- 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::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
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
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
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 > >