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 >
• 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::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::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::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
• 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