AbstractNonHomogeneousTreeLikelihood, bpp::ParametrizablePhyloTree
• setModel() : bpp::AbstractHomogeneousTreeLikelihood, bpp::HomogeneousTreeLikelihood, bpp::LikelihoodCalculationOnABranch, bpp::MixedSubstitutionModelSet::HyperNode, bpp::ModelPath, bpp::NonHomogeneousSubstitutionProcess, bpp::OnABranchPhyloLikelihood
• setModelCategories() : bpp::CategorySubstitutionRegister
• setModelName() : bpp::MvaFrequencySet
• setModelScenario() : bpp::AbstractAutonomousSubstitutionProcess, bpp::AutonomousSubstitutionProcessInterface, bpp::NonHomogeneousSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, bpp::SimpleSubstitutionProcess, bpp::SubstitutionProcessCollectionMember
• setModelToNode() : bpp::NonHomogeneousSubstitutionProcess
• setMuBounds() : bpp::TwoParameterBinarySubstitutionModel
• setName() : bpp::Node, bpp::PairedSiteLikelihoods, bpp::PhyloDAG, bpp::PhyloNode, bpp::PhyloTree, bpp::Tree, bpp::TreeTemplate< N >
• setNamespace() : bpp::AbstractBiblioTransitionModel, bpp::AbstractCodonAAFitnessSubstitutionModel, bpp::AbstractCodonAARateSubstitutionModel, bpp::AbstractCodonFitnessSubstitutionModel, bpp::AbstractCodonFrequenciesSubstitutionModel, bpp::AbstractCodonPhaseFrequenciesSubstitutionModel, bpp::AbstractCodonSubstitutionModel, bpp::AbstractFromSubstitutionModelTransitionModel, bpp::AbstractParametrizableSequencePhyloLikelihood, bpp::AbstractWordSubstitutionModel, bpp::AlignedPhyloLikelihoodAutoCorrelation, bpp::AlignedPhyloLikelihoodHmm, bpp::AutoCorrelationProcessPhyloLikelihood, bpp::AutoCorrelationSequenceEvolution, bpp::CodonAdHocSubstitutionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonDistanceSubstitutionModel, bpp::CodonSameAARateSubstitutionModel, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::DSO78, bpp::FromMixtureSubstitutionModel, bpp::FromModelFrequencySet, bpp::FullCodonFrequencySet, bpp::FullFrequencySet, bpp::FullPerAACodonFrequencySet, bpp::G2001, bpp::gBGC, bpp::HmmLikelihood_DF, bpp::HmmProcessPhyloLikelihood, bpp::HmmSequenceEvolution, bpp::InMixedSubstitutionModel, bpp::JCprot, bpp::JTT92, bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::KroneckerCodonDistanceSubstitutionModel, bpp::LG08, bpp::MarkovModulatedSubstitutionModel, bpp::MixtureSequenceEvolution, bpp::POMO, bpp::RE08, bpp::SENCA, bpp::SubstitutionProcessCollection, bpp::UserProteinSubstitutionModel, bpp::WAG01, bpp::WordFromIndependentFrequencySet, bpp::WordFromUniqueFrequencySet, bpp::YpR
• setNbrOfAxes() : bpp::MvaFrequencySet
• setNData() : bpp::AbstractSingleDataPhyloLikelihood
• setNode() : bpp::DRASDRTreeLikelihoodLeafData, bpp::DRASDRTreeLikelihoodNodeData, bpp::DRASRTreeLikelihoodNodeData, bpp::DRTreeParsimonyLeafData, bpp::DRTreeParsimonyNodeData, bpp::TreeLikelihoodNodeData, bpp::TreeParsimonyNodeDataInterface
• setNodeName() : bpp::Tree, bpp::TreeTemplate< N >
• setNodeProperties() : bpp::Nhx
• setNodeProperty() : bpp::Node, bpp::Tree, bpp::TreeTemplate< N >
• setNodeState() : bpp::DRTreeParsimonyScore, bpp::StochasticMapping
• setNodeToModel() : bpp::SubstitutionModelSet
• setNProbability() : bpp::AbstractBiblioMixedTransitionModel, bpp::AbstractMixedTransitionModel, bpp::MixedTransitionModelInterface
• setNumberOfSites() : bpp::AbstractAlignedPhyloLikelihood, bpp::AbstractMapping, bpp::LegacyAbstractMapping, bpp::LegacyProbabilisticRewardMapping, bpp::LegacyProbabilisticSubstitutionMapping, bpp::PhyloBranchMapping, bpp::PhyloBranchReward, bpp::ProbabilisticRewardMapping, bpp::ProbabilisticSubstitutionMapping
• setNumberOfSitesAndTypes() : bpp::PhyloBranchMapping, bpp::ProbabilisticSubstitutionMapping
• setNumberOfSubstitutionTypes() : bpp::AbstractSubstitutionMapping, bpp::ProbabilisticSubstitutionMapping, bpp::SubstitutionMapping
• setNumberOfTypes() : bpp::PhyloBranchMapping
• setNumericalDerivateConfiguration() : bpp::LikelihoodCalculationSingleProcess
• setNumericalOptimizationCounter() : bpp::NNITopologyListener2, bpp::NNITopologyListener
• setOptimizer() : bpp::DistanceEstimation
• setParameters() : bpp::AbstractPhyloLikelihood, bpp::BranchLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::GlobalClockTreeLikelihoodFunctionWrapper, bpp::HmmLikelihood_DF, bpp::LegacyOptimizationTools::ScaleFunction, bpp::MultiProcessSequenceEvolution, bpp::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood
• setParamValues() : bpp::MvaFrequencySet
• setPatterns_() : bpp::LikelihoodCalculationSingleProcess
• setPhyloProb() : bpp::AlignedPhyloLikelihoodMixture
• setPhyloTree() : bpp::AbstractAutonomousSubstitutionProcess, bpp::AutonomousSubstitutionProcessInterface
• setPosition() : bpp::TreeDrawingNodeInfo
• setProbability() : bpp::MixedSubstitutionModelSet::HyperNode, bpp::ModelPath, bpp::RNonHomogeneousMixedTreeLikelihood
• setProcess() : bpp::DistanceEstimation
• setProperty() : bpp::PhyloBranch, bpp::PhyloNode
• setRate() : bpp::AbstractMixedTransitionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractTransitionModel, bpp::BranchModelInterface, bpp::G2001, bpp::InMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::MultinomialFromTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::OneChangeTransitionModel, bpp::RegisterRatesSubstitutionModel, bpp::TransitionFromTransitionModel, bpp::TS98
• setRegStates_() : bpp::RegisterRatesSubstitutionModel
• setRootFrequencies() : bpp::BackwardLikelihoodTree, bpp::SubstitutionModelSet, bpp::SubstitutionProcessCollectionMember
• setRootFrequencySet() : bpp::AbstractAutonomousSubstitutionProcess, bpp::AutonomousSubstitutionProcessInterface
• setRootNode() : bpp::TreeTemplate< N >
• setScalable() : bpp::AbstractSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::SubstitutionModelInterface
• setScale() : bpp::AbstractSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::SubstitutionModelInterface
• setSiteLikelihoods() : bpp::AlignedLikelihoodCalculation
• setSitePosition() : bpp::AbstractMapping, bpp::LegacyAbstractMapping, bpp::LegacyMappingInterface, bpp::MappingInterface
• setSiteReward() : bpp::PhyloBranchReward
• setSiteTypeCount() : bpp::PhyloBranchMapping
• setSon() : bpp::AwareNode, bpp::Node
• setSpeciesMapIndexes_() : bpp::ForwardLikelihoodTree
• setStationarity() : bpp::CategorySubstitutionRegister
• setSubProcessProb() : bpp::MixtureSequenceEvolution
• setSubstitutionModel() : bpp::DecompositionMethods, bpp::DecompositionReward, bpp::DecompositionSubstitutionCount, bpp::LabelSubstitutionCount, bpp::LaplaceSubstitutionCount, bpp::NaiveSubstitutionCount, bpp::OneJumpSubstitutionCount, bpp::Reward, bpp::SubstitutionCountInterface, bpp::UniformizationSubstitutionCount
• setSubstitutionModelParametersInitialValuesWithAliases() : bpp::LegacyPhylogeneticsApplicationTools
• setSubstitutionModelSet() : bpp::AbstractNonHomogeneousTreeLikelihood, bpp::LegacyPhylogeneticsApplicationTools, bpp::NonHomogeneousTreeLikelihood
• setSubstitutionRegister() : bpp::AbstractSinglePhyloSubstitutionMapping, bpp::AbstractSubstitutionCount, bpp::LabelSubstitutionCount, bpp::LaplaceSubstitutionCount, bpp::OneJumpSubstitutionCount, bpp::SubstitutionCountInterface
• settings_ : bpp::AbstractTreeDrawing, bpp::BasicTreeDrawingDisplayControler, bpp::BootstrapValuesTreeDrawingListener, bpp::BranchLengthsTreeDrawingListener, bpp::LeafNamesTreeDrawingListener, bpp::NodesIdTreeDrawingListener
• setTransitionMatrix() : bpp::ProcessEdge
• setTransposeMatrixOfPpalAxes() : bpp::MvaFrequencySet
• setTree() : bpp::AbstractTreeDrawing, bpp::AbstractTreeParsimonyData, bpp::CladogramPlot, bpp::DRASDRTreeLikelihoodData, bpp::DRASRTreeLikelihoodData, bpp::DRTreeParsimonyData, bpp::LegacyAbstractMapping, bpp::LegacyProbabilisticRewardMapping, bpp::LegacyProbabilisticSubstitutionMapping, bpp::PhylogramPlot, bpp::PhyloStatistics, bpp::TreeDrawing
• setTreeNumber() : bpp::SubstitutionProcessCollectionMember
• setValue() : bpp::ConfiguredParameter, bpp::NumericMutable< T >, bpp::ShiftParameter
• setVectorOfColumnWeights() : bpp::MvaFrequencySet
• setVerbose() : bpp::AbstractAgglomerativeDistanceMethod, bpp::BppOFrequencySetFormat, bpp::BppOSubstitutionModelFormat, bpp::DistanceEstimation, bpp::DistanceMethodInterface
• setVerboseLevel() : bpp::AbstractTransitionModel
• setVerticalOrientation() : bpp::AbstractDendrogramPlot
• setVoidBranchLengths() : bpp::Tree, bpp::TreeTemplate< N >, bpp::TreeTemplateTools, bpp::TreeTools
• setVRates() : bpp::AbstractBiblioMixedTransitionModel, bpp::AbstractMixedTransitionModel, bpp::MixedTransitionModelInterface, bpp::MixtureOfTransitionModels
• setWeighted() : bpp::PGMA
• setWeights() : bpp::AbstractWeightedSubstitutionCount, bpp::WeightedSubstitutionCount
• setX() : bpp::TreeDrawingNodeInfo
• setXUnit() : bpp::AbstractTreeDrawing, bpp::TreeDrawing
• setY() : bpp::TreeDrawingNodeInfo
• setYUnit() : bpp::AbstractTreeDrawing, bpp::TreeDrawing
• sFreq_ : bpp::FullCodonFrequencySet, bpp::FullFrequencySet
• shape() : bpp::CWiseAdd< R, std::tuple< T0, T1 > >, bpp::CWiseApply< R, T, F >, bpp::CWiseDiv< R, std::tuple< T0, T1 > >, bpp::CWiseMean< R, ReductionOf< T >, P >, bpp::CWiseMean< R, ReductionOf< T >, ReductionOf< P > >, bpp::CWiseMul< R, std::tuple< T0, T1 > >, bpp::MatrixProduct< R, T0, T1 >, bpp::Node_DF, bpp::TransitionFunctionFromModel, bpp::TransitionMatrixFromModel, bpp::TransitionMatrixFromTransitionMatrix
• shareParameters() : bpp::AbstractPhyloLikelihood
• ShiftDelta() : bpp::ShiftDelta< T >
• ShiftParameter() : bpp::ShiftParameter
• shrinkSiteSet() : bpp::PatternTools
• shrunkData() : bpp::DRASDRTreeLikelihoodData, bpp::LikelihoodCalculationSingleProcess
• shrunkData_ : bpp::DRASDRTreeLikelihoodData, bpp::DRASRTreeLikelihoodData, bpp::DRTreeParsimonyData, bpp::LikelihoodCalculationSingleProcess
• sigma_ : bpp::RN95
• Sij() : bpp::AbstractSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::SubstitutionModelInterface
• SimData() : bpp::SimData
• SimpleBranchIterator() : bpp::AbstractTreeLikelihood::SimpleBranchIterator
• simpleExchangeabilities_ : bpp::RE08
• simpleGenerator_ : bpp::RE08
• simpleModel_ : bpp::RE08
• SimpleMutationProcess() : bpp::SimpleMutationProcess
• SimpleSiteIterator() : bpp::AbstractTreeLikelihood::SimpleSiteIterator
• SimpleSubstitutionProcess() : bpp::SimpleSubstitutionProcess
• SimpleSubstitutionProcessSequenceSimulator() : bpp::SimpleSubstitutionProcessSequenceSimulator
• SimpleSubstitutionProcessSiteSimulator() : bpp::SimpleSubstitutionProcessSiteSimulator, bpp::SimProcessEdge, bpp::SimProcessNode
• simplex() : bpp::MixtureSequenceEvolution
• simplex_ : bpp::AlignedPhyloLikelihoodMixture, bpp::ConfiguredSimplex, bpp::MixtureProcessPhyloLikelihood, bpp::MixtureSequenceEvolution
• SimProcessEdge() : bpp::SimProcessEdge
• SimProcessNode() : bpp::SimProcessNode
• simulate() : bpp::GivenDataSubstitutionProcessSequenceSimulator, bpp::NonHomogeneousSequenceSimulator, bpp::SequenceSimulatorInterface, bpp::SimpleSubstitutionProcessSequenceSimulator, bpp::SubstitutionProcessSequenceSimulator
• simulateSite() : bpp::NonHomogeneousSequenceSimulator, bpp::SimpleSubstitutionProcessSiteSimulator, bpp::SiteSimulatorInterface
• simulateSites() : bpp::SequenceSimulationTools
• SINGLE : bpp::HierarchicalClustering
• SingleDataPhyloLikelihoodInterface() : bpp::SingleDataPhyloLikelihoodInterface
• SingleProcessPhyloLikelihood() : bpp::SingleProcessPhyloLikelihood
• SingleProcessSubstitutionMapping() : bpp::SingleProcessSubstitutionMapping
• siteLik_ : bpp::LikelihoodCalculationOnABranch::RateCategoryEdge
• siteLikelihoods_ : bpp::AlignedLikelihoodCalculation
• siteModelDescription_ : bpp::AbstractHomogeneousTreeLikelihood::ConstHomogeneousSiteModelIterator
• siteModelDescriptions_ : bpp::AbstractNonHomogeneousTreeLikelihood::ConstNonHomogeneousSiteModelIterator
• siteP : bpp::SitePatterns::SortableSite
• SitePatterns() : bpp::SitePatterns
• siteS : bpp::SitePatterns::SortableSite
• sites_ : bpp::DistanceEstimation, bpp::SitePatterns
• siteSim_ : bpp::SimpleSubstitutionProcessSequenceSimulator
• SiteSimulationResult() : bpp::SiteSimulationResult
• siteSimulator() : bpp::GivenDataSubstitutionProcessSequenceSimulator, bpp::NonHomogeneousSequenceSimulator, bpp::SequenceSimulatorInterface, bpp::SimpleSubstitutionProcessSequenceSimulator, bpp::SubstitutionProcessSequenceSimulator
• SiteSimulatorInterface() : bpp::SiteSimulatorInterface
• sitesPositions_ : bpp::AbstractMapping, bpp::LegacyAbstractMapping
• size() : bpp::Context, bpp::ExtendedFloatEigen< R, C, EigenType >, bpp::MixedSubstitutionModelSet::HyperNode::Node, bpp::ModelList, bpp::ModelPath, 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
• son() : bpp::Node
• sons_ : bpp::AwareNode, bpp::Node, bpp::SimProcessNode
• SortableSite() : bpp::SitePatterns::SortableSite
• sortByPartitionSize() : bpp::BipartitionList
• sorted_ : bpp::BipartitionList
• sortElements() : 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_
• SSR() : bpp::SSR
• state : bpp::SimData
• state_ : bpp::SimProcessNode
• stateMap() : bpp::AbstractFrequencySet, bpp::AbstractSubstitutionRegister, bpp::AbstractTransitionModel, bpp::AbstractTreeParsimonyScore, bpp::AbstractWrappedModel, bpp::BranchModelInterface, bpp::FrequencySetInterface, bpp::LikelihoodCalculationOnABranch, bpp::LikelihoodCalculationSingleProcess, bpp::MarkovModulatedSubstitutionModel, bpp::NonHomogeneousSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, bpp::RegisterRatesSubstitutionModel, bpp::SequenceEvolution, bpp::SimpleSubstitutionProcess, bpp::SubstitutionModelSet, bpp::SubstitutionProcessCollectionMember, bpp::SubstitutionProcessInterface, bpp::SubstitutionRegisterInterface, bpp::TreeParsimonyScoreInterface
• 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
• statFromNode_() : bpp::PhyloTreeTools, bpp::TreeTools
• stationarity_ : bpp::CategorySubstitutionRegister, bpp::SubstitutionModelSet
• StochasticMapping() : bpp::StochasticMapping
• storeAllNumbersOfSubstitutions() : bpp::DecompositionSubstitutionCount, bpp::LabelSubstitutionCount, bpp::LaplaceSubstitutionCount, bpp::NaiveSubstitutionCount, bpp::OneJumpSubstitutionCount, bpp::SubstitutionCountInterface, bpp::UniformizationSubstitutionCount
• storeAllRewards() : bpp::DecompositionReward, bpp::Reward
• str : StringAndInt
• strictConsensus() : bpp::TreeTools
• StringAndInt() : StringAndInt
• stringToProperty_() : bpp::Nhx
• subModel() : bpp::MixtureOfASubstitutionModel, bpp::MixtureOfSubstitutionModels
• subModel_ : bpp::AbstractFromSubstitutionModelTransitionModel, bpp::FromMixtureSubstitutionModel, bpp::MultinomialFromTransitionModel, bpp::TransitionFromTransitionModel
• subModelNumber_ : bpp::InMixedSubstitutionModel
• subModelNumbers() : bpp::ProcessComputationEdge
• subNModel() : bpp::MixtureOfASubstitutionModel
• subsProc_ : bpp::OneProcessSequenceEvolution
• substitutionCount_ : bpp::LegacyProbabilisticSubstitutionMapping
• SubstitutionCountInterface() : bpp::SubstitutionCountInterface
• SubstitutionMapping() : bpp::SubstitutionMapping
• SubstitutionMappingTools() : bpp::SubstitutionMappingTools
• substitutionModel() : bpp::AbstractFromSubstitutionModelTransitionModel, bpp::AbstractTreeLikelihood::ConstNoPartitionBranchModelDescription, bpp::AbstractTreeLikelihood::ConstNoPartitionSiteModelDescription, bpp::FromMixtureSubstitutionModel, bpp::GY94, bpp::InMixedSubstitutionModel, bpp::KCM, bpp::MG94, bpp::RegisterRatesSubstitutionModel, bpp::SubstitutionModelSet, bpp::TreeLikelihoodInterface::ConstBranchModelDescription, bpp::TreeLikelihoodInterface::ConstSiteModelDescription, bpp::WrappedSubstitutionModelInterface, bpp::YN98
• substitutionModel_() : bpp::AbstractFromSubstitutionModelTransitionModel, bpp::AbstractWrappedSubstitutionModel, bpp::FromMixtureSubstitutionModel, bpp::GY94, bpp::InMixedSubstitutionModel, bpp::KCM, bpp::MG94, bpp::RegisterRatesSubstitutionModel, bpp::YN98
• SubstitutionModelInterface() : bpp::SubstitutionModelInterface
• substitutionModelSet() : bpp::AbstractNonHomogeneousTreeLikelihood, bpp::NonHomogeneousSequenceSimulator, bpp::NonHomogeneousTreeLikelihood
• SubstitutionModelSet() : bpp::SubstitutionModelSet
• substitutionProcess() : bpp::LikelihoodCalculationSingleProcess, bpp::MultiProcessSequenceEvolution, bpp::OneProcessSequenceEvolution, bpp::OneProcessSequencePhyloLikelihood, bpp::SequenceEvolution, bpp::SingleProcessPhyloLikelihood, bpp::SubstitutionProcessCollection
• SubstitutionProcessCollection() : bpp::SubstitutionProcessCollection, bpp::SubstitutionProcessCollectionMember
• SubstitutionProcessCollectionMember() : bpp::SubstitutionProcessCollectionMember
• SubstitutionProcessSequenceSimulator() : bpp::SubstitutionProcessSequenceSimulator
• substitutionRegister() : bpp::AbstractSinglePhyloSubstitutionMapping
• substitutionRegisterHasChanged() : bpp::AbstractSubstitutionCount, bpp::DecompositionSubstitutionCount, bpp::LabelSubstitutionCount, bpp::LaplaceSubstitutionCount, bpp::NaiveSubstitutionCount, bpp::OneJumpSubstitutionCount, bpp::UniformizationSubstitutionCount
• SubstitutionRegisterInterface() : bpp::SubstitutionRegisterInterface
• sum() : bpp::ExtendedFloatEigen< R, C, EigenType >, bpp::ExtendedFloatVectorwiseOp< DerivedEF, MatType, Direction >, bpp::PhyloTreeTools::Moments_, bpp::TreeTemplateTools::Moments_, bpp::TreeTools::Moments_
• sumDist_ : bpp::NeighborJoining
• SumOfLogarithms() : bpp::SumOfLogarithms< F >
• supportedChars_ : bpp::LabelSubstitutionCount, bpp::NaiveSubstitutionCount
• supportedProperties_ : bpp::Nhx
• supportedStates_ : bpp::NonHomogeneousSequenceSimulator
• swap() : bpp::AwareNode, bpp::Node
• swapNodes() : bpp::Tree, bpp::TreeTemplate< N >
• SWSubstitutionRegister() : bpp::SWSubstitutionRegister
• synfrom_ : bpp::DFP07, bpp::YNGP_M
• synto_ : bpp::DFP07, bpp::YNGP_M