- a -

• AbstractBiblioMixedTransitionModel : bpp::MixedTransitionModelInterface
• AbstractFromSubstitutionModelTransitionModel : bpp::AbstractLkTransitionModel , bpp::TransitionModelInterface
• AbstractTotallyWrappedTransitionModel : bpp::AbstractLkTransitionModel , bpp::TransitionModelInterface
• AlignedPhyloLikelihoodSet : bpp::AlignedPhyloLikelihoodInterface

- c -

• Context : bpp::Node_DF

- d -

• DRHomogeneousMixedTreeLikelihood : bpp::DRHomogeneousTreeLikelihood
• DRNonHomogeneousMixedTreeLikelihood : bpp::DRNonHomogeneousTreeLikelihood

- e -

• Eigen::internal::nullary_wrapper : bpp::ExtendedFloat
• ExtendedFloatEigen : bpp::ExtendedFloatEigen< R, C, EigenType >::OwnedExtendedFloat

- f -

• ForwardHmmD2Likelihood_DF : bpp::CondLikelihood
• ForwardHmmDLikelihood_DF : bpp::CondLikelihood
• ForwardHmmLikelihood_DF : bpp::CondLikelihood

- g -

• GivenDataSubstitutionProcessSiteSimulator : bpp::SimProcessEdge , bpp::SimProcessNode

- i -

• InMixedSubstitutionModel : bpp::AbstractLkTransitionModel , bpp::MixedTransitionModelInterface , bpp::TransitionModelInterface

- l -

• LikelihoodCalculationOnABranch : bpp::LikelihoodCalculationSingleProcess
• LikelihoodCalculationSingleProcess : bpp::BackwardLikelihoodTree , bpp::ForwardLikelihoodTree

- o -

• OneChangeRegisterTransitionModel : bpp::AbstractSubstitutionModel
• operator<< : bpp::ExtendedFloatEigen< R, C, EigenType >

- p -

• ParametrizablePhyloTree : bpp::PhyloBranchParam
• PNStopCondition : bpp::PseudoNewtonOptimizer
• ProbabilityDAG : bpp::ForwardLikelihoodTree

- r -

• RHomogeneousMixedTreeLikelihood : bpp::RHomogeneousTreeLikelihood
• RNonHomogeneousMixedTreeLikelihood : bpp::RNonHomogeneousTreeLikelihood

- s -

• SimpleSubstitutionProcessSiteSimulator : bpp::SimProcessEdge , bpp::SimProcessNode
• SubstitutionProcessCollection : bpp::SubstitutionProcessCollectionMember

- t -

• TreeTemplateTools : bpp::NodeTemplate< NodeInfos >