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• AbstractAgglomerativeDistanceMethod() : bpp::AbstractAgglomerativeDistanceMethod
• AbstractBiblioMixedSubstitutionModel() : bpp::AbstractBiblioMixedSubstitutionModel
• AbstractBiblioSubstitutionModel() : bpp::AbstractBiblioSubstitutionModel
• AbstractCodonDistanceSubstitutionModel() : bpp::AbstractCodonDistanceSubstitutionModel
• AbstractCodonFitnessSubstitutionModel() : bpp::AbstractCodonFitnessSubstitutionModel
• AbstractCodonFrequenciesSubstitutionModel() : bpp::AbstractCodonFrequenciesSubstitutionModel
• AbstractCodonPhaseFrequenciesSubstitutionModel() : bpp::AbstractCodonPhaseFrequenciesSubstitutionModel
• AbstractCodonSubstitutionModel() : bpp::AbstractCodonSubstitutionModel
• AbstractDendrogramPlot() : bpp::AbstractDendrogramPlot
• AbstractDiscreteRatesAcrossSitesTreeLikelihood() : bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood
• AbstractFrequenciesSet() : bpp::AbstractFrequenciesSet
• AbstractHomogeneousTreeLikelihood() : bpp::AbstractHomogeneousTreeLikelihood
• AbstractIDistanceMatrix() : bpp::AbstractIDistanceMatrix
• AbstractIMultiTree() : bpp::AbstractIMultiTree
• AbstractITree() : bpp::AbstractITree
• AbstractMixedSubstitutionModel() : bpp::AbstractMixedSubstitutionModel
• AbstractMutationProcess() : bpp::AbstractMutationProcess
• AbstractNonHomogeneousTreeLikelihood() : bpp::AbstractNonHomogeneousTreeLikelihood
• AbstractODistanceMatrix() : bpp::AbstractODistanceMatrix
• AbstractOMultiTree() : bpp::AbstractOMultiTree
• AbstractOTree() : bpp::AbstractOTree
• AbstractReversibleSubstitutionModel() : bpp::AbstractReversibleSubstitutionModel
• AbstractStateMap() : bpp::AbstractStateMap
• AbstractSubstitutionCount() : bpp::AbstractSubstitutionCount
• AbstractSubstitutionMapping() : bpp::AbstractSubstitutionMapping
• AbstractSubstitutionModel() : bpp::AbstractSubstitutionModel
• AbstractSubstitutionRegister() : bpp::AbstractSubstitutionRegister
• AbstractTreeDrawing() : bpp::AbstractTreeDrawing
• AbstractTreeLikelihood() : bpp::AbstractTreeLikelihood
• AbstractTreeLikelihoodData() : bpp::AbstractTreeLikelihoodData
• AbstractTreeParsimonyData() : bpp::AbstractTreeParsimonyData
• AbstractTreeParsimonyScore() : bpp::AbstractTreeParsimonyScore
• AbstractWeightedSubstitutionCount() : bpp::AbstractWeightedSubstitutionCount
• AbstractWordFrequenciesSet() : bpp::AbstractWordFrequenciesSet
• AbstractWordSubstitutionModel() : bpp::AbstractWordSubstitutionModel
• addBipartition() : bpp::BipartitionList
• addEmptyHyperNode() : bpp::MixedSubstitutionModelSet
• addEvent() : bpp::MutationPath
• addHyperNode() : bpp::MixedSubstitutionModelSet
• addListener() : bpp::TreeDrawingDisplayControler
• addModel() : bpp::SubstitutionModelSet
• addNode() : bpp::SiteSimulationResult
• addRateParameter() : bpp::AbstractBiblioSubstitutionModel , bpp::AbstractSubstitutionModel , bpp::G2001 , bpp::TS98 , bpp::SubstitutionModel
• addSon() : bpp::Node
• addToHyperNode() : bpp::MixedSubstitutionModelSet
• addToModel() : bpp::MixedSubstitutionModelSet::HyperNode
• addTopologyListener() : bpp::TopologySearch , bpp::NNITopologySearch
• addTreeDrawingListener() : bpp::AbstractTreeDrawing , bpp::TreeDrawing
• addTrivialBipartitions() : bpp::BipartitionList
• addX() : bpp::Cursor
• addY() : bpp::Cursor
• afterDrawBranch() : bpp::TreeDrawingListener , bpp::BootstrapValuesTreeDrawingListener , bpp::BranchLengthsTreeDrawingListener , bpp::TreeDrawingListenerAdapter
• afterDrawNode() : bpp::LabelInnerNodesTreeDrawingListener , bpp::LeafNamesTreeDrawingListener , bpp::LabelCollapsedNodesTreeDrawingListener , bpp::TreeDrawingListener , bpp::NodesIdTreeDrawingListener , bpp::TreeDrawingListenerAdapter
• afterDrawTree() : bpp::TreeDrawingListenerAdapter , bpp::TreeDrawingListener
• AgglomerativeDistanceMethod() : bpp::AgglomerativeDistanceMethod
• allowWithin() : bpp::CategorySubstitutionRegister
• AncestralStateReconstruction() : bpp::AncestralStateReconstruction
• appendModel() : bpp::PairedSiteLikelihoods
• appendModels() : bpp::PairedSiteLikelihoods
• applyParameters() : bpp::RHomogeneousClockTreeLikelihood , bpp::AbstractHomogeneousTreeLikelihood , bpp::AbstractNonHomogeneousTreeLikelihood , bpp::TwoTreeLikelihood
• areAllCompatible() : bpp::BipartitionList
• areAllCompatibleWith() : bpp::BipartitionList
• areCompatible() : bpp::BipartitionTools , bpp::BipartitionList
• areIdentical() : bpp::BipartitionList , bpp::BipartitionTools