bpp-phyl3
3.0.0
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- 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
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