- d -

• d2CondLik_ : bpp::ForwardHmmD2Likelihood_DF
• d2Pi_ : bpp::MultinomialFromTransitionModel , bpp::TransitionFromTransitionModel
• d2Pij_dt2 : bpp::MultinomialFromTransitionModel , bpp::TransitionFromTransitionModel
• d2pij_t : bpp::AbstractFromSubstitutionModelTransitionModel
• d2pijt_ : bpp::AbstractTransitionModel , bpp::MarkovModulatedSubstitutionModel
• d2pxy_ : bpp::AbstractHomogeneousTreeLikelihood , bpp::AbstractNonHomogeneousTreeLikelihood
• d_ : bpp::GTR
• data_ : bpp::AbstractTreeLikelihood , bpp::AbstractTreeParsimonyScore
• dCondLik_ : bpp::ForwardHmmDLikelihood_DF
• DEFAULT_SETTINGS : bpp::AbstractTreeDrawing
• defaultOptimizer_ : bpp::DistanceEstimation
• delta : bpp::NumericalDerivativeConfiguration
• delta_ : bpp::RN95 , bpp::RN95s , bpp::SSR
• dependencyNodes_ : bpp::Node_DF
• dependentNodes_ : bpp::Node_DF
• der_ : bpp::ExtendedFloatEigenBase< Derived >
• dist_ : bpp::DistanceEstimation
• DISTANCEMETHOD_INIT : bpp::OptimizationTools
• DISTANCEMETHOD_ITERATIONS : bpp::OptimizationTools
• DISTANCEMETHOD_PAIRWISE : bpp::OptimizationTools
• distances_ : bpp::AbstractSinglePhyloSubstitutionMapping , bpp::AbstractSubstitutionDistance
• distanceToFather_ : bpp::AwareNode , bpp::Node
• distColl_ : bpp::CollectionNodes , bpp::SubstitutionProcessCollection
• distrib_ : bpp::ConfiguredDistribution
• distributionMap_ : bpp::MixtureOfATransitionModel
• DNA : bpp::BppOFrequencySetFormat , bpp::BppOSubstitutionModelFormat
• dParCondLik_ : bpp::ForwardHmmDLikelihood_DF
• dPi_ : bpp::MultinomialFromTransitionModel , bpp::TransitionFromTransitionModel
• dPij_dt : bpp::MultinomialFromTransitionModel , bpp::TransitionFromTransitionModel
• dpij_t : bpp::AbstractFromSubstitutionModelTransitionModel
• dpijt_ : bpp::AbstractTransitionModel , bpp::MarkovModulatedSubstitutionModel
• dpxy_ : bpp::AbstractHomogeneousTreeLikelihood , bpp::AbstractNonHomogeneousTreeLikelihood