- a -

• a_ : bpp::GTR
• algorithm_ : bpp::NNITopologySearch
• ALL : bpp::BppOFrequencySetFormat , bpp::BppOSubstitutionModelFormat
• allowComments_ : bpp::ExtendedNewick , bpp::Newick
• allowConstant_ : bpp::BppORateDistributionFormat
• allowCovarions_ : bpp::BppOSubstitutionModelFormat
• allowed_product_without_normalization : bpp::ExtendedFloat
• allowGaps_ : bpp::BppOSubstitutionModelFormat
• allowMixed_ : bpp::BppOSubstitutionModelFormat
• allowSelf_ : bpp::NaiveSubstitutionCount
• alpha_ : bpp::AbstractCodonDistanceSubstitutionModel , bpp::L95 , bpp::RN95 , bpp::RN95s , bpp::SitePatterns
• alphabet_ : bpp::AbstractFrequencySet , bpp::AbstractStateMap , bpp::AbstractTransitionModel , bpp::AbstractTreeLikelihoodData , bpp::AbstractTreeParsimonyScore , bpp::LegacyMarginalAncestralStateReconstruction , bpp::MarginalAncestralReconstruction , bpp::MutationPath , bpp::NonHomogeneousSequenceSimulator , bpp::SubstitutionModelSet
• alphabetCode_ : bpp::BppOFrequencySetFormat , bpp::BppOSubstitutionModelFormat
• alphIndex_ : bpp::AbstractReward
• ancestralStates_ : bpp::SiteSimulationResult
• angle_ : bpp::Cursor
• annotation : bpp::IODAG::Element , bpp::IOTree::Element
• array1_ : bpp::BranchLikelihood
• array2_ : bpp::BranchLikelihood
• assign_ : bpp::AbstractCodonClusterAASubstitutionModel
• autoCorrTransMat_ : bpp::AutoCorrelationSequenceEvolution
• autonomous_ : bpp::TreeDrawingListenerAdapter
• AVERAGE : bpp::HierarchicalClustering