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• Identity() : bpp::ExtendedFloatEigen< R, C, EigenType > , bpp::Identity< R >
• IFrequencySet() : bpp::IFrequencySet
• IMultiPhyloDAG() : bpp::IMultiPhyloDAG
• IMultiPhyloTree() : bpp::IMultiPhyloTree
• IMultiTree() : bpp::IMultiTree
• incrementAllIds() : bpp::TreeTemplateTools
• init() : bpp::DRTreeParsimonyData , bpp::GivenDataSubstitutionProcessSiteSimulator , bpp::KrKcSubstitutionRegister , bpp::NonHomogeneousSequenceSimulator , bpp::RNonHomogeneousMixedTreeLikelihood , bpp::SimpleSubstitutionProcessSiteSimulator , bpp::TreeIterator
• init_() : bpp::AbstractHomogeneousTreeLikelihood , bpp::AbstractNonHomogeneousTreeLikelihood , bpp::AbstractTreeParsimonyScore , bpp::DistanceEstimation , bpp::DRHomogeneousTreeLikelihood , bpp::DRNonHomogeneousTreeLikelihood , bpp::DRTreeParsimonyData , bpp::DRTreeParsimonyScore , bpp::RHomogeneousTreeLikelihood , bpp::RNonHomogeneousTreeLikelihood , bpp::SitePatterns
• initBMatrices_() : bpp::DecompositionMethods , bpp::UniformizationSubstitutionCount
• initBranchLengthsGrafen() : bpp::PhyloTreeTools , bpp::TreeTools
• initBranchLengthsParameters() : bpp::AbstractHomogeneousTreeLikelihood , bpp::AbstractNonHomogeneousTreeLikelihood
• initCounts_() : bpp::DecompositionSubstitutionCount
• initGenerators_() : bpp::AbstractKroneckerWordSubstitutionModel
• initialize() : bpp::AbstractHomogeneousTreeLikelihood , bpp::AbstractNonHomogeneousTreeLikelihood , bpp::AbstractTreeLikelihood , bpp::DRHomogeneousMixedTreeLikelihood , bpp::ForwardLikelihoodTree , bpp::RHomogeneousMixedTreeLikelihood , bpp::RNonHomogeneousMixedTreeLikelihood , bpp::TreeLikelihoodInterface
• initialize_() : bpp::BppOFrequencySetFormat , bpp::BppOSubstitutionModelFormat
• initLikelihoods() : bpp::BranchLikelihood , bpp::DRASDRTreeLikelihoodData , bpp::DRASRTreeLikelihoodData
• initLikelihoodsWithPatterns() : bpp::DRASRTreeLikelihoodData
• initModel() : bpp::BranchLikelihood
• initParameters() : bpp::AbstractHomogeneousTreeLikelihood , bpp::AbstractNonHomogeneousTreeLikelihood
• initParameters_() : bpp::GlobalClockTreeLikelihoodFunctionWrapper
• initRewards_() : bpp::DecompositionReward
• initSet() : bpp::MvaFrequencySet
• initStates_() : bpp::DecompositionMethods
• InMixedSubstitutionModel() : bpp::InMixedSubstitutionModel
• InOrderTreeIterator() : bpp::InOrderTreeIterator
• insertN() : bpp::MixedSubstitutionModelSet::HyperNode::Node , bpp::ModelPath::PathNode
• intersects() : bpp::MixedSubstitutionModelSet::HyperNode , bpp::MixedSubstitutionModelSet::HyperNode::Node , bpp::ModelPath , bpp::ModelPath::PathNode
• invalidateRecursively() : bpp::Node_DF
• IODAG() : bpp::IODAG
• IoFrequencySet() : bpp::IoFrequencySet
• IOFrequencySetFactory() : bpp::IOFrequencySetFactory
• IoSubstitutionModel() : bpp::IoSubstitutionModel
• IOSubstitutionModelFactory() : bpp::IOSubstitutionModelFactory
• IOTree() : bpp::IOTree
• IOTreeFactory() : bpp::IOTreeFactory
• IPhyloDAG() : bpp::IPhyloDAG
• IPhyloTree() : bpp::IPhyloTree
• isAutonomous() : bpp::TreeDrawingListener , bpp::TreeDrawingListenerAdapter
• isCollapsed() : bpp::TreeDrawingNodeInfo
• isCompatibleWith() : bpp::AbstractSubstitutionProcess , bpp::MultiProcessSequenceEvolution , bpp::OneProcessSequenceEvolution , bpp::SequenceEvolution , bpp::SubstitutionProcessInterface
• isComplete() : bpp::MixedSubstitutionModelSet::HyperNode
• isDiagonalizable() : bpp::AbstractSubstitutionModel , bpp::AbstractTotallyWrappedSubstitutionModel , bpp::InMixedSubstitutionModel , bpp::MarkovModulatedSubstitutionModel , bpp::SubstitutionModelInterface
• isEmpty() : bpp::LegacyAbstractMapping , bpp::LegacyMappingInterface
• isEnabled() : bpp::TreeDrawingListener , bpp::TreeDrawingListenerAdapter
• isFullySetUp() : bpp::NonHomogeneousSubstitutionProcess , bpp::SubstitutionProcessCollectionMember
• isFullySetUpFor() : bpp::SubstitutionModelSet
• isInitialized() : bpp::AbstractPhyloLikelihood , bpp::AbstractPhyloLikelihoodSet , bpp::AbstractTreeLikelihood , bpp::LikelihoodCalculation , bpp::MultiProcessSequencePhyloLikelihood , bpp::OnABranchPhyloLikelihood , bpp::OneProcessSequencePhyloLikelihood , bpp::PhyloLikelihoodInterface , bpp::SingleProcessPhyloLikelihood , bpp::TreeLikelihoodInterface
• isLeaf() : bpp::AwareNode , bpp::Node , bpp::Tree , bpp::TreeTemplate< N >
• isListenerEnabled() : bpp::TreeDrawingDisplayControler
• isMixture() : bpp::NodeEvent , bpp::ProcessComputationNode
• isMultifurcating() : bpp::Tree , bpp::TreeTemplate< N > , bpp::TreeTemplateTools
• isNeighbor() : bpp::DRASDRTreeLikelihoodNodeData , bpp::DRTreeParsimonyNodeData
• isNodeCollapsed() : bpp::AbstractTreeDrawing , bpp::TreeDrawing
• isNonSingular() : bpp::AbstractSubstitutionModel , bpp::AbstractTotallyWrappedSubstitutionModel , bpp::InMixedSubstitutionModel , bpp::MarkovModulatedSubstitutionModel , bpp::SubstitutionModelInterface
• isRoot() : bpp::Tree , bpp::TreeTemplate< N > , bpp::TreeTemplateTools
• isRooted() : bpp::Tree , bpp::TreeTemplate< N >
• isScalable() : bpp::AbstractSubstitutionModel , bpp::AbstractTotallyWrappedSubstitutionModel , bpp::InMixedSubstitutionModel , bpp::MarkovModulatedSubstitutionModel , bpp::SubstitutionModelInterface
• isSorted() : bpp::BipartitionList
• isSpeciation() : bpp::NodeEvent , bpp::ProcessComputationNode
• isStationary() : bpp::CategorySubstitutionRegister , bpp::SubstitutionModelSet , bpp::SubstitutionProcessCollectionMember
• isToleranceReached() : bpp::PseudoNewtonOptimizer::PNStopCondition
• ISubstitutionModel() : bpp::ISubstitutionModel
• isValid() : bpp::Node_DF
• isVerbose() : bpp::AbstractAgglomerativeDistanceMethod , bpp::DistanceMethodInterface
• isWeighted() : bpp::PGMA
• ITree() : bpp::ITree