Here is a list of all class members with links to the classes they belong to:

- t -

• T : bpp::CategoryFromDiscreteDistribution , bpp::EquilibriumFrequenciesFromModel , bpp::EquilibriumFrequenciesFromTransitionMatrix , bpp::FrequenciesFromFrequencySet , bpp::FrequenciesFromSimplex , bpp::ProbabilitiesFromDiscreteDistribution , bpp::ProbabilitiesFromMixedModel , bpp::ProbabilityFromDiscreteDistribution , bpp::ProbabilityFromMixedModel , bpp::Sequence_DF , bpp::TransitionFunctionFromModel , bpp::TransitionMatrixFromModel , bpp::TransitionMatrixFromTransitionMatrix , bpp::ValueFromConfiguredParameter
• T92() : bpp::T92
• tag : bpp::Nhx::Property
• Target : bpp::ConfiguredDistribution , bpp::ConfiguredFrequencySet , bpp::ConfiguredModel , bpp::ConfiguredParameter , bpp::ConfiguredSimplex , bpp::ConfiguredTransitionMatrix
• targetDimension_ : bpp::BackwardHmmLikelihood_DF , bpp::CombineDeltaShifted< T > , bpp::CondLikelihood , bpp::ConstantOne< T > , bpp::ConstantZero< T > , bpp::Convert< R, F > , bpp::CWiseAdd< R, T > , bpp::CWiseAdd< R, ReductionOf< T > > , bpp::CWiseAdd< R, std::tuple< T0, T1 > > , bpp::CWiseApply< R, T, F > , bpp::CWiseCompound< R, ReductionOf< T > > , bpp::CWiseConstantPow< T > , bpp::CWiseDiv< R, std::tuple< T0, T1 > > , bpp::CWiseExp< T > , bpp::CWiseFill< R, T > , bpp::CWiseInverse< T > , bpp::CWiseLog< T > , bpp::CWiseMatching< R, ReductionOf< T > > , bpp::CWiseMean< R, ReductionOf< T >, P > , bpp::CWiseMean< R, ReductionOf< T >, ReductionOf< P > > , bpp::CWiseMul< R, ReductionOf< T > > , bpp::CWiseMul< R, std::tuple< T0, T1 > > , bpp::CWiseNegate< T > , bpp::CWisePattern< R > , bpp::CWiseSub< R, std::tuple< T0, T1 > > , bpp::EquilibriumFrequenciesFromModel , bpp::EquilibriumFrequenciesFromTransitionMatrix , bpp::ForwardHmmD2Likelihood_DF , bpp::ForwardHmmDLikelihood_DF , bpp::ForwardHmmLikelihood_DF , bpp::FrequenciesFromFrequencySet , bpp::FrequenciesFromSimplex , bpp::Identity< R > , bpp::MatrixProduct< R, T0, T1 > , bpp::ShiftDelta< T > , bpp::TransitionFunctionFromModel , bpp::TransitionMatrixFromModel , bpp::TransitionMatrixFromTransitionMatrix
• targetValue() : bpp::Value< T >
• td_ : bpp::DrawBranchEvent , bpp::DrawNodeEvent , bpp::DrawTreeEvent
• temp_ : bpp::SumOfLogarithms< F >
• templateTree_ : bpp::NonHomogeneousSequenceSimulator
• testBit() : bpp::BipartitionTools
• testNNI() : bpp::DRTreeParsimonyScore , bpp::NNIHomogeneousTreeLikelihood , bpp::NNISearchable
• theta1_ : bpp::F81 , bpp::F84 , bpp::GTR , bpp::HKY85 , bpp::TN93
• theta2_ : bpp::F81 , bpp::F84 , bpp::GTR , bpp::HKY85 , bpp::TN93
• theta_ : bpp::F81 , bpp::F84 , bpp::GTR , bpp::HKY85 , bpp::L95 , bpp::SSR , bpp::T92 , bpp::TN93
• thresholdConsensus() : bpp::TreeTools
• time : bpp::PGMAInfos
• times_ : bpp::MutationPath
• tl_ : bpp::GlobalClockTreeLikelihoodFunctionWrapper , bpp::LegacyOptimizationTools::ScaleFunction
• tmp_ : bpp::ExtendedFloatCol< R, C, EigenType > , bpp::ExtendedFloatRow< R, C, EigenType > , bpp::OneJumpSubstitutionCount
• tmpMat_ : bpp::AbstractSubstitutionModel
• TN93() : bpp::TN93
• to() : bpp::MixtureOfATransitionModel
• to_ : bpp::MixtureOfATransitionModel
• to_string() : bpp::ModelPath::PathNode
• tolerance : bpp::OptimizationTools::OptimizationOptions
• tolerance_ : bpp::NNITopologyListener2 , bpp::NNITopologyListener
• toMatrix() : bpp::BipartitionList
• topoListeners_ : bpp::NNITopologySearch
• topology() : bpp::DRTreeParsimonyScore , bpp::NNIHomogeneousTreeLikelihood , bpp::NNISearchable , bpp::NNITopologySearch
• TopologyChangeEvent() : bpp::TopologyChangeEvent
• topologyChangePerformed() : bpp::TopologyListener
• topologyChangeSuccessful() : bpp::DRTreeParsimonyScore , bpp::NNIHomogeneousTreeLikelihood , bpp::NNITopologyListener2 , bpp::NNITopologyListener , bpp::TopologyListener
• topologyChangeTested() : bpp::DRTreeParsimonyScore , bpp::NNIHomogeneousTreeLikelihood , bpp::NNITopologyListener2 , bpp::NNITopologyListener , bpp::TopologyListener
• TopologyListener() : bpp::TopologyListener
• TopologySearch() : bpp::TopologySearch
• topoSearch_ : bpp::NNITopologyListener2 , bpp::NNITopologyListener
• toString() : bpp::ModelPath , bpp::ModelScenario , bpp::NodeEvent
• totalDepth_ : bpp::CladogramPlot , bpp::PhylogramPlot
• TotalSubstitutionRegister() : bpp::TotalSubstitutionRegister
• totalTime_ : bpp::MutationPath
• toTree() : bpp::BipartitionList
• tPpalAxes_ : bpp::MvaFrequencySet
• tr_ : bpp::AbstractDFPSubstitutionModel
• transform() : bpp::NumericalDependencyTransform< T > , bpp::NumericalDependencyTransform< Transposed< T > >
• TransitionFromTransitionModel() : bpp::TransitionFromTransitionModel
• TransitionFunctionFromModel() : bpp::TransitionFunctionFromModel
• transitionMatrix_ : bpp::ProcessEdge
• TransitionMatrixFromModel() : bpp::TransitionMatrixFromModel
• TransitionMatrixFromTransitionMatrix() : bpp::TransitionMatrixFromTransitionMatrix
• transitionModel() : bpp::AbstractBiblioMixedTransitionModel , bpp::AbstractFromSubstitutionModelTransitionModel , bpp::AbstractWrappedSubstitutionModel , bpp::MultinomialFromTransitionModel , bpp::RegisterRatesSubstitutionModel , bpp::TransitionFromTransitionModel , bpp::WrappedTransitionModelInterface
• transitionModel_() : bpp::AbstractBiblioMixedTransitionModel , bpp::AbstractFromSubstitutionModelTransitionModel , bpp::AbstractWrappedSubstitutionModel , bpp::AbstractWrappedTransitionModel , bpp::RegisterRatesSubstitutionModel , bpp::TransitionFromTransitionModel
• TransitionModelInterface() : bpp::TransitionModelInterface
• transpose() : bpp::ExtendedFloatEigen< R, C, EigenType >
• tree() : bpp::AbstractAgglomerativeDistanceMethod , bpp::AbstractTreeLikelihood , bpp::AbstractTreeParsimonyData , bpp::AbstractTreeParsimonyScore , bpp::DistanceMethodInterface , bpp::LegacyAbstractMapping , bpp::LegacyMappingInterface , bpp::NonHomogeneousSequenceSimulator , bpp::OneProcessSequenceEvolution , bpp::OneProcessSequencePhyloLikelihood , bpp::SingleProcessPhyloLikelihood , bpp::SubstitutionProcessCollection
• Tree() : bpp::Tree
• tree() : bpp::TreeLikelihoodInterface , bpp::TreeParsimonyDataInterface , bpp::TreeParsimonyScoreInterface
• tree_ : bpp::AbstractAgglomerativeDistanceMethod , bpp::AbstractTreeDrawing , bpp::AbstractTreeLikelihood , bpp::AbstractTreeLikelihoodData , bpp::AbstractTreeParsimonyData , bpp::AbstractTreeParsimonyScore , bpp::LegacyAbstractMapping , bpp::LegacyMarginalAncestralStateReconstruction , bpp::MarginalAncestralReconstruction , bpp::NonHomogeneousSequenceSimulator , bpp::PhyloTreeException , bpp::SimpleSubstitutionProcessSiteSimulator , bpp::SiteSimulationResult , bpp::StochasticMapping , bpp::TreeException , bpp::TreeIterator
• treeColl_ : bpp::CollectionNodes , bpp::SubstitutionProcessCollection
• TreeDrawing() : bpp::TreeDrawing
• TreeDrawingDisplayControler() : bpp::TreeDrawingDisplayControler
• TreeDrawingListenerAdapter() : bpp::TreeDrawingListenerAdapter
• TreeDrawingNodeInfo() : bpp::TreeDrawingNodeInfo
• TreeDrawingSettings() : bpp::TreeDrawingSettings
• TreeException() : bpp::TreeException
• treeHasChanged() : bpp::AbstractTreeDrawing , bpp::CladogramPlot , bpp::PhylogramPlot
• TreeIterator() : bpp::TreeIterator
• TreeLikelihoodData() : bpp::TreeLikelihoodData
• TreeLikelihoodInterface() : bpp::TreeLikelihoodInterface
• TreeLikelihoodNodeData() : bpp::TreeLikelihoodNodeData
• treeLikelihoodsContainer_ : bpp::DRHomogeneousMixedTreeLikelihood , bpp::RHomogeneousMixedTreeLikelihood
• TreeLikelihoodTools() : bpp::TreeLikelihoodTools
• treeNode_ : bpp::LikelihoodCalculationSingleProcess::ProcessNodes
• TreeParsimonyDataInterface() : bpp::TreeParsimonyDataInterface
• TreeParsimonyNodeDataInterface() : bpp::TreeParsimonyNodeDataInterface
• TreeParsimonyScoreInterface() : bpp::TreeParsimonyScoreInterface
• treePtr_ : bpp::AbstractTreeParsimonyScore
• treeTemplate() : bpp::AbstractTreeParsimonyScore
• TreeTemplate() : bpp::TreeTemplate< N >
• treeTemplate_() : bpp::AbstractTreeParsimonyScore
• TreeTemplateTools : bpp::NodeTemplate< NodeInfos > , bpp::TreeTemplateTools
• TreeTools() : bpp::TreeTools
• treeToParenthesis() : bpp::Newick , bpp::Nhx , bpp::TreeTemplateTools , bpp::TreeTools
• tref_ : bpp::MultinomialFromTransitionModel , bpp::TransitionFromTransitionModel
• TripletSubstitutionModel() : bpp::TripletSubstitutionModel
• TrivialSitePartition() : bpp::TrivialSitePartition
• trr_ : bpp::AbstractDFPSubstitutionModel
• trv_ : bpp::AbstractDFPSubstitutionModel
• TS98() : bpp::TS98
• TsTvSubstitutionRegister() : bpp::TsTvSubstitutionRegister
• tsub_ : bpp::AbstractDFPSubstitutionModel
• tvv_ : bpp::AbstractDFPSubstitutionModel
• TwoParameterBinarySubstitutionModel() : bpp::TwoParameterBinarySubstitutionModel
• type : bpp::Nhx::Property , bpp::NumericalDerivativeConfiguration
• types_ : bpp::GeneralSubstitutionRegister , bpp::KrKcSubstitutionRegister