- t -
- T92() : bpp::T92
- targetValue() : bpp::Value< T >
- testBit() : bpp::BipartitionTools
- testNNI() : bpp::DRTreeParsimonyScore, bpp::NNIHomogeneousTreeLikelihood, bpp::NNISearchable
- thresholdConsensus() : bpp::TreeTools
- TN93() : bpp::TN93
- to() : bpp::MixtureOfATransitionModel
- to_string() : bpp::ModelPath::PathNode
- toMatrix() : bpp::BipartitionList
- 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
- toString() : bpp::ModelPath, bpp::ModelScenario, bpp::NodeEvent
- TotalSubstitutionRegister() : bpp::TotalSubstitutionRegister
- toTree() : bpp::BipartitionList
- transform() : bpp::NumericalDependencyTransform< T >, bpp::NumericalDependencyTransform< Transposed< T > >
- TransitionFromTransitionModel() : bpp::TransitionFromTransitionModel
- TransitionFunctionFromModel() : bpp::TransitionFunctionFromModel
- 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::AbstractTreeParsimonyScore
- 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
- TreeLikelihoodTools() : bpp::TreeLikelihoodTools
- TreeParsimonyDataInterface() : bpp::TreeParsimonyDataInterface
- TreeParsimonyNodeDataInterface() : bpp::TreeParsimonyNodeDataInterface
- TreeParsimonyScoreInterface() : bpp::TreeParsimonyScoreInterface
- treeTemplate() : bpp::AbstractTreeDrawing, bpp::AbstractTreeParsimonyScore
- TreeTemplate() : bpp::TreeTemplate< N >
- treeTemplate_() : bpp::AbstractTreeParsimonyScore
- TreeTemplateTools() : bpp::TreeTemplateTools
- TreeTools() : bpp::TreeTools
- treeToParenthesis() : bpp::Newick, bpp::Nhx, bpp::TreeTemplateTools, bpp::TreeTools
- TripletSubstitutionModel() : bpp::TripletSubstitutionModel
- TrivialSitePartition() : bpp::TrivialSitePartition
- TS98() : bpp::TS98
- TsTvSubstitutionRegister() : bpp::TsTvSubstitutionRegister
- TwoParameterBinarySubstitutionModel() : bpp::TwoParameterBinarySubstitutionModel