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

- p -

• p_ : bpp::BinarySubstitutionModel
• P_ : bpp::CoalaCore
• p_ : bpp::EquiprobableSubstitutionModel , bpp::F81 , bpp::F84 , bpp::GTR , bpp::HKY85 , bpp::JCnuc , bpp::JCprot , bpp::K80 , bpp::RE08 , bpp::T92 , bpp::TN93 , bpp::TwoParameterBinarySubstitutionModel
• pAAmodel_ : bpp::AbstractCodonAARateSubstitutionModel , bpp::CodonSameAARateSubstitutionModel
• PairedSiteLikelihoods() : bpp::PairedSiteLikelihoods
• param_ : bpp::Coala
• parameter() : bpp::LegacyOptimizationTools::ScaleFunction
• parameters : bpp::OptimizationTools::OptimizationOptions
• parameters_ : bpp::DistanceEstimation , bpp::NNITopologyListener2 , bpp::NNITopologyListener
• parametrizablePhyloTree() : bpp::AbstractAutonomousSubstitutionProcess
• ParametrizablePhyloTree() : bpp::ParametrizablePhyloTree , bpp::PhyloBranchParam
• parametrizablePhyloTree() : bpp::SubstitutionProcessCollectionMember , bpp::SubstitutionProcessInterface
• params_ : bpp::PseudoNewtonOptimizer
• paramValues_ : bpp::CoalaCore , bpp::MvaFrequencySet
• parCondLik_ : bpp::ForwardHmmLikelihood_DF
• parenthesisToNode() : bpp::ExtendedNewick , bpp::Newick , bpp::Nhx , bpp::TreeTemplateTools
• parenthesisToPhyloDAG() : bpp::ExtendedNewick
• parenthesisToPhyloTree() : bpp::Newick , bpp::Nhx
• parenthesisToTree() : bpp::Nhx , bpp::TreeTemplateTools
• parsimonyData_ : bpp::DRTreeParsimonyScore
• PartitionProcessPhyloLikelihood() : bpp::PartitionProcessPhyloLikelihood
• PartitionSequenceEvolution() : bpp::PartitionSequenceEvolution
• path_ : bpp::UserFrequencySet , bpp::UserProteinSubstitutionModel
• PathNode() : bpp::ModelPath::PathNode
• paths_ : bpp::SiteSimulationResult
• pattern_ : bpp::CWisePattern< R >::pattern_functor
• pattern_functor() : bpp::CWisePattern< R >::pattern_functor
• patternedSiteLikelihoods_ : bpp::AlignedLikelihoodCalculation
• patternLinks_ : bpp::DRASRTreeLikelihoodData
• pCodonModel_ : bpp::CodonSameAARateSubstitutionModel
• pdistance_ : bpp::AbstractCodonDistanceSubstitutionModel
• pfitness_ : bpp::POMO
• pfitset_ : bpp::AbstractCodonAAFitnessSubstitutionModel , bpp::AbstractCodonFitnessSubstitutionModel
• pFreq_ : bpp::CodonSameAARateSubstitutionModel , bpp::WordFromUniqueFrequencySet
• pfreqset_ : bpp::AbstractCodonFrequenciesSubstitutionModel
• pgc_ : bpp::CodonFromIndependentFrequencySet , bpp::CodonFromUniqueFrequencySet , bpp::FixedCodonFrequencySet , bpp::FullCodonFrequencySet , bpp::FullPerAACodonFrequencySet , bpp::UserCodonFrequencySet
• pgencode_ : bpp::AbstractCodonAAFitnessSubstitutionModel , bpp::AbstractCodonAARateSubstitutionModel , bpp::AbstractCodonBGCSubstitutionModel , bpp::AbstractCodonClusterAASubstitutionModel , bpp::AbstractCodonDistanceSubstitutionModel , bpp::AbstractCodonFitnessSubstitutionModel , bpp::CodonSameAARateSubstitutionModel
• PGMA() : bpp::PGMA
• phi_ : bpp::CodonSameAARateSubstitutionModel
• phylAlph_ : bpp::HmmPhyloEmissionProbabilities
• PhyloBranch() : bpp::PhyloBranch
• PhyloBranchException() : bpp::PhyloBranchException
• PhyloBranchMapping() : bpp::PhyloBranchMapping
• PhyloBranchNotFoundException() : bpp::PhyloBranchNotFoundException
• PhyloBranchParam() : bpp::PhyloBranchParam
• PhyloBranchPException() : bpp::PhyloBranchPException
• PhyloBranchPropertyNotFoundException() : bpp::PhyloBranchPropertyNotFoundException
• PhyloBranchReward() : bpp::PhyloBranchReward
• PhylogeneticsApplicationTools() : bpp::PhylogeneticsApplicationTools
• PhylogramDrawBranchEvent() : bpp::PhylogramDrawBranchEvent
• PhylogramPlot() : bpp::PhylogramPlot
• PhyloLikelihoodContainer() : bpp::PhyloLikelihoodContainer
• PhyloLikelihoodFormula() : bpp::PhyloLikelihoodFormula
• PhyloLikelihoodInterface() : bpp::PhyloLikelihoodInterface
• PhyloNode() : bpp::PhyloNode
• PhyloNodeException() : bpp::PhyloNodeException
• PhyloNodeNotFoundException() : bpp::PhyloNodeNotFoundException
• PhyloNodePException() : bpp::PhyloNodePException
• PhyloNodePropertyNotFoundException() : bpp::PhyloNodePropertyNotFoundException
• PhyloStatistics() : bpp::PhyloStatistics
• PhyloSubstitutionMapping() : bpp::PhyloSubstitutionMapping
• phyloTree : bpp::LikelihoodCalculationSingleProcess::RateCategoryTrees
• PhyloTree() : bpp::PhyloTree
• phyloTree_ : bpp::NonHomogeneousSequenceSimulator , bpp::SimpleSubstitutionProcessSiteSimulator
• PhyloTreeException() : bpp::PhyloTreeException
• PhyloTreeTools() : bpp::PhyloTreeTools
• PHYML : bpp::NNITopologySearch
• pi0_ : bpp::TwoParameterBinarySubstitutionModel
• Pi_ : bpp::MultinomialFromTransitionModel , bpp::TransitionFromTransitionModel
• piA_ : bpp::F81 , bpp::F84 , bpp::GTR , bpp::HKY85 , bpp::SSR , bpp::T92 , bpp::TN93
• piC_ : bpp::F81 , bpp::F84 , bpp::GTR , bpp::HKY85 , bpp::SSR , bpp::T92 , bpp::TN93
• piG_ : bpp::F81 , bpp::F84 , bpp::GTR , bpp::HKY85 , bpp::SSR , bpp::T92 , bpp::TN93
• pij_t : bpp::AbstractFromSubstitutionModelTransitionModel
• Pij_t() : bpp::AbstractTotallyWrappedTransitionModel , bpp::AbstractTransitionModel , bpp::BinarySubstitutionModel , bpp::EquiprobableSubstitutionModel , bpp::F81 , bpp::F84 , bpp::HKY85 , bpp::InMixedSubstitutionModel , bpp::JCnuc , bpp::JCprot , bpp::K80 , bpp::MarkovModulatedSubstitutionModel , bpp::MultinomialFromTransitionModel , bpp::OneChangeRegisterTransitionModel , bpp::OneChangeTransitionModel , bpp::RE08 , bpp::T92 , bpp::TN93 , bpp::TransitionFromTransitionModel , bpp::TransitionModelInterface , bpp::TwoParameterBinarySubstitutionModel
• pijt_ : bpp::AbstractTransitionModel , bpp::MarkovModulatedSubstitutionModel
• piR_ : bpp::F81 , bpp::F84 , bpp::HKY85 , bpp::TN93
• piT_ : bpp::F81 , bpp::F84 , bpp::GTR , bpp::HKY85 , bpp::SSR , bpp::T92 , bpp::TN93
• piY_ : bpp::F81 , bpp::F84 , bpp::HKY85 , bpp::TN93
• plot() : bpp::AbstractDendrogramPlot , bpp::TreeDrawing
• pMod_ : bpp::ModelBranch
• pmodel_ : bpp::GY94 , bpp::KCM , bpp::MG94 , bpp::POMO , bpp::YN98 , bpp::YpR
• PNStopCondition : bpp::PseudoNewtonOptimizer , bpp::PseudoNewtonOptimizer::PNStopCondition
• pointArea : bpp::TreeDrawingSettings
• pointSize : bpp::TreeDrawingSettings
• POMO() : bpp::POMO
• pOPSP_ : bpp::OneProcessSequenceSubstitutionMapping
• pos : bpp::ProcPos
• pos_ : bpp::GCPositionSubstitutionRegister , bpp::GivenDataSubstitutionProcessSiteSimulator , bpp::TreeDrawingNodeInfo
• posFreqSet_ : bpp::AbstractCodonPhaseFrequenciesSubstitutionModel
• positiveLengths_ : bpp::NeighborJoining
• PostOrderTreeIterator() : bpp::PostOrderTreeIterator
• pow() : bpp::ExtendedFloat
• power_ : bpp::UniformizationSubstitutionCount
• ppfs_ : bpp::FullPerAACodonFrequencySet
• pPhyloCont_ : bpp::AbstractPhyloLikelihoodSet
• pReg_ : bpp::AbstractSinglePhyloSubstitutionMapping
• preg_ : bpp::CompleteSubstitutionRegister
• PreOrderTreeIterator() : bpp::PreOrderTreeIterator
• previousPoint_ : bpp::PseudoNewtonOptimizer
• previousValue_ : bpp::PseudoNewtonOptimizer
• printAnalysisInformation() : bpp::PhylogeneticsApplicationTools
• printParameters() : bpp::LegacyPhylogeneticsApplicationTools , bpp::PhylogeneticsApplicationTools
• proba_ : bpp::MixedSubstitutionModelSet::HyperNode , bpp::ModelPath
• ProbabilisticRewardMapping() : bpp::ProbabilisticRewardMapping
• ProbabilisticSubstitutionMapping() : bpp::ProbabilisticSubstitutionMapping
• ProbabilitiesFromDiscreteDistribution() : bpp::ProbabilitiesFromDiscreteDistribution
• ProbabilitiesFromMixedModel() : bpp::ProbabilitiesFromMixedModel
• ProbabilityDAG : bpp::ForwardLikelihoodTree , bpp::ProbabilityDAG
• ProbabilityFromDiscreteDistribution() : bpp::ProbabilityFromDiscreteDistribution
• ProbabilityFromMixedModel() : bpp::ProbabilityFromMixedModel
• probas_ : bpp::DRHomogeneousMixedTreeLikelihood , bpp::RHomogeneousMixedTreeLikelihood
• process() : bpp::DistanceEstimation
• process_ : bpp::DistanceEstimation , bpp::LikelihoodCalculationSingleProcess , bpp::ProcessComputationTree , bpp::SimpleSubstitutionProcessSiteSimulator
• processColl_ : bpp::HmmProcessAlphabet , bpp::MultiProcessSequenceEvolution
• ProcessComputationEdge() : bpp::ProcessComputationEdge
• ProcessComputationNode() : bpp::ProcessComputationNode
• ProcessComputationTree() : bpp::ProcessComputationTree
• processDistsInSubtree_() : bpp::TreeTemplateTools
• ProcessEdge() : bpp::ProcessEdge
• processNodes_ : bpp::LikelihoodCalculationSingleProcess
• ProcessTree() : bpp::ProcessTree
• processTree_ : bpp::BackwardLikelihoodTree , bpp::ForwardLikelihoodTree
• prodMatrixVector() : bpp::CoalaCore
• profiler : bpp::OptimizationTools::OptimizationOptions
• profiler_ : bpp::NNITopologyListener2 , bpp::NNITopologyListener
• properties_ : bpp::PhyloBranch , bpp::PhyloNode
• propertiesToParenthesis() : bpp::Nhx
• Property() : bpp::Nhx::Property
• PROPERTY_BOOTSTRAP_VALUES : bpp::BasicTreeDrawingDisplayControler
• PROPERTY_BRANCH_LENGTHS : bpp::BasicTreeDrawingDisplayControler
• PROPERTY_LEAF_NAMES : bpp::BasicTreeDrawingDisplayControler
• PROPERTY_NODE_IDS : bpp::BasicTreeDrawingDisplayControler
• propertyName_ : bpp::PhyloBranchPropertyNotFoundException , bpp::PhyloNodePropertyNotFoundException , bpp::PropertyNotFoundException
• PropertyNotFoundException() : bpp::PropertyNotFoundException
• propertyToString_() : bpp::Nhx
• proportion_ : bpp::LG10_EX_EHO::EmbeddedModel , bpp::LGL08_CAT::EmbeddedModel , bpp::LLG08_EHO::EmbeddedModel , bpp::LLG08_EX2::EmbeddedModel , bpp::LLG08_EX3::EmbeddedModel , bpp::LLG08_UL2::EmbeddedModel , bpp::LLG08_UL3::EmbeddedModel
• PROTEIN : bpp::BppOFrequencySetFormat , bpp::BppOSubstitutionModelFormat
• proteinFrequencySet() : bpp::FullPerAACodonFrequencySet
• proteinModel() : bpp::CodonSameAARateSubstitutionModel , bpp::DFP07
• protStateMap_ : bpp::AbstractCodonAAFitnessSubstitutionModel
• pruneTree() : bpp::PhyloTree
• PseudoNewtonOptimizer() : bpp::PseudoNewtonOptimizer
• psites_ : bpp::LikelihoodCalculationSingleProcess
• pSPP_ : bpp::SingleProcessSubstitutionMapping
• pSubProColl_ : bpp::SubstitutionProcessCollectionMember
• pTree_ : bpp::AbstractAutonomousSubstitutionProcess
• pxy_ : bpp::AbstractHomogeneousTreeLikelihood , bpp::AbstractNonHomogeneousTreeLikelihood , bpp::BranchLikelihood