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• 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
• mapOfProcessSites() : bpp::PartitionSequenceEvolution
• MappingInterface() : bpp::MappingInterface
• MarginalAncestralReconstruction() : bpp::MarginalAncestralReconstruction
• MarkovModulatedFrequencySet() : bpp::MarkovModulatedFrequencySet
• MarkovModulatedStateMap() : bpp::MarkovModulatedStateMap
• MarkovModulatedSubstitutionModel() : bpp::MarkovModulatedSubstitutionModel
• matching_functor() : bpp::CWiseMatching< R, ReductionOf< T > >::matching_functor
• matchParametersValues() : bpp::AbstractSinglePhyloSubstitutionMapping , bpp::DistanceEstimation , bpp::PhyloSubstitutionMapping , bpp::ProcessTree , bpp::SubstitutionProcessCollectionMember
• 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 >
• maxCoeff() : bpp::ExtendedFloatEigen< R, C, EigenType >
• mean() : bpp::ExtendedFloatEigen< R, C, EigenType > , bpp::ExtendedFloatVectorwiseOp< DerivedEF, MatType, Direction >
• mergeBipartitionLists() : bpp::BipartitionTools
• MG94() : bpp::MG94
• midpointRooting() : bpp::TreeTools
• midRoot() : bpp::TreeTemplateTools
• mixedModel() : bpp::AbstractBiblioMixedTransitionModel , bpp::InMixedSubstitutionModel
• mixedModel_() : bpp::AbstractBiblioMixedTransitionModel , bpp::InMixedSubstitutionModel
• MixedSubstitutionModelSet() : bpp::MixedSubstitutionModelSet
• MixedTransitionModelInterface() : bpp::MixedTransitionModelInterface
• MixtureOfASubstitutionModel() : bpp::MixtureOfASubstitutionModel
• MixtureOfATransitionModel() : bpp::MixtureOfATransitionModel
• MixtureOfSubstitutionModels() : bpp::MixtureOfSubstitutionModels
• MixtureOfTransitionModels() : bpp::MixtureOfTransitionModels
• MixtureProcessPhyloLikelihood() : bpp::MixtureProcessPhyloLikelihood
• MixtureSequenceEvolution() : bpp::MixtureSequenceEvolution
• 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::SimpleSubstitutionProcess , bpp::SubstitutionModelSet , bpp::SubstitutionProcessCollection , bpp::SubstitutionProcessCollectionMember , bpp::SubstitutionProcessInterface , bpp::TransitionFromTransitionModel , bpp::TreeLikelihoodInterface::ConstBranchModelDescription , bpp::TreeLikelihoodInterface::ConstSiteModelDescription , bpp::WrappedModelInterface
• model_() : bpp::AbstractFromSubstitutionModelTransitionModel , bpp::AbstractWrappedTransitionModel , bpp::TransitionFromTransitionModel
• ModelList() : bpp::ModelList
• ModelPath() : bpp::ModelPath
• ModelScenario() : bpp::ModelScenario
• modify() : bpp::Value< T >
• Moments_() : bpp::PhyloTreeTools::Moments_ , bpp::TreeTools::Moments_
• MRP() : bpp::TreeTools
• MRPEncode() : bpp::BipartitionTools , bpp::TreeTools
• MRPEncodeMultilabel() : bpp::BipartitionTools , bpp::TreeTools
• MRPMultilabel() : bpp::TreeTools
• 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