- a -
- AbstractAgglomerativeDistanceMethod()
: bpp::AbstractAgglomerativeDistanceMethod
- AbstractBiblioMixedSubstitutionModel()
: bpp::AbstractBiblioMixedSubstitutionModel
- AbstractBiblioSubstitutionModel()
: bpp::AbstractBiblioSubstitutionModel
- AbstractCodonDistanceSubstitutionModel()
: bpp::AbstractCodonDistanceSubstitutionModel
- AbstractCodonFitnessSubstitutionModel()
: bpp::AbstractCodonFitnessSubstitutionModel
- AbstractCodonFrequenciesSubstitutionModel()
: bpp::AbstractCodonFrequenciesSubstitutionModel
- AbstractCodonPhaseFrequenciesSubstitutionModel()
: bpp::AbstractCodonPhaseFrequenciesSubstitutionModel
- AbstractCodonSubstitutionModel()
: bpp::AbstractCodonSubstitutionModel
- AbstractDendrogramPlot()
: bpp::AbstractDendrogramPlot
- AbstractDiscreteRatesAcrossSitesTreeLikelihood()
: bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood
- AbstractFrequenciesSet()
: bpp::AbstractFrequenciesSet
- AbstractHomogeneousTreeLikelihood()
: bpp::AbstractHomogeneousTreeLikelihood
- AbstractIDistanceMatrix()
: bpp::AbstractIDistanceMatrix
- AbstractIMultiTree()
: bpp::AbstractIMultiTree
- AbstractITree()
: bpp::AbstractITree
- AbstractMixedSubstitutionModel()
: bpp::AbstractMixedSubstitutionModel
- AbstractMutationProcess()
: bpp::AbstractMutationProcess
- AbstractNonHomogeneousTreeLikelihood()
: bpp::AbstractNonHomogeneousTreeLikelihood
- AbstractODistanceMatrix()
: bpp::AbstractODistanceMatrix
- AbstractOMultiTree()
: bpp::AbstractOMultiTree
- AbstractOTree()
: bpp::AbstractOTree
- AbstractReversibleSubstitutionModel()
: bpp::AbstractReversibleSubstitutionModel
- AbstractStateMap()
: bpp::AbstractStateMap
- AbstractSubstitutionCount()
: bpp::AbstractSubstitutionCount
- AbstractSubstitutionMapping()
: bpp::AbstractSubstitutionMapping
- AbstractSubstitutionModel()
: bpp::AbstractSubstitutionModel
- AbstractSubstitutionRegister()
: bpp::AbstractSubstitutionRegister
- AbstractTreeDrawing()
: bpp::AbstractTreeDrawing
- AbstractTreeLikelihood()
: bpp::AbstractTreeLikelihood
- AbstractTreeLikelihoodData()
: bpp::AbstractTreeLikelihoodData
- AbstractTreeParsimonyData()
: bpp::AbstractTreeParsimonyData
- AbstractTreeParsimonyScore()
: bpp::AbstractTreeParsimonyScore
- AbstractWeightedSubstitutionCount()
: bpp::AbstractWeightedSubstitutionCount
- AbstractWordFrequenciesSet()
: bpp::AbstractWordFrequenciesSet
- AbstractWordSubstitutionModel()
: bpp::AbstractWordSubstitutionModel
- addBipartition()
: bpp::BipartitionList
- addEmptyHyperNode()
: bpp::MixedSubstitutionModelSet
- addEvent()
: bpp::MutationPath
- addHyperNode()
: bpp::MixedSubstitutionModelSet
- addListener()
: bpp::TreeDrawingDisplayControler
- addModel()
: bpp::SubstitutionModelSet
- addNode()
: bpp::SiteSimulationResult
- addRateParameter()
: bpp::AbstractBiblioSubstitutionModel
, bpp::AbstractSubstitutionModel
, bpp::G2001
, bpp::TS98
, bpp::SubstitutionModel
- addSon()
: bpp::Node
- addToHyperNode()
: bpp::MixedSubstitutionModelSet
- addToModel()
: bpp::MixedSubstitutionModelSet::HyperNode
- addTopologyListener()
: bpp::TopologySearch
, bpp::NNITopologySearch
- addTreeDrawingListener()
: bpp::AbstractTreeDrawing
, bpp::TreeDrawing
- addTrivialBipartitions()
: bpp::BipartitionList
- addX()
: bpp::Cursor
- addY()
: bpp::Cursor
- afterDrawBranch()
: bpp::TreeDrawingListener
, bpp::BootstrapValuesTreeDrawingListener
, bpp::BranchLengthsTreeDrawingListener
, bpp::TreeDrawingListenerAdapter
- afterDrawNode()
: bpp::LabelInnerNodesTreeDrawingListener
, bpp::LeafNamesTreeDrawingListener
, bpp::LabelCollapsedNodesTreeDrawingListener
, bpp::TreeDrawingListener
, bpp::NodesIdTreeDrawingListener
, bpp::TreeDrawingListenerAdapter
- afterDrawTree()
: bpp::TreeDrawingListenerAdapter
, bpp::TreeDrawingListener
- AgglomerativeDistanceMethod()
: bpp::AgglomerativeDistanceMethod
- allowWithin()
: bpp::CategorySubstitutionRegister
- AncestralStateReconstruction()
: bpp::AncestralStateReconstruction
- appendModel()
: bpp::PairedSiteLikelihoods
- appendModels()
: bpp::PairedSiteLikelihoods
- applyParameters()
: bpp::RHomogeneousClockTreeLikelihood
, bpp::AbstractHomogeneousTreeLikelihood
, bpp::AbstractNonHomogeneousTreeLikelihood
, bpp::TwoTreeLikelihood
- areAllCompatible()
: bpp::BipartitionList
- areAllCompatibleWith()
: bpp::BipartitionList
- areCompatible()
: bpp::BipartitionTools
, bpp::BipartitionList
- areIdentical()
: bpp::BipartitionList
, bpp::BipartitionTools