- 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
- param_ : bpp::Coala
- parameters : bpp::OptimizationTools::OptimizationOptions
- parameters_ : bpp::DistanceEstimation, bpp::NNITopologyListener2, bpp::NNITopologyListener
- params_ : bpp::PseudoNewtonOptimizer
- paramValues_ : bpp::CoalaCore, bpp::MvaFrequencySet
- parCondLik_ : bpp::ForwardHmmLikelihood_DF
- PARSIMONY_SOLUTION_STATE : bpp::DRTreeParsimonyScore
- parsimonyData_ : bpp::DRTreeParsimonyScore
- path_ : bpp::UserFrequencySet, bpp::UserProteinSubstitutionModel
- paths_ : bpp::SiteSimulationResult
- pattern_ : 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
- phi_ : bpp::CodonSameAARateSubstitutionModel
- phylAlph_ : bpp::HmmPhyloEmissionProbabilities
- phyloTree : bpp::LikelihoodCalculationSingleProcess::RateCategoryTrees
- phyloTree_ : bpp::NonHomogeneousSequenceSimulator, bpp::SimpleSubstitutionProcessSiteSimulator
- 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::MultinomialFromTransitionModel, bpp::TransitionFromTransitionModel
- 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
- pMod_ : bpp::ModelBranch
- pmodel_ : bpp::GY94, bpp::KCM, bpp::MG94, bpp::POMO, bpp::YN98, bpp::YpR
- pointArea : bpp::TreeDrawingSettings
- pointSize : bpp::TreeDrawingSettings
- pOPSP_ : bpp::OneProcessSequenceSubstitutionMapping
- pos : bpp::ProcPos
- pos_ : bpp::GCPositionSubstitutionRegister, bpp::GivenDataSubstitutionProcessSiteSimulator, bpp::TreeDrawingNodeInfo
- posFreqSet_ : bpp::AbstractCodonPhaseFrequenciesSubstitutionModel
- positiveLengths_ : bpp::NeighborJoining
- power_ : bpp::UniformizationSubstitutionCount
- ppfs_ : bpp::FullPerAACodonFrequencySet
- pPhyloCont_ : bpp::AbstractPhyloLikelihoodSet
- pReg_ : bpp::AbstractSinglePhyloSubstitutionMapping
- preg_ : bpp::CompleteSubstitutionRegister
- previousPoint_ : bpp::PseudoNewtonOptimizer
- previousValue_ : bpp::PseudoNewtonOptimizer
- proba_ : bpp::MixedSubstitutionModelSet::HyperNode, bpp::ModelPath
- probas_ : bpp::DRHomogeneousMixedTreeLikelihood, bpp::RHomogeneousMixedTreeLikelihood
- process_ : bpp::DistanceEstimation, bpp::LikelihoodCalculationSingleProcess, bpp::ProcessComputationTree, bpp::SimpleSubstitutionProcessSiteSimulator
- processColl_ : bpp::HmmProcessAlphabet, bpp::MultiProcessSequenceEvolution
- processNodes_ : bpp::LikelihoodCalculationSingleProcess
- processTree_ : bpp::BackwardLikelihoodTree, bpp::ForwardLikelihoodTree
- profiler : bpp::OptimizationTools::OptimizationOptions
- profiler_ : bpp::NNITopologyListener2, bpp::NNITopologyListener
- properties_ : bpp::PhyloBranch, bpp::PhyloNode
- 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
- 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
- protStateMap_ : bpp::AbstractCodonAAFitnessSubstitutionModel
- psites_ : bpp::LikelihoodCalculationSingleProcess
- pSPP_ : bpp::SingleProcessSubstitutionMapping
- pSubProColl_ : bpp::SubstitutionProcessCollectionMember
- pTree_ : bpp::AbstractAutonomousSubstitutionProcess
- pxy_ : bpp::AbstractHomogeneousTreeLikelihood, bpp::AbstractNonHomogeneousTreeLikelihood, bpp::BranchLikelihood