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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
• isHybridization() : bpp::NodeEvent
• 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