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

- d -

• D1WalkSubstitutionModel() : bpp::D1WalkSubstitutionModel
• d2CondLik_ : bpp::ForwardHmmD2Likelihood_DF
• d2Lik_dt2() : bpp::AbstractLkTransitionModel , bpp::BranchModelInterface , bpp::MultinomialFromTransitionModel , bpp::TransitionFromTransitionModel , bpp::TransitionModelInterface
• d2Pi_ : bpp::MultinomialFromTransitionModel , bpp::TransitionFromTransitionModel
• d2Pij_dt2() : bpp::AbstractTotallyWrappedTransitionModel , bpp::AbstractTransitionModel , bpp::BinarySubstitutionModel , bpp::EquiprobableSubstitutionModel , bpp::F81 , bpp::F84 , bpp::HKY85 , bpp::InMixedSubstitutionModel , bpp::JCnuc , bpp::JCprot , bpp::K80 , bpp::MarkovModulatedSubstitutionModel , bpp::MultinomialFromTransitionModel , bpp::OneChangeRegisterTransitionModel , bpp::OneChangeTransitionModel , bpp::RE08 , bpp::T92 , bpp::TN93 , bpp::TransitionFromTransitionModel , bpp::TransitionModelInterface , bpp::TwoParameterBinarySubstitutionModel
• d2pij_t : bpp::AbstractFromSubstitutionModelTransitionModel
• d2pijt_ : bpp::AbstractTransitionModel , bpp::MarkovModulatedSubstitutionModel
• d2pxy_ : bpp::AbstractHomogeneousTreeLikelihood , bpp::AbstractNonHomogeneousTreeLikelihood
• d_ : bpp::GTR
• DAClass : bpp::BackwardLikelihoodTree , bpp::ForwardLikelihoodTree
• dagToParenthesis() : bpp::ExtendedNewick
• data() : bpp::AbstractTreeLikelihood , bpp::DistanceEstimation , bpp::LikelihoodCalculationSingleProcess , bpp::TreeLikelihoodInterface
• data_ : bpp::AbstractTreeLikelihood , bpp::AbstractTreeParsimonyScore
• dCondLik_ : bpp::ForwardHmmDLikelihood_DF
• debugInfo() : 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::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
• DecompositionMethods() : bpp::DecompositionMethods
• DecompositionReward() : bpp::DecompositionReward
• DecompositionSubstitutionCount() : bpp::DecompositionSubstitutionCount
• DEFAULT_SETTINGS : bpp::AbstractTreeDrawing
• defaultOptimizer_ : bpp::DistanceEstimation
• defineParameters() : bpp::MvaFrequencySet
• degree() : bpp::Node
• deleteBipartition() : bpp::BipartitionList
• deleteBranchLengths() : bpp::TreeTemplateTools
• deleteBranchProperties() : bpp::Node , bpp::TreeTemplateTools
• deleteBranchProperty() : bpp::Node
• deleteDistanceToFather() : bpp::Node , bpp::Tree , bpp::TreeTemplate< N >
• deleteLength() : bpp::PhyloBranch
• deleteName() : bpp::Node , bpp::PhyloNode
• deleteNodeName() : bpp::Tree , bpp::TreeTemplate< N >
• deleteNodeProperties() : bpp::Node , bpp::TreeTemplateTools
• deleteNodeProperty() : bpp::Node
• deleteProperties() : bpp::PhyloBranch , bpp::PhyloNode
• deleteProperty() : bpp::PhyloBranch , bpp::PhyloNode
• deleteSubtree() : bpp::TreeTemplateTools
• delta : bpp::NumericalDerivativeConfiguration
• delta_ : bpp::RN95 , bpp::RN95s , bpp::SSR
• denorm_add() : bpp::ExtendedFloat , bpp::ExtendedFloatEigen< R, C, EigenType >
• denorm_div() : bpp::ExtendedFloat , bpp::ExtendedFloatEigen< R, C, EigenType >
• denorm_mul() : bpp::ExtendedFloat , bpp::ExtendedFloatEigen< R, C, EigenType >
• denorm_pow() : bpp::ExtendedFloat , bpp::ExtendedFloatEigen< R, C, EigenType >
• denorm_sub() : bpp::ExtendedFloat , bpp::ExtendedFloatEigen< R, C, EigenType >
• Dep : bpp::CategoryFromDiscreteDistribution , bpp::EquilibriumFrequenciesFromModel , bpp::EquilibriumFrequenciesFromTransitionMatrix , bpp::ProbabilitiesFromDiscreteDistribution , bpp::ProbabilitiesFromMixedModel , bpp::ProbabilityFromDiscreteDistribution , bpp::ProbabilityFromMixedModel , bpp::TransitionFunctionFromModel , bpp::TransitionMatrixFromModel , bpp::TransitionMatrixFromTransitionMatrix , bpp::ValueFromConfiguredParameter
• dependencies() : bpp::Node_DF
• dependency() : bpp::Node_DF
• dependencyNodes_ : bpp::Node_DF
• dependentNodes() : bpp::Node_DF
• dependentNodes_ : bpp::Node_DF
• DepF : bpp::Convert< R, F >
• DepT0 : bpp::MatrixProduct< R, T0, T1 >
• DepT1 : bpp::MatrixProduct< R, T0, T1 >
• DepType : bpp::NumericalDependencyTransform< T > , bpp::NumericalDependencyTransform< Transposed< T > >
• der_ : bpp::ExtendedFloatEigenBase< Derived >
• derive() : 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::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
• deriveAsValue() : bpp::Value< T >
• derived() : bpp::ExtendedFloatEigenBase< Derived >
• description() : bpp::CombineDeltaShifted< T > , 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::MatrixProduct< R, T0, T1 > , bpp::Node_DF , bpp::NumericConstant< T > , bpp::NumericMutable< T > , bpp::Sequence_DF , bpp::ShiftParameter , bpp::TransitionFunctionFromModel , bpp::TransitionMatrixFromModel , bpp::TransitionMatrixFromTransitionMatrix , bpp::ValueFromConfiguredParameter
• detailedEvolve() : bpp::AbstractMutationProcess , bpp::MutationProcess
• DetailedSiteSimulatorInterface() : bpp::DetailedSiteSimulatorInterface
• dEvolve() : bpp::NonHomogeneousSequenceSimulator
• dEvolveInternal() : bpp::NonHomogeneousSequenceSimulator
• DFP07() : bpp::DFP07
• DFPDistanceFrequenciesSubstitutionModel() : bpp::DFPDistanceFrequenciesSubstitutionModel
• Dimension() : bpp::Dimension< char > , bpp::Dimension< double > , bpp::Dimension< Eigen::Matrix< T, Rows, Cols > > , bpp::Dimension< ExtendedFloat > , bpp::Dimension< ExtendedFloatEigen< R, C, EigenType > > , bpp::Dimension< float > , bpp::Dimension< Parameter > , bpp::Dimension< size_t > , bpp::Dimension< std::string > , bpp::Dimension< TransitionFunction > , bpp::Dimension< uint >
• disableCG() : bpp::PseudoNewtonOptimizer
• disableExtendedBootstrapProperty() : bpp::Newick
• DiscreteRatesAcrossSitesTreeLikelihoodInterface() : bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface
• displayLikelihood() : bpp::DRHomogeneousMixedTreeLikelihood , bpp::DRHomogeneousTreeLikelihood , bpp::DRNonHomogeneousTreeLikelihood , bpp::RHomogeneousMixedTreeLikelihood , bpp::RHomogeneousTreeLikelihood , bpp::RNonHomogeneousTreeLikelihood
• displayLikelihoodArray() : bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood
• displayParameters() : bpp::BppPhylogeneticsApplication
• dist_ : bpp::DistanceEstimation
• DistanceEstimation() : bpp::DistanceEstimation
• DISTANCEMETHOD_INIT : bpp::OptimizationTools
• DISTANCEMETHOD_ITERATIONS : bpp::OptimizationTools
• DISTANCEMETHOD_PAIRWISE : bpp::OptimizationTools
• DistanceMethodInterface() : bpp::DistanceMethodInterface
• distances_ : bpp::AbstractSinglePhyloSubstitutionMapping , bpp::AbstractSubstitutionDistance
• distancesHaveChanged() : bpp::AbstractSubstitutionDistance , bpp::DecompositionSubstitutionCount , bpp::UniformizationSubstitutionCount
• distanceToFather_ : bpp::AwareNode , bpp::Node
• distColl_ : bpp::CollectionNodes , bpp::SubstitutionProcessCollection
• distrib_ : bpp::ConfiguredDistribution
• distribution() : bpp::MixtureOfATransitionModel
• distributionMap_ : bpp::MixtureOfATransitionModel
• dLik_dt() : bpp::AbstractLkTransitionModel , bpp::BranchModelInterface , bpp::MultinomialFromTransitionModel , bpp::TransitionFromTransitionModel , bpp::TransitionModelInterface
• DNA : bpp::BppOFrequencySetFormat , bpp::BppOSubstitutionModelFormat
• DnDsSubstitutionRegister() : bpp::DnDsSubstitutionRegister
• doInit() : bpp::PseudoNewtonOptimizer
• doNNI() : bpp::DRTreeParsimonyScore , bpp::NNIHomogeneousTreeLikelihood , bpp::NNISearchable
• doStep() : bpp::InOrderTreeIterator , bpp::PseudoNewtonOptimizer
• dot() : bpp::ExtendedFloatEigen< R, C, EigenType >
• dParCondLik_ : bpp::ForwardHmmDLikelihood_DF
• dPi_ : bpp::MultinomialFromTransitionModel , bpp::TransitionFromTransitionModel
• dPij_dt() : bpp::AbstractTotallyWrappedTransitionModel , bpp::AbstractTransitionModel , bpp::BinarySubstitutionModel , bpp::EquiprobableSubstitutionModel , bpp::F81 , bpp::F84 , bpp::HKY85 , bpp::InMixedSubstitutionModel , bpp::JCnuc , bpp::JCprot , bpp::K80 , bpp::MarkovModulatedSubstitutionModel , bpp::MultinomialFromTransitionModel , bpp::OneChangeRegisterTransitionModel , bpp::OneChangeTransitionModel , bpp::RE08 , bpp::T92 , bpp::TN93 , bpp::TransitionFromTransitionModel , bpp::TransitionModelInterface , bpp::TwoParameterBinarySubstitutionModel
• dpij_t : bpp::AbstractFromSubstitutionModelTransitionModel
• dpijt_ : bpp::AbstractTransitionModel , bpp::MarkovModulatedSubstitutionModel
• dpxy_ : bpp::AbstractHomogeneousTreeLikelihood , bpp::AbstractNonHomogeneousTreeLikelihood
• DRASDRTreeLikelihoodData() : bpp::DRASDRTreeLikelihoodData
• DRASDRTreeLikelihoodLeafData() : bpp::DRASDRTreeLikelihoodLeafData
• DRASDRTreeLikelihoodNodeData() : bpp::DRASDRTreeLikelihoodNodeData
• DRASRTreeLikelihoodData() : bpp::DRASRTreeLikelihoodData
• DRASRTreeLikelihoodNodeData() : bpp::DRASRTreeLikelihoodNodeData
• drawAtBranch() : bpp::AbstractTreeDrawing
• drawAtNode() : bpp::AbstractTreeDrawing
• DrawBranchEvent() : bpp::DrawBranchEvent
• drawDendrogram_() : bpp::AbstractDendrogramPlot , bpp::CladogramPlot , bpp::PhylogramPlot
• DrawIBranchEvent() : bpp::DrawIBranchEvent
• DrawINodeEvent() : bpp::DrawINodeEvent
• DrawNodeEvent() : bpp::DrawNodeEvent
• DrawTreeEvent() : bpp::DrawTreeEvent
• DRHomogeneousMixedTreeLikelihood() : bpp::DRHomogeneousMixedTreeLikelihood , bpp::DRHomogeneousTreeLikelihood
• DRHomogeneousTreeLikelihood() : bpp::DRHomogeneousTreeLikelihood
• DRNonHomogeneousMixedTreeLikelihood : bpp::DRNonHomogeneousTreeLikelihood
• DRNonHomogeneousTreeLikelihood() : bpp::DRNonHomogeneousTreeLikelihood
• dropLeaf() : bpp::TreeTemplateTools
• dropSubtree() : bpp::TreeTemplateTools
• DRTreeLikelihoodInterface() : bpp::DRTreeLikelihoodInterface
• DRTreeParsimonyData() : bpp::DRTreeParsimonyData
• DRTreeParsimonyLeafData() : bpp::DRTreeParsimonyLeafData
• DRTreeParsimonyNodeData() : bpp::DRTreeParsimonyNodeData
• DRTreeParsimonyScore() : bpp::DRTreeParsimonyScore
• dSimulateSite() : bpp::DetailedSiteSimulatorInterface , bpp::NonHomogeneousSequenceSimulator , bpp::SimpleSubstitutionProcessSiteSimulator
• DSO78() : bpp::DSO78