bpp-phyl3
3.0.0
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- 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
Generated on Tue Jun 10 2025 12:12:11 for bpp-phyl3 by
1.9.4