- d -

D1WalkSubstitutionModel() : bpp::D1WalkSubstitutionModel
d2Lik_dt2() : bpp::AbstractLkTransitionModel, bpp::BranchModelInterface, bpp::MultinomialFromTransitionModel, bpp::TransitionFromTransitionModel, bpp::TransitionModelInterface
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::OneChangeRegisterTransitionModel, bpp::OneChangeTransitionModel, bpp::RE08, bpp::T92, bpp::TN93, bpp::TransitionModelInterface, bpp::TwoParameterBinarySubstitutionModel
dagToParenthesis() : bpp::ExtendedNewick
data() : bpp::AbstractTreeLikelihood, bpp::DistanceEstimation, bpp::LikelihoodCalculationSingleProcess, bpp::TreeLikelihoodInterface
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
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
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 >
dependencies() : bpp::Node_DF
dependency() : bpp::Node_DF
dependentNodes() : bpp::Node_DF
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
displaySettings() : bpp::AbstractTreeDrawing, bpp::TreeDrawing
DistanceEstimation() : bpp::DistanceEstimation
DistanceMethodInterface() : bpp::DistanceMethodInterface
distancesHaveChanged() : bpp::AbstractSubstitutionDistance, bpp::DecompositionSubstitutionCount, bpp::UniformizationSubstitutionCount
distribution() : bpp::MixtureOfATransitionModel
dLik_dt() : bpp::AbstractLkTransitionModel, bpp::BranchModelInterface, bpp::MultinomialFromTransitionModel, bpp::TransitionFromTransitionModel, bpp::TransitionModelInterface
DnDsSubstitutionRegister() : bpp::DnDsSubstitutionRegister
doInit() : bpp::PseudoNewtonOptimizer
doNNI() : bpp::DRTreeParsimonyScore, bpp::NNIHomogeneousTreeLikelihood, bpp::NNISearchable
doStep() : bpp::InOrderTreeIterator, bpp::PseudoNewtonOptimizer
dot() : bpp::ExtendedFloatEigen< R, C, EigenType >
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::OneChangeRegisterTransitionModel, bpp::OneChangeTransitionModel, bpp::RE08, bpp::T92, bpp::TN93, bpp::TransitionModelInterface, bpp::TwoParameterBinarySubstitutionModel
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
DRHomogeneousTreeLikelihood() : bpp::DRHomogeneousTreeLikelihood
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