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

- c -

• c_ : bpp::GTR
• cached() : bpp::Context
• CachedNodeRef() : bpp::Context::CachedNodeRef
• calcul_ : bpp::GivenDataSubstitutionProcessSequenceSimulator, bpp::GivenDataSubstitutionProcessSiteSimulator
• CanonicalStateMap() : bpp::CanonicalStateMap
• categories_ : bpp::CategorySubstitutionRegister
• categoryCorrespondance_ : bpp::AAExteriorSubstitutionRegister, bpp::AAInteriorSubstitutionRegister
• CategoryFromDiscreteDistribution() : bpp::CategoryFromDiscreteDistribution
• categoryNames_ : bpp::CategorySubstitutionRegister, bpp::SelectedSubstitutionRegister
• CategorySubstitutionRegister() : bpp::CategorySubstitutionRegister
• catProb_ : bpp::LikelihoodCalculationOnABranch, bpp::LikelihoodCalculationSingleProcess
• CENTROID : bpp::HierarchicalClustering
• changeModel() : bpp::ModelPath, bpp::ModelScenario
• changeNamesToTags() : bpp::Nhx
• changeTagsToNames() : bpp::Nhx
• checkChangingPositions_() : bpp::AbstractKroneckerWordSubstitutionModel
• checkEstimatedParameters() : bpp::PhylogeneticsApplicationTools
• checkIds() : bpp::TreeTools
• checkModel() : bpp::YpR
• checkNodesId_() : bpp::Nhx
• checkOrphanModels() : bpp::SubstitutionModelSet
• checkOrphanNodes() : bpp::NonHomogeneousSubstitutionProcess, bpp::SubstitutionModelSet, bpp::SubstitutionProcessCollectionMember
• checkUnknownNodes() : bpp::NonHomogeneousSubstitutionProcess, bpp::SubstitutionModelSet, bpp::SubstitutionProcessCollectionMember
• CladogramDrawBranchEvent() : bpp::CladogramDrawBranchEvent
• CladogramPlot() : bpp::CladogramPlot
• cleanAllLikelihoods() : bpp::AlignedLikelihoodCalculation, bpp::LikelihoodCalculation, bpp::LikelihoodCalculationOnABranch, bpp::LikelihoodCalculationSingleProcess
• clear() : bpp::Context, bpp::MixedSubstitutionModelSet, bpp::ModelScenario, bpp::MutationPath, bpp::NonHomogeneousSubstitutionProcess, bpp::SubstitutionModelSet, bpp::SubstitutionProcessCollection, bpp::SubstitutionProcessCollectionMember
• clone() : bpp::AAExteriorSubstitutionRegister, bpp::AAInteriorSubstitutionRegister, bpp::AbstractCodonAAFitnessSubstitutionModel, bpp::AbstractCodonAARateSubstitutionModel, bpp::AbstractCodonBGCSubstitutionModel, bpp::AbstractCodonClusterAASubstitutionModel, bpp::AbstractCodonCpGSubstitutionModel, bpp::AbstractCodonDistanceSubstitutionModel, bpp::AbstractCodonFitnessSubstitutionModel, bpp::AbstractCodonFrequenciesSubstitutionModel, bpp::AbstractCodonPhaseFrequenciesSubstitutionModel, bpp::AbstractCodonSubstitutionModel, bpp::AbstractDFPSubstitutionModel, bpp::AbstractKroneckerCodonSubstitutionModel, bpp::AbstractMixedTransitionModel, bpp::AbstractNucleotideSubstitutionModel, bpp::AbstractProteinSubstitutionModel, bpp::AbstractReversibleNucleotideSubstitutionModel, bpp::AbstractReversibleProteinSubstitutionModel, bpp::AbstractReversibleSubstitutionModel, bpp::AbstractRewardMapping, bpp::AbstractSubstitutionMapping, bpp::AbstractWordFrequencySet, bpp::AgglomerativeDistanceMethodInterface, bpp::AlignedLikelihoodCalculation, bpp::AlignedPhyloLikelihoodAutoCorrelation, bpp::AlignedPhyloLikelihoodHmm, bpp::AlignedPhyloLikelihoodInterface, bpp::AlignedPhyloLikelihoodMixture, bpp::AlignedPhyloLikelihoodProduct, bpp::AlignedPhyloLikelihoodSetInterface, bpp::AnonymousSubstitutionModel, bpp::AutoCorrelationProcessPhyloLikelihood, bpp::AutoCorrelationSequenceEvolution, bpp::AwareNode, bpp::BinarySubstitutionModel, bpp::BioNJ, bpp::BipartitionList, bpp::BootstrapValuesTreeDrawingListener, bpp::BranchLengthsTreeDrawingListener, bpp::BranchLikelihood, bpp::BranchModelInterface, bpp::CanonicalStateMap, bpp::CladogramPlot, bpp::Coala, bpp::CoalaCore, bpp::CodonAdHocSubstitutionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonDistanceSubstitutionModel, bpp::CodonFrequencySetInterface, bpp::CodonFromIndependentFrequencySet, bpp::CodonFromUniqueFrequencySet, bpp::CodonReversibleSubstitutionModelInterface, bpp::CodonSameAARateSubstitutionModel, bpp::CodonSubstitutionModelInterface, bpp::CollectionNodes, bpp::CompleteSubstitutionRegister, bpp::ComprehensiveSubstitutionRegister, bpp::ConfiguredDistribution, bpp::ConfiguredFrequencySet, bpp::ConfiguredModel, bpp::ConfiguredParameter, bpp::ConfiguredSimplex, bpp::ConfiguredTransitionMatrix, bpp::ConstantRateDistribution, bpp::CoreCodonSubstitutionModelInterface, bpp::D1WalkSubstitutionModel, bpp::DecompositionMethods, bpp::DecompositionReward, bpp::DecompositionSubstitutionCount, bpp::DetailedSiteSimulatorInterface, bpp::DFP07, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::DistanceEstimation, bpp::DistanceMethodInterface, bpp::DnDsSubstitutionRegister, bpp::DRASDRTreeLikelihoodData, bpp::DRASDRTreeLikelihoodLeafData, bpp::DRASDRTreeLikelihoodNodeData, bpp::DRASRTreeLikelihoodData, bpp::DRASRTreeLikelihoodNodeData, bpp::DRHomogeneousMixedTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::DRTreeLikelihoodInterface, bpp::DRTreeParsimonyData, bpp::DRTreeParsimonyLeafData, bpp::DRTreeParsimonyNodeData, bpp::DRTreeParsimonyScore, bpp::DSO78, bpp::EquiprobableSubstitutionModel, bpp::EvolutionSequenceSimulator, bpp::ExponentialDiscreteRateDistribution, bpp::F81, bpp::F84, bpp::FixedCodonFrequencySet, bpp::FixedFrequencySet, bpp::FixedNucleotideFrequencySet, bpp::FixedProteinFrequencySet, bpp::FrequencySetInterface, bpp::FromMixtureSubstitutionModel, bpp::FromModelFrequencySet, bpp::FullCodonFrequencySet, bpp::FullFrequencySet, bpp::FullNucleotideFrequencySet, bpp::FullPerAACodonFrequencySet, bpp::FullProteinFrequencySet, bpp::G2001, bpp::GammaDiscreteRateDistribution, bpp::GaussianDiscreteRateDistribution, bpp::gBGC, bpp::GCFrequencySet, bpp::GCPositionSubstitutionRegister, bpp::GCSubstitutionRegister, bpp::GCSynonymousSubstitutionRegister, bpp::GeneralSubstitutionRegister, bpp::GivenDataSubstitutionProcessSequenceSimulator, bpp::GivenDataSubstitutionProcessSiteSimulator, bpp::GlobalClockTreeLikelihoodFunctionWrapper, bpp::GTR, bpp::GY94, bpp::HierarchicalClustering, bpp::HKY85, bpp::HmmEmissionProbabilities_Eigen, bpp::HmmLikelihood_DF, bpp::HmmPhyloAlphabet, bpp::HmmPhyloEmissionProbabilities, bpp::HmmProcessAlphabet, bpp::HmmProcessPhyloLikelihood, bpp::HmmSequenceEvolution, bpp::HomogeneousTreeLikelihood, bpp::InMixedSubstitutionModel, bpp::JCnuc, bpp::JCprot, bpp::JTT92, bpp::K80, bpp::KCM, bpp::KrKcSubstitutionRegister, bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::KroneckerCodonDistanceSubstitutionModel, bpp::KroneckerWordSubstitutionModel, bpp::L95, bpp::LabelCollapsedNodesTreeDrawingListener, bpp::LabelInnerNodesTreeDrawingListener, bpp::LabelSubstitutionCount, bpp::LaplaceSubstitutionCount, bpp::LeafNamesTreeDrawingListener, bpp::LegacyAbstractMapping, bpp::LegacyAbstractRewardMapping, bpp::LegacyAbstractSubstitutionMapping, bpp::LegacyMappingInterface, bpp::LegacyMarginalAncestralStateReconstruction, bpp::LegacyOptimizationTools::ScaleFunction, bpp::LegacyProbabilisticRewardMapping, bpp::LegacyProbabilisticSubstitutionMapping, bpp::LegacyRewardMappingInterface, bpp::LegacySubstitutionMappingInterface, bpp::LG08, bpp::LG10_EX_EHO, bpp::LG10_EX_EHO::EmbeddedModel, bpp::LGL08_CAT, bpp::LGL08_CAT::EmbeddedModel, bpp::LikelihoodCalculation, bpp::LikelihoodCalculationOnABranch, bpp::LikelihoodCalculationSingleProcess, bpp::LLG08_EHO, bpp::LLG08_EHO::EmbeddedModel, bpp::LLG08_EX2, bpp::LLG08_EX2::EmbeddedModel, bpp::LLG08_EX3, bpp::LLG08_EX3::EmbeddedModel, bpp::LLG08_UL2, bpp::LLG08_UL2::EmbeddedModel, bpp::LLG08_UL3, bpp::LLG08_UL3::EmbeddedModel, bpp::MappingInterface, bpp::MarginalAncestralReconstruction, bpp::MarkovModulatedFrequencySet, bpp::MarkovModulatedStateMap, bpp::MarkovModulatedSubstitutionModel, bpp::MG94, bpp::MixedSubstitutionModelSet, bpp::MixedTransitionModelInterface, bpp::MixtureOfASubstitutionModel, bpp::MixtureOfATransitionModel, bpp::MixtureOfSubstitutionModels, bpp::MixtureOfTransitionModels, bpp::MixtureProcessPhyloLikelihood, bpp::MixtureSequenceEvolution, bpp::MultinomialFromTransitionModel, bpp::MvaFrequencySet, bpp::NaiveSubstitutionCount, bpp::NeighborJoining, bpp::NNIHomogeneousTreeLikelihood, bpp::NNISearchable, bpp::NNITopologyListener2, bpp::NNITopologyListener, bpp::Node, bpp::NodeEvent, bpp::NodesIdTreeDrawingListener, bpp::NodeTemplate< NodeInfos >, bpp::NonHomogeneousSequenceSimulator, bpp::NonHomogeneousSubstitutionProcess, bpp::NonHomogeneousTreeLikelihood, bpp::NucleotideFrequencySetInterface, bpp::NucleotideReversibleSubstitutionModelInterface, bpp::NucleotideSubstitutionModelInterface, bpp::OnABranchPhyloLikelihood, bpp::OneChangeRegisterTransitionModel, bpp::OneChangeTransitionModel, bpp::OneJumpSubstitutionCount, bpp::OneProcessSequenceEvolution, bpp::OneProcessSequencePhyloLikelihood, bpp::OneProcessSequenceSubstitutionMapping, bpp::ParametrizablePhyloTree, bpp::PartitionProcessPhyloLikelihood, bpp::PartitionSequenceEvolution, bpp::PGMA, bpp::PhyloBranch, bpp::PhyloBranchMapping, bpp::PhyloBranchParam, bpp::PhyloBranchReward, bpp::PhyloDAG, bpp::PhylogramPlot, bpp::PhyloLikelihoodContainer, bpp::PhyloLikelihoodFormula, bpp::PhyloLikelihoodInterface, bpp::PhyloLikelihoodSetInterface, bpp::PhyloNode, bpp::PhyloStatistics, bpp::PhyloSubstitutionMapping, bpp::PhyloTree, bpp::POMO, bpp::ProbabilisticRewardMapping, bpp::ProbabilisticSubstitutionMapping, bpp::ProcessTree, bpp::ProteinFrequencySetInterface, bpp::ProteinReversibleSubstitutionModelInterface, bpp::ProteinSubstitutionModelInterface, bpp::PseudoNewtonOptimizer, bpp::PseudoNewtonOptimizer::PNStopCondition, bpp::RateAcrossSitesSubstitutionProcess, bpp::RE08, bpp::RE08Codon, bpp::RE08Nucleotide, bpp::RE08Protein, bpp::RegisterRatesSubstitutionModel, bpp::RELAX, bpp::ReversibleSubstitutionModelInterface, bpp::Reward, bpp::RewardMappingInterface, bpp::RHomogeneousMixedTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::RN95, bpp::RN95s, bpp::RNonHomogeneousMixedTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, bpp::SelectedSubstitutionRegister, bpp::SENCA, bpp::SequenceEvolution, bpp::SequencePhyloLikelihoodInterface, bpp::SequenceSimulatorInterface, bpp::SimpleSubstitutionProcess, bpp::SimpleSubstitutionProcessSequenceSimulator, bpp::SimpleSubstitutionProcessSiteSimulator, bpp::SingleDataPhyloLikelihoodInterface, bpp::SingleProcessPhyloLikelihood, bpp::SingleProcessSubstitutionMapping, bpp::SitePartition, bpp::SitePartitionHomogeneousTreeLikelihood, bpp::SitePatterns, bpp::SiteSimulatorInterface, bpp::SSR, bpp::StateMapInterface, bpp::StochasticMapping, bpp::SubstitutionCountInterface, bpp::SubstitutionMapping, bpp::SubstitutionModelInterface, bpp::SubstitutionModelSet, bpp::SubstitutionProcessCollection, bpp::SubstitutionProcessCollectionMember, bpp::SubstitutionProcessInterface, bpp::SubstitutionProcessSequenceSimulator, bpp::SubstitutionRegisterInterface, bpp::SWSubstitutionRegister, bpp::T92, bpp::TN93, bpp::TopologyListener, bpp::TotalSubstitutionRegister, bpp::TransitionFromTransitionModel, bpp::TransitionModelInterface, bpp::Tree, bpp::TreeDrawing, bpp::TreeDrawingListener, bpp::TreeLikelihoodData, bpp::TreeLikelihoodInterface, bpp::TreeLikelihoodNodeData, bpp::TreeParsimonyDataInterface, bpp::TreeParsimonyNodeDataInterface, bpp::TreeParsimonyScoreInterface, bpp::TreeTemplate< N >, bpp::TripletSubstitutionModel, bpp::TrivialSitePartition, bpp::TS98, bpp::TsTvSubstitutionRegister, bpp::TwoParameterBinarySubstitutionModel, bpp::UniformizationSubstitutionCount, bpp::UserCodonFrequencySet, bpp::UserFrequencySet, bpp::UserNucleotideFrequencySet, bpp::UserProteinFrequencySet, bpp::UserProteinSubstitutionModel, bpp::VectorOfSubstitutionRegisters, bpp::WAG01, bpp::WordFrequencySetInterface, bpp::WordFromIndependentFrequencySet, bpp::WordFromUniqueFrequencySet, bpp::WordSubstitutionModel, bpp::YN98, bpp::YNGP_M10, bpp::YNGP_M1, bpp::YNGP_M2, bpp::YNGP_M3, bpp::YNGP_M7, bpp::YNGP_M8, bpp::YNGP_M9, bpp::YNGP_M, bpp::YpR_Gen, bpp::YpR_Sym
• cloneSubtree() : bpp::Tree, bpp::TreeTemplate< N >, bpp::TreeTemplateTools
• clt : bpp::LikelihoodCalculationSingleProcess::RateCategoryTrees
• ClusterInfos() : bpp::ClusterInfos
• Coala() : bpp::Coala
• CoalaCore() : bpp::CoalaCore
• CODON : bpp::BppOFrequencySetFormat, bpp::BppOSubstitutionModelFormat
• CodonAdHocSubstitutionModel() : bpp::CodonAdHocSubstitutionModel
• CodonDistanceFrequenciesSubstitutionModel() : bpp::CodonDistanceFrequenciesSubstitutionModel
• CodonDistancePhaseFrequenciesSubstitutionModel() : bpp::CodonDistancePhaseFrequenciesSubstitutionModel
• CodonDistanceSubstitutionModel() : bpp::CodonDistanceSubstitutionModel
• codonFrequencySet() : bpp::AbstractCodonAAFitnessSubstitutionModel, bpp::AbstractCodonAARateSubstitutionModel, bpp::AbstractCodonBGCSubstitutionModel, bpp::AbstractCodonClusterAASubstitutionModel, bpp::AbstractCodonCpGSubstitutionModel, bpp::AbstractCodonDistanceSubstitutionModel, bpp::AbstractCodonFitnessSubstitutionModel, bpp::AbstractCodonFrequenciesSubstitutionModel, bpp::AbstractCodonPhaseFrequenciesSubstitutionModel, bpp::CodonAdHocSubstitutionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonSameAARateSubstitutionModel, bpp::CoreCodonSubstitutionModelInterface, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::KCM, bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::MG94, bpp::RE08Codon, bpp::SENCA, bpp::YN98
• CodonFromIndependentFrequencySet() : bpp::CodonFromIndependentFrequencySet
• CodonFromUniqueFrequencySet() : bpp::CodonFromUniqueFrequencySet
• codonModel() : bpp::CodonSameAARateSubstitutionModel
• CodonReversibleSubstitutionModelInterface() : bpp::CodonReversibleSubstitutionModelInterface
• CodonSameAARateSubstitutionModel() : bpp::CodonSameAARateSubstitutionModel
• CodonSubstitutionModelInterface() : bpp::CodonSubstitutionModelInterface
• coeffs_ : bpp::CombineDeltaShifted< T >
• col() : bpp::ExtendedFloatEigen< R, C, EigenType >
• collapse() : bpp::TreeDrawingNodeInfo
• collapsed_ : bpp::TreeDrawingNodeInfo
• collapseNode() : bpp::AbstractTreeDrawing, bpp::TreeDrawing
• collection() : bpp::CollectionNodes, bpp::MultiProcessSequenceEvolution, bpp::SubstitutionProcessCollectionMember
• collection_ : bpp::CollectionNodes
• CollectionNodes() : bpp::CollectionNodes
• collectionNodes_ : bpp::PhyloLikelihoodContainer
• color() : bpp::CategoryFromDiscreteDistribution, bpp::ConfiguredDistribution, bpp::ConfiguredFrequencySet, bpp::ConfiguredModel, bpp::ConfiguredParameter, bpp::ConfiguredSimplex, bpp::ConfiguredTransitionMatrix, 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::EquilibriumFrequenciesFromModel, bpp::EquilibriumFrequenciesFromTransitionMatrix, bpp::FrequenciesFromFrequencySet, bpp::FrequenciesFromSimplex, bpp::MatrixProduct< R, T0, T1 >, bpp::Node_DF, bpp::NumericConstant< T >, bpp::ProbabilitiesFromDiscreteDistribution, bpp::ProbabilitiesFromMixedModel, bpp::ProbabilityFromDiscreteDistribution, bpp::ProbabilityFromMixedModel, bpp::Sequence_DF, bpp::ShiftParameter, bpp::TransitionFunctionFromModel, bpp::TransitionMatrixFromModel, bpp::TransitionMatrixFromTransitionMatrix, bpp::ValueFromConfiguredParameter
• cols() : bpp::ExtendedFloatEigen< R, C, EigenType >, bpp::MatrixDimension
• columnWeights_ : bpp::MvaFrequencySet
• colWeights_ : bpp::CoalaCore
• colwise() : bpp::ExtendedFloatEigen< R, C, EigenType >
• CombineDeltaShifted() : bpp::CombineDeltaShifted< T >
• compareAdditionalArguments() : bpp::BackwardHmmLikelihood_DF, bpp::CategoryFromDiscreteDistribution, bpp::CombineDeltaShifted< T >, bpp::CondLikelihood, 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::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::Node_DF, bpp::NumericConstant< 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
• compFreq_ : bpp::MarkovModulatedSubstitutionModel
• COMPLETE : bpp::HierarchicalClustering
• complete() : bpp::MixedSubstitutionModelSet, bpp::ModelScenario
• completeMatrices_() : bpp::AbstractCodonSubstitutionModel, bpp::AbstractKroneckerCodonSubstitutionModel, bpp::AbstractWordSubstitutionModel, bpp::KroneckerWordSubstitutionModel, bpp::WordSubstitutionModel
• completeMixedSubstitutionModelSet() : bpp::LegacyPhylogeneticsApplicationTools
• CompleteSubstitutionRegister() : bpp::CompleteSubstitutionRegister
• compound_functor() : bpp::CWiseCompound< R, ReductionOf< T > >::compound_functor
• ComprehensiveSubstitutionRegister() : bpp::ComprehensiveSubstitutionRegister
• compTree_ : bpp::PhyloLikelihoodFormula
• compute() : bpp::BackwardHmmLikelihood_DF, bpp::CategoryFromDiscreteDistribution, bpp::CombineDeltaShifted< T >, bpp::CondLikelihood, 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 > >::compound_functor, 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::CWiseMatching< R, ReductionOf< T > >::matching_functor, 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::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::Node_DF, 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
• compute_() : bpp::CodonSameAARateSubstitutionModel
• compute_d2Multinomial_dt2_() : bpp::MultinomialFromTransitionModel
• compute_dMultinomial_dt_() : bpp::MultinomialFromTransitionModel
• compute_Multinomial_() : bpp::MultinomialFromTransitionModel
• computeAllTransitionProbabilities() : bpp::AbstractHomogeneousTreeLikelihood, bpp::AbstractNonHomogeneousTreeLikelihood, bpp::BranchLikelihood, bpp::RHomogeneousMixedTreeLikelihood
• computeBootstrapValues() : bpp::TreeTools
• computeBranchLengthsForPair() : bpp::AbstractAgglomerativeDistanceMethod, bpp::HierarchicalClustering, bpp::NeighborJoining, bpp::PGMA
• computeBranchLengthsFromHeights_() : bpp::GlobalClockTreeLikelihoodFunctionWrapper
• computeBranchLengthsGrafen() : bpp::PhyloTreeTools, bpp::TreeTools
• computeCOA() : bpp::CoalaCore
• ComputeConditionals() : bpp::StochasticMapping
• computeCoordsFirstSpaceCOA() : bpp::MvaFrequencySet
• computeCoordsFirstSpacePCA() : bpp::MvaFrequencySet
• computeCounts() : bpp::LaplaceSubstitutionCount, bpp::OneProcessSequenceSubstitutionMapping, bpp::PhyloSubstitutionMapping, bpp::SingleProcessSubstitutionMapping, bpp::SubstitutionMappingTools
• computeCounts_() : bpp::DecompositionSubstitutionCount, bpp::UniformizationSubstitutionCount
• computeCountsPerSitePerBranch() : bpp::LegacySubstitutionMappingTools
• computeCountsPerSitePerBranchPerType() : bpp::LegacySubstitutionMappingTools
• computeCountsPerSitePerType() : bpp::LegacySubstitutionMappingTools
• computeCountsPerTypePerBranch() : bpp::LegacySubstitutionMappingTools, bpp::SubstitutionMappingTools
• computeDistancesFromPair() : bpp::AbstractAgglomerativeDistanceMethod, bpp::BioNJ, bpp::HierarchicalClustering, bpp::NeighborJoining, bpp::PGMA
• computeDownSubtreeD2Likelihood() : bpp::RHomogeneousMixedTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousMixedTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood
• computeDownSubtreeDLikelihood() : bpp::RHomogeneousMixedTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousMixedTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood
• computeEquilibriumFrequencies() : bpp::Coala
• computeExpectations() : bpp::DecompositionMethods
• computeExpectedLikelihoodWeights() : bpp::PairedSiteLikelihoods
• computeFirstOrderDerivatives_ : bpp::AbstractTreeLikelihood
• computeForSubtree_() : bpp::PhyloStatistics
• computeFractionals() : bpp::StochasticMapping
• computeFreq_ : bpp::AbstractSubstitutionModel
• computeFrequencies() : bpp::AbstractFromSubstitutionModelTransitionModel, bpp::AbstractMixedTransitionModel, bpp::AbstractSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractTransitionModel, bpp::InMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::TransitionModelInterface
• computeHyperNodesProbabilities() : bpp::MixedSubstitutionModelSet
• computeLikelihoodAtNode() : bpp::DRHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::DRTreeLikelihoodInterface
• computeLikelihoodAtNode_() : bpp::DRHomogeneousMixedTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood
• computeLikelihoodFromArrays() : bpp::DRHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood
• computeLogLikelihood() : bpp::BranchLikelihood
• computeMatrix() : bpp::DistanceEstimation
• computeModelPathsProbabilities() : bpp::ModelScenario
• computeNormalizations() : bpp::OneProcessSequenceSubstitutionMapping, bpp::PhyloSubstitutionMapping, bpp::SingleProcessSubstitutionMapping, bpp::SubstitutionMappingTools
• computeNormalizedCounts() : bpp::SubstitutionMappingTools
• computeNormForSite() : bpp::LegacySubstitutionMappingTools
• computeOneJumpCounts() : bpp::SubstitutionMappingTools
• computeOneJumpProbabilityVectors() : bpp::LegacySubstitutionMappingTools
• computeProducts_() : bpp::DecompositionMethods
• computeRecursively() : bpp::Node_DF
• computeReverseCOA() : bpp::MvaFrequencySet
• computeReversePCA() : bpp::MvaFrequencySet
• computeRewards_() : bpp::DecompositionReward
• computeRewardVectors() : bpp::LegacyRewardMappingTools, bpp::RewardMappingTools
• computeRootLikelihood() : bpp::DRHomogeneousMixedTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood
• computeScores() : bpp::DRTreeParsimonyScore
• computeScoresForNode() : bpp::DRTreeParsimonyScore
• computeScoresFromArrays() : bpp::DRTreeParsimonyScore
• computeScoresPostorder() : bpp::DRTreeParsimonyScore
• computeScoresPostorderForNode() : bpp::DRTreeParsimonyScore
• computeScoresPreorder() : bpp::DRTreeParsimonyScore
• computeScoresPreorderForNode() : bpp::DRTreeParsimonyScore
• computeSecondOrderDerivatives_ : bpp::AbstractTreeLikelihood
• computeSolution() : bpp::DRTreeParsimonyScore
• computeStatesFrequencies() : bpp::StochasticMapping
• computeSubstitutionVectors() : bpp::LegacySubstitutionMappingTools
• computeSubstitutionVectorsMarginal() : bpp::LegacySubstitutionMappingTools
• computeSubstitutionVectorsNoAveraging() : bpp::LegacySubstitutionMappingTools
• computeSubstitutionVectorsNoAveragingMarginal() : bpp::LegacySubstitutionMappingTools
• computeSubtreeLikelihood() : bpp::RHomogeneousMixedTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousMixedTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood
• computeSubtreeLikelihoodPostfix() : bpp::DRHomogeneousMixedTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood
• computeSubtreeLikelihoodPrefix() : bpp::DRHomogeneousMixedTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood
• computeSumForBranch() : bpp::LegacyRewardMappingTools, bpp::LegacySubstitutionMappingTools, bpp::RewardMappingTools
• computeSumForSite() : bpp::LegacyRewardMappingTools, bpp::LegacySubstitutionMappingTools, bpp::RewardMappingTools
• computeTotalSubstitutionVectorForSitePerBranch() : bpp::LegacySubstitutionMappingTools
• computeTotalSubstitutionVectorForSitePerType() : bpp::LegacySubstitutionMappingTools
• computeTransitionProbabilitiesForNode() : bpp::AbstractHomogeneousTreeLikelihood, bpp::AbstractNonHomogeneousTreeLikelihood, bpp::RHomogeneousMixedTreeLikelihood, bpp::RNonHomogeneousMixedTreeLikelihood
• computeTree() : bpp::AbstractAgglomerativeDistanceMethod, bpp::BioNJ, bpp::DistanceMethodInterface
• computeTreeD2Likelihood() : bpp::RHomogeneousMixedTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousMixedTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood
• computeTreeD2LikelihoodAtNode() : bpp::DRHomogeneousMixedTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood
• computeTreeD2Likelihoods() : bpp::DRHomogeneousMixedTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood
• computeTreeDLikelihood() : bpp::RHomogeneousMixedTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousMixedTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood
• computeTreeDLikelihoodAtNode() : bpp::DRHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood
• computeTreeDLikelihoods() : bpp::DRHomogeneousMixedTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood
• computeTreeLikelihood() : bpp::DRHomogeneousMixedTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::RHomogeneousMixedTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood
• ConditionalProbabilities_ : bpp::StochasticMapping
• condLik_ : bpp::ForwardHmmLikelihood_DF
• CondLikelihood() : bpp::CondLikelihood
• condLikelihoodTree_ : bpp::LikelihoodCalculationSingleProcess
• config : bpp::ConfiguredDistribution, bpp::ConfiguredFrequencySet, bpp::ConfiguredModel, bpp::ConfiguredSimplex, bpp::ConfiguredTransitionMatrix
• ConfiguredDistribution() : bpp::ConfiguredDistribution
• ConfiguredFrequencySet() : bpp::ConfiguredFrequencySet
• ConfiguredModel() : bpp::ConfiguredModel
• ConfiguredParameter() : bpp::ConfiguredParameter
• ConfiguredSimplex() : bpp::ConfiguredSimplex
• ConfiguredTransitionMatrix() : bpp::ConfiguredTransitionMatrix
• Constant() : bpp::ExtendedFloatEigen< R, C, EigenType >
• ConstantOne() : bpp::ConstantOne< T >
• ConstantRateDistribution() : bpp::ConstantRateDistribution
• ConstantTransitionFunction() : bpp::ConstantTransitionFunction
• ConstantZero() : bpp::ConstantZero< T >
• ConstHomogeneousSiteModelIterator() : bpp::AbstractHomogeneousTreeLikelihood::ConstHomogeneousSiteModelIterator
• ConstNonHomogeneousSiteModelIterator() : bpp::AbstractNonHomogeneousTreeLikelihood::ConstNonHomogeneousSiteModelIterator
• ConstNoPartitionBranchModelDescription() : bpp::AbstractTreeLikelihood::ConstNoPartitionBranchModelDescription
• ConstNoPartitionBranchModelIterator() : bpp::AbstractTreeLikelihood::ConstNoPartitionBranchModelIterator
• ConstNoPartitionSiteModelDescription() : bpp::AbstractTreeLikelihood::ConstNoPartitionSiteModelDescription
• constrainedMidPointRooting() : bpp::PhyloTreeTools, bpp::TreeTools
• containsBipartition() : bpp::BipartitionList
• content : bpp::IODAG::Element, bpp::IOTree::Element, bpp::TreeTemplateTools::Element
• context() : bpp::AbstractPhyloLikelihood, bpp::CollectionNodes
• Context() : bpp::Context, bpp::Node_DF
• context() : bpp::PhyloLikelihoodInterface
• context_ : bpp::AbstractPhyloLikelihood, bpp::BackwardLikelihoodTree, bpp::CollectionNodes, bpp::ConfiguredParameter, bpp::ForwardLikelihoodTree, bpp::HmmLikelihood_DF, bpp::HmmPhyloAlphabet, bpp::HmmPhyloEmissionProbabilities, bpp::LikelihoodCalculation, bpp::PhyloLikelihoodContainer, bpp::ProbabilityDAG, bpp::ProcessTree
• continuousRates_ : bpp::NonHomogeneousSequenceSimulator, bpp::SimpleSubstitutionProcessSiteSimulator
• Convert() : bpp::Convert< R, F >
• convert() : bpp::ExtendedFloat
• convertToClockTree() : bpp::PhyloTreeTools, bpp::TreeTools
• convertToClockTree2() : bpp::PhyloTreeTools, bpp::TreeTools
• CoreCodonSubstitutionModelInterface() : bpp::CoreCodonSubstitutionModelInterface
• countMultiple_ : bpp::DnDsSubstitutionRegister
• counts() : bpp::AbstractSinglePhyloSubstitutionMapping, bpp::PhyloSubstitutionMapping
• counts_ : bpp::AbstractSinglePhyloSubstitutionMapping, bpp::DecompositionSubstitutionCount, bpp::PhyloBranchMapping, bpp::UniformizationSubstitutionCount
• countsPerformed() : bpp::AbstractSinglePhyloSubstitutionMapping, bpp::PhyloSubstitutionMapping
• create() : bpp::BackwardHmmLikelihood_DF, bpp::CategoryFromDiscreteDistribution, bpp::CombineDeltaShifted< T >, bpp::CondLikelihood, bpp::ConfiguredParameter, 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::ForwardHmmD2Likelihood_DF, bpp::ForwardHmmDLikelihood_DF, bpp::ForwardHmmLikelihood_DF, 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::ValueFromConfiguredParameter
• createConfigured() : bpp::ConfiguredParametrizable
• createDouble() : bpp::ConfiguredParametrizable
• createHomogeneousModelSet() : bpp::SubstitutionModelSetTools
• createHomogeneousSubstitutionProcess() : bpp::NonHomogeneousSubstitutionProcess
• createMatrix() : bpp::ConfiguredParametrizable
• createNonHomogeneousModelSet() : bpp::SubstitutionModelSetTools
• createNonHomogeneousSubstitutionProcess() : bpp::NonHomogeneousSubstitutionProcess
• createReader() : bpp::IOFrequencySetFactory, bpp::IOSubstitutionModelFactory, bpp::IOTreeFactory
• createRowVector() : bpp::ConfiguredParametrizable
• createVector() : bpp::ConfiguredParametrizable
• createWriter() : bpp::IOFrequencySetFactory, bpp::IOSubstitutionModelFactory, bpp::IOTreeFactory
• cumProb_ : bpp::SimProcessNode
• cumpxy : bpp::SimData
• cumpxy_ : bpp::SimProcessEdge
• currentIndex_ : bpp::SiteSimulationResult
• currentLength_ : bpp::DecompositionReward, bpp::DecompositionSubstitutionCount, bpp::LaplaceSubstitutionCount, bpp::UniformizationSubstitutionCount
• currentNodes_ : bpp::AbstractAgglomerativeDistanceMethod
• currNode_ : bpp::TreeIterator
• Cursor() : bpp::Cursor
• cursor_ : bpp::DrawBranchEvent, bpp::DrawNodeEvent
• cutOff_ : bpp::LaplaceSubstitutionCount
• CWiseAdd() : bpp::CWiseAdd< R, T >, bpp::CWiseAdd< R, ReductionOf< T > >, bpp::CWiseAdd< R, std::tuple< T0, T1 > >
• CWiseApply() : bpp::CWiseApply< R, T, F >
• CWiseCompound() : bpp::CWiseCompound< R, ReductionOf< T > >
• CWiseConstantPow() : bpp::CWiseConstantPow< T >
• CWiseDiv() : bpp::CWiseDiv< R, std::tuple< T0, T1 > >
• CWiseExp() : bpp::CWiseExp< T >
• CWiseFill() : bpp::CWiseFill< R, T >
• CWiseInverse() : bpp::CWiseInverse< T >
• CWiseLog() : bpp::CWiseLog< T >
• CWiseMatching() : bpp::CWiseMatching< R, ReductionOf< T > >
• CWiseMean() : bpp::CWiseMean< R, ReductionOf< T >, P >, bpp::CWiseMean< R, ReductionOf< T >, ReductionOf< P > >
• CWiseMul() : bpp::CWiseMul< R, ReductionOf< T > >, bpp::CWiseMul< R, std::tuple< T0, T1 > >
• CWiseNegate() : bpp::CWiseNegate< T >
• CWisePattern() : bpp::CWisePattern< R >
• CWiseSub() : bpp::CWiseSub< R, std::tuple< T0, T1 > >