- 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