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

- m -

• m_ : bpp::LaplaceSubstitutionCount
• m_arg_ : bpp::CWiseCompound< R, ReductionOf< T > >::compound_functor , bpp::CWiseMatching< R, ReductionOf< T > >::matching_functor , bpp::CWisePattern< R >::pattern_functor
• main_ : bpp::RNonHomogeneousMixedTreeLikelihood
• majorityConsensus() : bpp::TreeTools
• makeBackwardLikelihoodAtEdge() : bpp::BackwardLikelihoodTree
• makeBackwardLikelihoodAtNode() : bpp::BackwardLikelihoodTree
• makeForwardLikelihoodAtEdge() : bpp::ForwardLikelihoodTree
• makeForwardLikelihoodAtNode() : bpp::ForwardLikelihoodTree
• makeForwardLikelihoodTree_() : bpp::LikelihoodCalculationSingleProcess
• makeInitialConditionalLikelihood() : bpp::ForwardLikelihoodTree
• makeInvalid() : bpp::Node_DF
• makeLikCal_() : bpp::PartitionProcessPhyloLikelihood
• makeLikelihoods() : bpp::AlignedLikelihoodCalculation , bpp::HmmLikelihood_DF , bpp::LikelihoodCalculation , bpp::LikelihoodCalculationOnABranch , bpp::LikelihoodCalculationSingleProcess , bpp::PhyloLikelihoodFormula
• makeLikelihoodsAtDAGNode_() : bpp::LikelihoodCalculationSingleProcess
• makeLikelihoodsAtNode_() : bpp::LikelihoodCalculationSingleProcess
• makeLikelihoodsAtRoot_() : bpp::LikelihoodCalculationSingleProcess
• makeLikelihoodsFromOperator() : bpp::PhyloLikelihoodFormula
• makeLikelihoodsTree() : bpp::LikelihoodCalculationSingleProcess
• makeProbaAtEdge_() : bpp::ProbabilityDAG
• makeProbaAtNode_() : bpp::ProbabilityDAG
• makeProcessNodes_() : bpp::LikelihoodCalculationSingleProcess
• makeProcessTree() : bpp::ProcessTree
• makeRootFreqs_() : bpp::LikelihoodCalculationSingleProcess
• makeValid() : bpp::Node_DF
• mapEdgesIndexes_ : bpp::ForwardLikelihoodTree
• mapFact_ : bpp::MultinomialFromTransitionModel
• mapNodesIndexes_ : bpp::ForwardLikelihoodTree
• mapOfProcessSites() : bpp::PartitionSequenceEvolution
• mapParNamesFromPmodel_ : bpp::AbstractBiblioTransitionModel
• mapping_ : bpp::LegacyProbabilisticRewardMapping , bpp::LegacyProbabilisticSubstitutionMapping
• MappingInterface() : bpp::MappingInterface
• mapTree : bpp::ProbabilisticRewardMapping , bpp::ProbabilisticSubstitutionMapping
• MarginalAncestralReconstruction() : bpp::MarginalAncestralReconstruction
• MarkovModulatedFrequencySet() : bpp::MarkovModulatedFrequencySet
• MarkovModulatedStateMap() : bpp::MarkovModulatedStateMap
• MarkovModulatedSubstitutionModel() : bpp::MarkovModulatedSubstitutionModel
• mat_ : bpp::ExtendedFloatEigen< R, C, EigenType >
• matching_ : bpp::CWiseMatching< R, ReductionOf< T > >::matching_functor
• matching_functor() : bpp::CWiseMatching< R, ReductionOf< T > >::matching_functor
• matchParametersValues() : bpp::AbstractSinglePhyloSubstitutionMapping , bpp::DistanceEstimation , bpp::PhyloSubstitutionMapping , bpp::ProcessTree , bpp::SubstitutionProcessCollectionMember
• matrix_ : bpp::AbstractAgglomerativeDistanceMethod , bpp::GeneralSubstitutionRegister , bpp::HmmLikelihood_DF
• MatrixDimension() : bpp::Dimension< Eigen::Matrix< T, Rows, Cols > > , bpp::Dimension< ExtendedFloatEigen< R, C, EigenType > > , bpp::MatrixDimension , bpp::RowVectorDimension , bpp::VectorDimension
• MatrixProduct() : bpp::MatrixProduct< R, T0, T1 >
• MatType : bpp::ExtendedFloatArrayWrapper< R, C > , bpp::ExtendedFloatEigen< R, C, EigenType >
• maxCoeff() : bpp::ExtendedFloatEigen< R, C, EigenType >
• maxCorrection_ : bpp::PseudoNewtonOptimizer
• maximumBrLen_ : bpp::AbstractHomogeneousTreeLikelihood , bpp::AbstractNonHomogeneousTreeLikelihood , bpp::ParametrizablePhyloTree
• maxIndex_ : bpp::AbstractTreeLikelihood::SimpleSiteIterator
• mData_ : bpp::PartitionProcessPhyloLikelihood
• mDistToSubPro_ : bpp::SubstitutionProcessCollection
• mean() : bpp::ExtendedFloatEigen< R, C, EigenType > , bpp::ExtendedFloatVectorwiseOp< DerivedEF, MatType, Direction >
• MEDIAN : bpp::HierarchicalClustering
• mergeBipartitionLists() : bpp::BipartitionTools
• message_ : bpp::TopologyChangeEvent
• messenger : bpp::OptimizationTools::OptimizationOptions
• messenger_ : bpp::NNITopologyListener2 , bpp::NNITopologyListener
• method_ : bpp::HierarchicalClustering
• mFreqToSubPro_ : bpp::SubstitutionProcessCollection
• MG94() : bpp::MG94
• mgmtStopCodon_ : bpp::CodonFromIndependentFrequencySet , bpp::CodonFromUniqueFrequencySet
• midpointRooting() : bpp::TreeTools
• midRoot() : bpp::TreeTemplateTools
• MIDROOT_SUM_OF_SQUARES : bpp::TreeTemplateTools
• MIDROOT_VARIANCE : bpp::TreeTemplateTools
• minimumBrLen_ : bpp::AbstractHomogeneousTreeLikelihood , bpp::AbstractNonHomogeneousTreeLikelihood , bpp::ParametrizablePhyloTree
• minusLogLik_ : bpp::AbstractPhyloLikelihood , bpp::DRHomogeneousTreeLikelihood , bpp::DRNonHomogeneousTreeLikelihood , bpp::RHomogeneousTreeLikelihood , bpp::RNonHomogeneousTreeLikelihood
• miu_ : bpp::UniformizationSubstitutionCount
• mixedModel() : bpp::AbstractBiblioMixedTransitionModel , bpp::InMixedSubstitutionModel
• mixedModel_() : bpp::AbstractBiblioMixedTransitionModel , bpp::InMixedSubstitutionModel
• mixedModelPtr_ : bpp::AbstractBiblioMixedTransitionModel , bpp::InMixedSubstitutionModel
• mixedSubModelPtr_ : bpp::DFP07 , bpp::YNGP_M
• MixedSubstitutionModelSet() : bpp::MixedSubstitutionModelSet
• MixedTransitionModelInterface() : bpp::MixedTransitionModelInterface
• mixtName_ : bpp::FromMixtureSubstitutionModel , bpp::InMixedSubstitutionModel
• mixtureEvent : bpp::NodeEvent
• MixtureOfASubstitutionModel() : bpp::MixtureOfASubstitutionModel
• MixtureOfATransitionModel() : bpp::MixtureOfATransitionModel
• MixtureOfSubstitutionModels() : bpp::MixtureOfSubstitutionModels
• MixtureOfTransitionModels() : bpp::MixtureOfTransitionModels
• MixtureProcessPhyloLikelihood() : bpp::MixtureProcessPhyloLikelihood
• MixtureSequenceEvolution() : bpp::MixtureSequenceEvolution
• mModBrid_ : bpp::AbstractSinglePhyloSubstitutionMapping
• mModelScenario_ : bpp::SubstitutionProcessCollection
• mModelToSubPro_ : bpp::SubstitutionProcessCollection
• mModPath_ : bpp::ModelPath
• model() : bpp::AbstractBiblioMixedTransitionModel , bpp::AbstractFromSubstitutionModelTransitionModel , bpp::AbstractTreeLikelihood::ConstNoPartitionBranchModelDescription , bpp::AbstractTreeLikelihood::ConstNoPartitionSiteModelDescription , bpp::AbstractWrappedTransitionModel , bpp::CollectionNodes , bpp::FromModelFrequencySet , bpp::MixedTransitionModelInterface , bpp::MixtureOfATransitionModel , bpp::MixtureOfTransitionModels , bpp::MultinomialFromTransitionModel , bpp::NonHomogeneousSubstitutionProcess , bpp::ProcessEdge , bpp::RateAcrossSitesSubstitutionProcess , bpp::SimData , bpp::SimpleSubstitutionProcess , bpp::SubstitutionModelSet , bpp::SubstitutionProcessCollection , bpp::SubstitutionProcessCollectionMember , bpp::SubstitutionProcessInterface , bpp::TransitionFromTransitionModel , bpp::TreeLikelihoodInterface::ConstBranchModelDescription , bpp::TreeLikelihoodInterface::ConstSiteModelDescription , bpp::WrappedModelInterface
• model_() : bpp::AbstractFromSubstitutionModelTransitionModel , bpp::AbstractHomogeneousTreeLikelihood , bpp::AbstractMutationProcess , bpp::AbstractTreeLikelihood::ConstNoPartitionBranchModelDescription , bpp::AbstractTreeLikelihood::ConstNoPartitionSiteModelDescription , bpp::AbstractWrappedTransitionModel , bpp::BranchLikelihood , bpp::ConfiguredModel , bpp::DecompositionMethods , bpp::FromModelFrequencySet , bpp::gBGC , bpp::LaplaceSubstitutionCount , bpp::LikelihoodCalculationOnABranch , bpp::MarkovModulatedSubstitutionModel , bpp::MvaFrequencySet , bpp::OneJumpSubstitutionCount , bpp::ProcessComputationEdge , bpp::ProcessEdge , bpp::RateAcrossSitesSubstitutionProcess , bpp::SimpleSubstitutionProcess , bpp::TransitionFromTransitionModel , bpp::UniformizationSubstitutionCount
• modelChanged_ : bpp::OneChangeRegisterTransitionModel
• modelColl_ : bpp::AbstractSinglePhyloSubstitutionMapping , bpp::CollectionNodes , bpp::SubstitutionProcessCollection
• ModelList() : bpp::ModelList
• modelNames_ : bpp::PairedSiteLikelihoods
• modelNode_ : bpp::LikelihoodCalculationSingleProcess::ProcessNodes
• modelParameters_ : bpp::NonHomogeneousSubstitutionProcess , bpp::SubstitutionModelSet
• ModelPath() : bpp::ModelPath
• models_ : bpp::ModelList
• ModelScenario() : bpp::ModelScenario
• modelScenario_ : bpp::AbstractAutonomousSubstitutionProcess
• modelsContainer_ : bpp::AbstractMixedTransitionModel
• modelSet_ : bpp::AbstractNonHomogeneousTreeLikelihood , bpp::NonHomogeneousSequenceSimulator , bpp::NonHomogeneousSubstitutionProcess , bpp::SubstitutionModelSet
• modelToNodes_ : bpp::NonHomogeneousSubstitutionProcess , bpp::SubstitutionModelSet , bpp::SubstitutionProcessCollectionMember
• modelTree : bpp::AbstractSinglePhyloSubstitutionMapping
• modify() : bpp::Value< T >
• Moments_() : bpp::PhyloTreeTools::Moments_ , bpp::TreeTools::Moments_
• mPhylo_ : bpp::PhyloLikelihoodContainer
• mProcess_ : bpp::SubstitutionProcessSequenceSimulator
• mProcPos_ : bpp::PartitionSequenceEvolution
• MRP() : bpp::TreeTools
• MRPEncode() : bpp::BipartitionTools , bpp::TreeTools
• MRPEncodeMultilabel() : bpp::BipartitionTools , bpp::TreeTools
• MRPMultilabel() : bpp::TreeTools
• mSeqEvol_ : bpp::MixtureProcessPhyloLikelihood , bpp::MultiProcessSequencePhyloLikelihood , bpp::OneProcessSequencePhyloLikelihood , bpp::PartitionProcessPhyloLikelihood
• mStopNeigh_ : bpp::CodonFromIndependentFrequencySet , bpp::CodonFromUniqueFrequencySet
• mSubProcess_ : bpp::SubstitutionProcessCollection
• mTargetDimension_ : bpp::LogSumExp< R, T0, T1 > , bpp::SumOfLogarithms< F >
• mTreeToSubPro_ : bpp::SubstitutionProcessCollection
• mu_ : bpp::RE08 , bpp::TwoParameterBinarySubstitutionModel
• MulCost : Eigen::NumTraits< bpp::ExtendedFloat >
• MultinomialFromTransitionModel() : bpp::MultinomialFromTransitionModel
• multipleEvolve() : bpp::NonHomogeneousSequenceSimulator
• multipleEvolveInternal() : bpp::NonHomogeneousSequenceSimulator
• MultiProcessSequenceEvolution() : bpp::MultiProcessSequenceEvolution
• MultiProcessSequencePhyloLikelihood() : bpp::MultiProcessSequencePhyloLikelihood
• mutate() : bpp::AbstractMutationProcess , bpp::MutationProcess
• mutationModel() : bpp::POMO
• MutationPath() : bpp::MutationPath
• MutationProcess() : bpp::MutationProcess
• MvaFrequencySet() : bpp::MvaFrequencySet
• mVConstDist_ : bpp::SubstitutionProcessCollection
• mvPosNames_ : bpp::SubstitutionProcessSequenceSimulator
• mvTreeLikelihoods_ : bpp::RNonHomogeneousMixedTreeLikelihood