- c -

cached() : bpp::Context
CachedNodeRef() : bpp::Context::CachedNodeRef
CanonicalStateMap() : bpp::CanonicalStateMap
CategoryFromDiscreteDistribution() : bpp::CategoryFromDiscreteDistribution
CategorySubstitutionRegister() : bpp::CategorySubstitutionRegister
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::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
ClusterInfos() : bpp::ClusterInfos
Coala() : bpp::Coala
CoalaCore() : bpp::CoalaCore
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
col() : bpp::ExtendedFloatEigen< R, C, EigenType >
collapse() : bpp::TreeDrawingNodeInfo
collapseNode() : bpp::AbstractTreeDrawing , bpp::TreeDrawing
collection() : bpp::CollectionNodes , bpp::MultiProcessSequenceEvolution , bpp::SubstitutionProcessCollectionMember
CollectionNodes() : bpp::CollectionNodes
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 > , 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 >
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 > , 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
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
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 > , 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
computeForSubtree_() : bpp::PhyloStatistics
computeFractionals() : bpp::StochasticMapping
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
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
CondLikelihood() : bpp::CondLikelihood
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
context() : bpp::AbstractPhyloLikelihood , bpp::CollectionNodes
Context() : bpp::Context
context() : bpp::PhyloLikelihoodInterface
Convert() : bpp::Convert< R, F >
convert() : bpp::ExtendedFloat
convertToClockTree() : bpp::PhyloTreeTools , bpp::TreeTools
convertToClockTree2() : bpp::PhyloTreeTools , bpp::TreeTools
CoreCodonSubstitutionModelInterface() : bpp::CoreCodonSubstitutionModelInterface
counts() : bpp::AbstractSinglePhyloSubstitutionMapping , bpp::PhyloSubstitutionMapping
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 > , 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
Cursor() : bpp::Cursor
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 >
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 > >