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

- d -

• d2Likelihoods_ : bpp::TwoTreeLikelihood
• d2Pij_dt2() : bpp::AbstractBiblioSubstitutionModel , bpp::BinarySubstitutionModel , bpp::JCnuc , bpp::SubstitutionModel , bpp::K80 , bpp::MarkovModulatedSubstitutionModel , bpp::RN95 , bpp::RN95s , bpp::AbstractSubstitutionModel , bpp::F84 , bpp::T92 , bpp::TN93 , bpp::HKY85 , bpp::JCprot , bpp::RE08
• d2pijt_ : bpp::AbstractSubstitutionModel , bpp::MarkovModulatedSubstitutionModel
• d2pxy_ : bpp::TwoTreeLikelihood , bpp::AbstractHomogeneousTreeLikelihood , bpp::AbstractNonHomogeneousTreeLikelihood
• d_ : bpp::GTR
• data_ : bpp::AbstractTreeLikelihood , bpp::AbstractTreeParsimonyScore
• DAYHOFF_SCHWARTZ_ORCUTT : bpp::SubstitutionModelFactory
• DecompositionSubstitutionCount() : bpp::DecompositionSubstitutionCount
• DEFAULT_SETTINGS : bpp::AbstractTreeDrawing
• defaultOptimizer_ : bpp::DistanceEstimation
• defineParameters() : bpp::MvaFrequenciesSet
• degree() : bpp::Node
• deleteBipartition() : bpp::BipartitionList
• deleteBranchLengths() : bpp::TreeTemplateTools
• deleteBranchProperties() : bpp::Node
• deleteBranchProperty() : bpp::Node
• deleteDistanceToFather() : bpp::Node , bpp::Tree , bpp::TreeTemplate< N >
• deleteName() : bpp::Node
• deleteNodeName() : bpp::Tree , bpp::TreeTemplate< N >
• deleteNodeProperties() : bpp::Node
• deleteNodeProperty() : bpp::Node
• deleteSubtree() : bpp::TreeTemplateTools
• delta_ : bpp::RN95 , bpp::RN95s , bpp::SSR
• detailedEvolve() : bpp::MutationProcess , bpp::AbstractMutationProcess
• DetailedSiteSimulator() : bpp::DetailedSiteSimulator
• dEvolve() : bpp::NonHomogeneousSequenceSimulator
• dEvolveInternal() : bpp::NonHomogeneousSequenceSimulator
• disableCG() : bpp::PseudoNewtonOptimizer
• disableExtendedBootstrapProperty() : bpp::Newick
• DiscreteRatesAcrossSitesTreeLikelihood() : bpp::DiscreteRatesAcrossSitesTreeLikelihood
• displayLikelihood() : bpp::DRHomogeneousMixedTreeLikelihood , bpp::DRHomogeneousTreeLikelihood , bpp::DRNonHomogeneousTreeLikelihood , bpp::RHomogeneousMixedTreeLikelihood , bpp::RHomogeneousTreeLikelihood , bpp::RNonHomogeneousTreeLikelihood
• displayLikelihoodArray() : bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood
• dist_ : bpp::DistanceEstimation
• DistanceEstimation() : bpp::DistanceEstimation
• DistanceMethod() : bpp::DistanceMethod
• DISTANCEMETHOD_INIT : bpp::OptimizationTools
• DISTANCEMETHOD_ITERATIONS : bpp::OptimizationTools
• DISTANCEMETHOD_PAIRWISE : bpp::OptimizationTools
• distanceToFather_ : bpp::Node
• distributionMap_ : bpp::MixtureOfASubstitutionModel
• dLikelihoods_ : bpp::TwoTreeLikelihood
• DNA : bpp::BppOFrequenciesSetFormat , bpp::BppOSubstitutionModelFormat
• DnDsSubstitutionRegister() : bpp::DnDsSubstitutionRegister
• doInit() : bpp::PseudoNewtonOptimizer
• doNNI() : bpp::NNIHomogeneousTreeLikelihood , bpp::NNISearchable , bpp::DRTreeParsimonyScore
• doStep() : bpp::PseudoNewtonOptimizer
• dPij_dt() : bpp::JCprot , bpp::F84 , bpp::RN95 , bpp::AbstractBiblioSubstitutionModel , bpp::AbstractSubstitutionModel , bpp::BinarySubstitutionModel , bpp::MarkovModulatedSubstitutionModel , bpp::HKY85 , bpp::JCnuc , bpp::K80 , bpp::RN95s , bpp::T92 , bpp::TN93 , bpp::RE08 , bpp::SubstitutionModel
• dpijt_ : bpp::AbstractSubstitutionModel , bpp::MarkovModulatedSubstitutionModel
• dpxy_ : bpp::TwoTreeLikelihood , 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 , bpp::DRHomogeneousMixedTreeLikelihood
• DRHomogeneousTreeLikelihood() : bpp::DRHomogeneousTreeLikelihood
• DRNonHomogeneousMixedTreeLikelihood : bpp::DRNonHomogeneousTreeLikelihood
• DRNonHomogeneousTreeLikelihood() : bpp::DRNonHomogeneousTreeLikelihood
• dropLeaf() : bpp::TreeTemplateTools
• dropSubtree() : bpp::TreeTemplateTools
• DRTreeLikelihood() : bpp::DRTreeLikelihood
• DRTreeParsimonyData() : bpp::DRTreeParsimonyData
• DRTreeParsimonyLeafData() : bpp::DRTreeParsimonyLeafData
• DRTreeParsimonyNodeData() : bpp::DRTreeParsimonyNodeData
• DRTreeParsimonyScore() : bpp::DRTreeParsimonyScore
• dSimulate() : bpp::DetailedSiteSimulator , bpp::NonHomogeneousSequenceSimulator , bpp::DetailedSiteSimulator , bpp::NonHomogeneousSequenceSimulator , bpp::DetailedSiteSimulator , bpp::NonHomogeneousSequenceSimulator
• DSO78() : bpp::DSO78