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::AbstractTreeDrawing, 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::TreeDrawing, 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::AbstractTreeDrawing, 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