- g -

• G2001() : bpp::G2001
• GammaDiscreteRateDistribution() : bpp::GammaDiscreteRateDistribution
• GaussianDiscreteRateDistribution() : bpp::GaussianDiscreteRateDistribution
• gBGC() : bpp::gBGC
• GCFrequenciesSet() : bpp::GCFrequenciesSet
• GCSubstitutionRegister() : bpp::GCSubstitutionRegister
• GCSynonymousSubstitutionRegister() : bpp::GCSynonymousSubstitutionRegister
• getAllAncestralStates() : bpp::AncestralStateReconstruction , bpp::MarginalAncestralStateReconstruction
• getAllNumbersOfSubstitutions() : bpp::NaiveSubstitutionCount , bpp::LabelSubstitutionCount , bpp::OneJumpSubstitutionCount , bpp::SubstitutionCount , bpp::UniformizationSubstitutionCount , bpp::DecompositionSubstitutionCount , bpp::LaplaceSubstitutionCount
• getAlphabet() : bpp::FixedCodonFrequenciesSet , bpp::FullPerAACodonFrequenciesSet , bpp::CodonFromIndependentFrequenciesSet , bpp::CodonFromUniqueFrequenciesSet , bpp::FrequenciesSet , bpp::AbstractFrequenciesSet , bpp::MvaFrequenciesSet , bpp::NucleotideFrequenciesSet , bpp::GCFrequenciesSet , bpp::FullNucleotideFrequenciesSet , bpp::AbstractTreeLikelihood , bpp::FixedNucleotideFrequenciesSet , bpp::ProteinFrequenciesSet , bpp::AbstractTreeLikelihoodData , bpp::FullProteinFrequenciesSet , bpp::FixedProteinFrequenciesSet , bpp::TreeLikelihood , bpp::WordFrequenciesSet , bpp::AbstractWordFrequenciesSet , bpp::TreeLikelihoodData , bpp::MarkovModulatedSubstitutionModel , bpp::StateMap , bpp::SubstitutionCount , bpp::AbstractStateMap , bpp::SubstitutionModel , bpp::SubstitutionRegister , bpp::SubstitutionModelSet , bpp::SiteSimulationResult , bpp::AbstractSubstitutionRegister , bpp::MutationPath , bpp::NonHomogeneousSequenceSimulator , bpp::AbstractBiblioSubstitutionModel , bpp::SequenceSimulator , bpp::SiteSimulator , bpp::AbstractSubstitutionModel , bpp::CodonFrequenciesSet , bpp::FullCodonFrequenciesSet
• getAlphabetChar() : bpp::AbstractBiblioSubstitutionModel , bpp::AbstractSubstitutionModel , bpp::MarkovModulatedSubstitutionModel , bpp::SubstitutionModel
• getAlphabetChars() : bpp::MarkovModulatedSubstitutionModel , bpp::SubstitutionModel , bpp::AbstractBiblioSubstitutionModel , bpp::AbstractSubstitutionModel
• getAncestors() : bpp::TreeTools
• getAncestorsId() : bpp::Tree , bpp::TreeTemplate< N > , bpp::TreeTemplateTools
• getAncestralFrequencies() : bpp::TreeLikelihoodTools
• getAncestralFrequencies_() : bpp::TreeLikelihoodTools
• getAncestralSequenceForNode() : bpp::AncestralStateReconstruction , bpp::MarginalAncestralStateReconstruction
• getAncestralSequences() : bpp::AncestralStateReconstruction , bpp::MarginalAncestralStateReconstruction
• getAncestralState() : bpp::SiteSimulationResult
• getAncestralStatesForNode() : bpp::AncestralStateReconstruction , bpp::MarginalAncestralStateReconstruction
• getAngle() : bpp::Cursor
• getArrayPosition() : bpp::DRASDRTreeLikelihoodData , bpp::DRASRTreeLikelihoodData , bpp::TreeLikelihoodData , bpp::DRTreeParsimonyData , bpp::TreeParsimonyData
• getArrayPositions() : bpp::DRASRTreeLikelihoodData
• getBestPair() : bpp::AbstractAgglomerativeDistanceMethod , bpp::HierarchicalClustering , bpp::NeighborJoining , bpp::PGMA
• getBestRootInSubtree() : bpp::TreeTemplateTools
• getBipartition() : bpp::BipartitionList
• getBitBipartition() : bpp::BipartitionList
• getBitBipartitionList() : bpp::BipartitionList
• getBitsetsArray() : bpp::DRTreeParsimonyLeafData , bpp::DRTreeParsimonyData
• getBitsetsArrayForNeighbor() : bpp::DRTreeParsimonyNodeData
• getBootstrapValue() : bpp::Node
• getBranchCursor() : bpp::CladogramDrawBranchEvent , bpp::PhylogramDrawBranchEvent , bpp::DrawBranchEvent
• getBranchesId() : bpp::Tree , bpp::TreeTemplate< N > , bpp::TreeTemplateTools
• getBranchLengths() : bpp::SubstitutionMapping , bpp::AbstractSubstitutionMapping , bpp::PhyloStatistics , bpp::Tree , bpp::TreeTemplate< N > , bpp::TreeTemplateTools , bpp::TreeTools
• getBranchLengthsParameters() : bpp::TwoTreeLikelihood , bpp::AbstractHomogeneousTreeLikelihood , bpp::AbstractNonHomogeneousTreeLikelihood , bpp::TreeLikelihood
• getBranchProperties() : bpp::TreeTemplateTools
• getBranchProperty() : bpp::Node , bpp::Tree , bpp::TreeTemplate< N >
• getBranchPropertyNames() : bpp::Node , bpp::Tree , bpp::TreeTemplate< N > , bpp::TreeTemplateTools
• getCategory() : bpp::CategorySubstitutionRegister
• getCategoryFrom() : bpp::CategorySubstitutionRegister
• getCategoryName() : bpp::CategorySubstitutionRegister
• getCategoryTo() : bpp::CategorySubstitutionRegister
• getCodonsMulRate() : bpp::AbstractCodonDistanceSubstitutionModel , bpp::AbstractCodonFitnessSubstitutionModel , bpp::AbstractCodonFrequenciesSubstitutionModel , bpp::AbstractCodonPhaseFrequenciesSubstitutionModel , bpp::AbstractCodonSubstitutionModel , bpp::CodonDistanceFitnessPhaseFrequenciesSubstitutionModel , bpp::CodonDistanceFrequenciesSubstitutionModel , bpp::CodonDistancePhaseFrequenciesSubstitutionModel , bpp::CodonDistanceSubstitutionModel , bpp::CodonRateFrequenciesSubstitutionModel , bpp::CodonRateSubstitutionModel , bpp::CodonSubstitutionModel
• getColumnRightEigenVectors() : bpp::AbstractBiblioSubstitutionModel , bpp::AbstractSubstitutionModel , bpp::MarkovModulatedSubstitutionModel , bpp::SubstitutionModel
• getColumnWeights() : bpp::CoalaCore
• getCurrentTolerance() : bpp::PseudoNewtonOptimizer::PNStopCondition
• getCursor() : bpp::DrawNodeEvent , bpp::DrawBranchEvent
• getD2LikelihoodArray() : bpp::DRASDRTreeLikelihoodNodeData , bpp::DRASDRTreeLikelihoodData , bpp::DRASRTreeLikelihoodNodeData , bpp::DRASRTreeLikelihoodData
• getD2LikelihoodArrayForNeighbor() : bpp::DRASDRTreeLikelihoodNodeData
• getD2LikelihoodForASite() : bpp::RHomogeneousTreeLikelihood , bpp::RNonHomogeneousTreeLikelihood
• getD2LikelihoodForASiteForARateClass() : bpp::RHomogeneousMixedTreeLikelihood , bpp::RHomogeneousTreeLikelihood , bpp::RNonHomogeneousTreeLikelihood
• getD2LogLikelihood() : bpp::RHomogeneousTreeLikelihood , bpp::RNonHomogeneousTreeLikelihood
• getD2LogLikelihoodForASite() : bpp::RHomogeneousTreeLikelihood , bpp::RNonHomogeneousTreeLikelihood
• getd2Pij_dt2() : bpp::AbstractBiblioSubstitutionModel , bpp::AbstractMixedSubstitutionModel , bpp::AbstractSubstitutionModel , bpp::BinarySubstitutionModel , bpp::MarkovModulatedSubstitutionModel , bpp::F84 , bpp::HKY85 , bpp::JCnuc , bpp::K80 , bpp::RN95 , bpp::RN95s , bpp::T92 , bpp::TN93 , bpp::JCprot , bpp::RE08 , bpp::SubstitutionModel , bpp::WordSubstitutionModel
• getData() : bpp::DistanceEstimation , bpp::AbstractTreeLikelihood , bpp::TreeLikelihood
• getDataType() : bpp::IODistanceMatrix , bpp::IoFrequenciesSet , bpp::IoSubstitutionModel , bpp::IOTree
• getDepth() : bpp::TreeTemplateTools , bpp::TreeTools
• getDepths() : bpp::TreeTemplateTools , bpp::TreeTools
• getDerivableParameters() : bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood , bpp::RHomogeneousClockTreeLikelihood , bpp::TreeLikelihood
• getDescription() : bpp::WordFromIndependentFrequenciesSet , bpp::WordFromUniqueFrequenciesSet
• getDisplaySettings() : bpp::AbstractTreeDrawing , bpp::TreeDrawing
• getDistanceBetweenAnyTwoNodes() : bpp::TreeTemplateTools , bpp::TreeTools
• getDistanceMatrix() : bpp::TreeTemplateTools , bpp::TreeTools
• getDistanceToFather() : bpp::Node , bpp::Tree , bpp::TreeTemplate< N >
• getDistribution() : bpp::MixtureOfASubstitutionModel
• getDLikelihoodArray() : bpp::DRASDRTreeLikelihoodNodeData , bpp::DRASDRTreeLikelihoodData , bpp::DRASRTreeLikelihoodNodeData , bpp::DRASRTreeLikelihoodData
• getDLikelihoodForASite() : bpp::RHomogeneousTreeLikelihood , bpp::RNonHomogeneousTreeLikelihood
• getDLikelihoodForASiteForARateClass() : bpp::RHomogeneousMixedTreeLikelihood , bpp::RHomogeneousTreeLikelihood , bpp::RNonHomogeneousTreeLikelihood
• getDLogLikelihood() : bpp::RHomogeneousTreeLikelihood , bpp::RNonHomogeneousTreeLikelihood
• getDLogLikelihoodForASite() : bpp::RHomogeneousTreeLikelihood , bpp::RNonHomogeneousTreeLikelihood
• getdPij_dt() : bpp::AbstractBiblioSubstitutionModel , bpp::AbstractMixedSubstitutionModel , bpp::AbstractSubstitutionModel , bpp::BinarySubstitutionModel , bpp::MarkovModulatedSubstitutionModel , bpp::F84 , bpp::HKY85 , bpp::JCnuc , bpp::K80 , bpp::RN95 , bpp::RN95s , bpp::T92 , bpp::TN93 , bpp::JCprot , bpp::RE08 , bpp::SubstitutionModel , bpp::WordSubstitutionModel
• getEigenValues() : bpp::AbstractBiblioSubstitutionModel , bpp::AbstractSubstitutionModel , bpp::MarkovModulatedSubstitutionModel , bpp::SubstitutionModel
• getElement() : bpp::Nhx , bpp::TreeTemplateTools
• getElementNames() : bpp::BipartitionList
• getEmpiricalMatrixFile() : bpp::Coala
• getEventCounts() : bpp::MutationPath
• getExch() : bpp::Coala
• getExchangeabilityMatrix() : bpp::AbstractBiblioSubstitutionModel , bpp::AbstractSubstitutionModel , bpp::MarkovModulatedSubstitutionModel , bpp::SubstitutionModel
• getFather() : bpp::Node , bpp::NodeTemplate< NodeInfos >
• getFatherId() : bpp::Node , bpp::Tree , bpp::TreeTemplate< N >
• getFinalState() : bpp::MutationPath
• getFinalStates() : bpp::SiteSimulationResult
• getFirstOrderDerivative() : bpp::TwoTreeLikelihood , bpp::DRHomogeneousMixedTreeLikelihood , bpp::DRHomogeneousTreeLikelihood , bpp::DRNonHomogeneousTreeLikelihood , bpp::GlobalClockTreeLikelihoodFunctionWrapper , bpp::RHomogeneousClockTreeLikelihood , bpp::RHomogeneousTreeLikelihood , bpp::RNonHomogeneousTreeLikelihood
• getFitness() : bpp::AbstractCodonFitnessSubstitutionModel
• getFormatDescription() : bpp::BppOFrequenciesSetFormat , bpp::BppOSubstitutionModelFormat , bpp::Newick , bpp::NexusIOTree , bpp::Nhx , bpp::PhylipDistanceMatrixFormat
• getFormatName() : bpp::BppOFrequenciesSetFormat , bpp::BppOSubstitutionModelFormat , bpp::Newick , bpp::NexusIOTree , bpp::Nhx , bpp::PhylipDistanceMatrixFormat
• getFreq() : bpp::AbstractCodonFitnessSubstitutionModel
• getFreq_() : bpp::AbstractFrequenciesSet
• getFrequencies() : bpp::AbstractBiblioSubstitutionModel , bpp::AbstractSubstitutionModel , bpp::FrequenciesSet , bpp::AbstractFrequenciesSet , bpp::MarkovModulatedSubstitutionModel , bpp::SubstitutionModel
• getFrequencies_() : bpp::AbstractFrequenciesSet
• getFrequenciesSet() : bpp::PhylogeneticsApplicationTools , bpp::AbstractBiblioSubstitutionModel , bpp::AbstractCodonFrequenciesSubstitutionModel , bpp::AbstractCodonPhaseFrequenciesSubstitutionModel , bpp::DSO78 , bpp::JCprot , bpp::JTT92 , bpp::LG08 , bpp::UserProteinSubstitutionModel , bpp::WAG01 , bpp::SubstitutionModel
• getFrequenciesSetForCodons() : bpp::CodonFrequenciesSet
• getFrequenciesSetForLetter() : bpp::WordFrequenciesSet , bpp::WordFromIndependentFrequenciesSet , bpp::WordFromUniqueFrequenciesSet
• getFunction() : bpp::PseudoNewtonOptimizer
• getFunction_() : bpp::PseudoNewtonOptimizer
• getFunctionValue() : bpp::PseudoNewtonOptimizer
• getGenerator() : bpp::AbstractBiblioSubstitutionModel , bpp::AbstractSubstitutionModel , bpp::MarkovModulatedSubstitutionModel , bpp::SubstitutionModel
• getGeneticCode() : bpp::AbstractCodonDistanceSubstitutionModel
• getGraphicDevice() : bpp::DrawNodeEvent , bpp::DrawBranchEvent , bpp::DrawTreeEvent
• getHeight() : bpp::CladogramPlot , bpp::PhylogramPlot , bpp::TreeDrawing , bpp::TreeTemplateTools , bpp::TreeTools
• getHeightParameters() : bpp::GlobalClockTreeLikelihoodFunctionWrapper
• getHeights() : bpp::TreeTemplateTools , bpp::TreeTools
• getHorizontalOrientation() : bpp::AbstractDendrogramPlot
• getHPos() : bpp::Cursor
• getHyperNode() : bpp::RNonHomogeneousMixedTreeLikelihood , bpp::MixedSubstitutionModelSet
• getHyperNodeProbability() : bpp::MixedSubstitutionModelSet
• getId() : bpp::Node , bpp::NodeNotFoundException
• getIEigenValues() : bpp::AbstractBiblioSubstitutionModel , bpp::AbstractSubstitutionModel , bpp::MarkovModulatedSubstitutionModel , bpp::SubstitutionModel
• getIndexes() : bpp::PatternTools
• getIndices() : bpp::SitePatterns
• getInfos() : bpp::NodeTemplate< NodeInfos >
• getInitialState() : bpp::MutationPath
• getInitValue() : bpp::AbstractBiblioSubstitutionModel , bpp::AbstractSubstitutionModel , bpp::MarkovModulatedSubstitutionModel , bpp::RE08 , bpp::SubstitutionModel
• getInnerNodes() : bpp::TreeTemplate< N > , bpp::TreeTemplateTools
• getInnerNodesId() : bpp::Tree , bpp::TreeTemplate< N > , bpp::TreeTemplateTools
• getINode() : bpp::DrawINodeEvent , bpp::DrawIBranchEvent
• getLastCommonAncestor() : bpp::TreeTools
• getLeafData() : bpp::DRASDRTreeLikelihoodData , bpp::DRTreeParsimonyData
• getLeafId() : bpp::Tree , bpp::TreeTemplate< N > , bpp::TreeTemplateTools , bpp::TreeTools
• getLeafLikelihoods() : bpp::DRASDRTreeLikelihoodData
• getLeafNode() : bpp::AbstractAgglomerativeDistanceMethod , bpp::HierarchicalClustering , bpp::PGMA
• getLeaveNames() : bpp::SiteSimulationResult
• getLeaves() : bpp::TreeTemplate< N > , bpp::TreeTemplateTools
• getLeavesId() : bpp::Tree , bpp::TreeTemplate< N > , bpp::TreeTemplateTools , bpp::TreeTools
• getLeavesNames() : bpp::Tree , bpp::TreeTemplate< N > , bpp::TreeTemplateTools
• getLength() : bpp::WordFrequenciesSet , bpp::AbstractWordFrequenciesSet , bpp::WordFromIndependentFrequenciesSet , bpp::WordFromUniqueFrequenciesSet
• getLikelihood() : bpp::TwoTreeLikelihood , bpp::DRHomogeneousMixedTreeLikelihood , bpp::DRHomogeneousTreeLikelihood , bpp::DRNonHomogeneousTreeLikelihood , bpp::RHomogeneousTreeLikelihood , bpp::RNonHomogeneousTreeLikelihood , bpp::TreeLikelihood
• getLikelihoodArray() : bpp::DRASDRTreeLikelihoodLeafData , bpp::DRASDRTreeLikelihoodData , bpp::DRASRTreeLikelihoodNodeData , bpp::DRASRTreeLikelihoodData
• getLikelihoodArrayForNeighbor() : bpp::DRASDRTreeLikelihoodNodeData
• getLikelihoodArrays() : bpp::DRASDRTreeLikelihoodNodeData , bpp::DRASDRTreeLikelihoodData
• getLikelihoodData() : bpp::TwoTreeLikelihood , bpp::DRHomogeneousTreeLikelihood , bpp::DRNonHomogeneousTreeLikelihood , bpp::DRTreeLikelihood , bpp::RHomogeneousTreeLikelihood , bpp::RNonHomogeneousTreeLikelihood , bpp::TreeLikelihood
• getLikelihoodForASite() : bpp::TwoTreeLikelihood , bpp::DRHomogeneousMixedTreeLikelihood , bpp::DRHomogeneousTreeLikelihood , bpp::DRNonHomogeneousTreeLikelihood , bpp::RHomogeneousTreeLikelihood , bpp::RNonHomogeneousTreeLikelihood , bpp::TreeLikelihood
• getLikelihoodForASiteForARateClass() : bpp::TwoTreeLikelihood , bpp::DiscreteRatesAcrossSitesTreeLikelihood , bpp::DRHomogeneousMixedTreeLikelihood , bpp::DRHomogeneousTreeLikelihood , bpp::DRNonHomogeneousTreeLikelihood , bpp::RHomogeneousMixedTreeLikelihood , bpp::RHomogeneousTreeLikelihood , bpp::RNonHomogeneousTreeLikelihood
• getLikelihoodForASiteForARateClassForAState() : bpp::TwoTreeLikelihood , bpp::DiscreteRatesAcrossSitesTreeLikelihood , bpp::DRHomogeneousMixedTreeLikelihood , bpp::DRHomogeneousTreeLikelihood , bpp::DRNonHomogeneousTreeLikelihood , bpp::RHomogeneousMixedTreeLikelihood , bpp::RHomogeneousTreeLikelihood , bpp::RNonHomogeneousTreeLikelihood
• getLikelihoodForASiteForAState() : bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood , bpp::TreeLikelihood
• getLikelihoodForEachSite() : bpp::AbstractTreeLikelihood , bpp::TreeLikelihood
• getLikelihoodForEachSiteForEachRateClass() : bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood , bpp::DiscreteRatesAcrossSitesTreeLikelihood
• getLikelihoodForEachSiteForEachRateClassForEachState() : bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood , bpp::DiscreteRatesAcrossSitesTreeLikelihood
• getLikelihoodForEachSiteForEachState() : bpp::AbstractTreeLikelihood , bpp::TreeLikelihood
• getLikelihoods() : bpp::PairedSiteLikelihoods
• getLogLikelihood() : bpp::TwoTreeLikelihood , bpp::DRHomogeneousMixedTreeLikelihood , bpp::DRHomogeneousTreeLikelihood , bpp::DRNonHomogeneousTreeLikelihood , bpp::RHomogeneousTreeLikelihood , bpp::RNonHomogeneousTreeLikelihood , bpp::TreeLikelihood
• getLogLikelihoodForASite() : bpp::TwoTreeLikelihood , bpp::DRHomogeneousMixedTreeLikelihood , bpp::DRHomogeneousTreeLikelihood , bpp::DRNonHomogeneousTreeLikelihood , bpp::RHomogeneousTreeLikelihood , bpp::RNonHomogeneousTreeLikelihood , bpp::TreeLikelihood
• getLogLikelihoodForASiteForARateClass() : bpp::TwoTreeLikelihood , bpp::DiscreteRatesAcrossSitesTreeLikelihood , bpp::DRHomogeneousMixedTreeLikelihood , bpp::DRHomogeneousTreeLikelihood , bpp::DRNonHomogeneousTreeLikelihood , bpp::RHomogeneousMixedTreeLikelihood , bpp::RHomogeneousTreeLikelihood , bpp::RNonHomogeneousTreeLikelihood
• getLogLikelihoodForASiteForARateClassForAState() : bpp::TwoTreeLikelihood , bpp::DiscreteRatesAcrossSitesTreeLikelihood , bpp::DRHomogeneousMixedTreeLikelihood , bpp::DRHomogeneousTreeLikelihood , bpp::DRNonHomogeneousTreeLikelihood , bpp::RHomogeneousMixedTreeLikelihood , bpp::RHomogeneousTreeLikelihood , bpp::RNonHomogeneousTreeLikelihood
• getLogLikelihoodForASiteForAState() : bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood , bpp::TreeLikelihood
• getLogLikelihoodForEachSite() : bpp::AbstractTreeLikelihood , bpp::TreeLikelihood
• getLogLikelihoodForEachSiteForEachRateClass() : bpp::DiscreteRatesAcrossSitesTreeLikelihood , bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood
• getLogLikelihoodForEachSiteForEachRateClassForEachState() : bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood , bpp::DiscreteRatesAcrossSitesTreeLikelihood
• getLogLikelihoodForEachSiteForEachState() : bpp::AbstractTreeLikelihood , bpp::TreeLikelihood
• getMatrix() : bpp::DistanceEstimation
• getMaxId() : bpp::TreeTools
• getMaximumBranchLength() : bpp::AbstractHomogeneousTreeLikelihood , bpp::AbstractNonHomogeneousTreeLikelihood
• getMessage() : bpp::TopologyChangeEvent
• getMinimumBranchLength() : bpp::TwoTreeLikelihood , bpp::AbstractHomogeneousTreeLikelihood , bpp::AbstractNonHomogeneousTreeLikelihood
• getMixedModel() : bpp::AbstractBiblioMixedSubstitutionModel , bpp::YNGKP_M1 , bpp::YNGKP_M2 , bpp::YNGKP_M3 , bpp::YNGKP_M7 , bpp::YNGKP_M8 , bpp::LGL08_CAT , bpp::LLG08_EHO , bpp::LLG08_EX2 , bpp::LLG08_EX3 , bpp::LLG08_UL2 , bpp::LLG08_UL3
• getModel() : bpp::AbstractTreeLikelihood::ConstNoPartitionBranchModelDescription , bpp::AbstractTreeLikelihood::ConstNoPartitionSiteModelDescription , bpp::TreeLikelihood::ConstBranchModelDescription , bpp::TreeLikelihood::ConstSiteModelDescription , bpp::AbstractBiblioSubstitutionModel , bpp::GY94 , bpp::MG94 , bpp::YN98 , bpp::YNGKP_M1 , bpp::YNGKP_M2 , bpp::YNGKP_M3 , bpp::YNGKP_M7 , bpp::YNGKP_M8 , bpp::LGL08_CAT , bpp::LLG08_EHO , bpp::LLG08_EX2 , bpp::LLG08_EX3 , bpp::LLG08_UL2 , bpp::LLG08_UL3 , bpp::SubstitutionModelSet
• getModelForNode() : bpp::SubstitutionModelSet
• getModelIndexForNode() : bpp::SubstitutionModelSet
• getModelNames() : bpp::PairedSiteLikelihoods
• getModelParameters() : bpp::SubstitutionModelSet
• getModelStates() : bpp::AbstractBiblioSubstitutionModel , bpp::AbstractSubstitutionModel , bpp::MarkovModulatedSubstitutionModel , bpp::SubstitutionModel
• getMPNUId() : bpp::TreeTools
• getMultipleDistributionDefaultInstance() : bpp::PhylogeneticsApplicationTools
• getMutationPath() : bpp::SiteSimulationResult
• getName() : bpp::AbstractFrequenciesSet , bpp::WordSubstitutionModel , bpp::LLG08_UL2 , bpp::LLG08_EX2 , bpp::LGL08_CAT , bpp::YpR_Sym , bpp::RN95s , bpp::JCnuc , bpp::YNGKP_M3 , bpp::TripletSubstitutionModel , bpp::CladogramPlot , bpp::CodonDistanceFitnessPhaseFrequenciesSubstitutionModel , bpp::BioNJ , bpp::DistanceMethod , bpp::HierarchicalClustering , bpp::NeighborJoining , bpp::PGMA , bpp::PhylogramPlot , bpp::TreeDrawing , bpp::BinarySubstitutionModel , bpp::CodonDistanceFrequenciesSubstitutionModel , bpp::CodonDistancePhaseFrequenciesSubstitutionModel , bpp::CodonDistanceSubstitutionModel , bpp::CodonRateFrequenciesSubstitutionModel , bpp::CodonRateSubstitutionModel , bpp::GY94 , bpp::MG94 , bpp::YN98 , bpp::YNGKP_M1 , bpp::YNGKP_M2 , bpp::YNGKP_M7 , bpp::YNGKP_M8 , bpp::FrequenciesSet , bpp::G2001 , bpp::MixtureOfASubstitutionModel , bpp::MixtureOfSubstitutionModels , bpp::F84 , bpp::gBGC , bpp::GTR , bpp::HKY85 , bpp::K80 , bpp::L95 , bpp::RN95 , bpp::SSR , bpp::T92 , bpp::TN93 , bpp::YpR_Gen , bpp::Coala , bpp::DSO78 , bpp::JCprot , bpp::JTT92 , bpp::LG08 , bpp::LGL08_CAT::EmbeddedModel , bpp::LLG08_EHO::EmbeddedModel , bpp::LLG08_EHO , bpp::LLG08_EX2::EmbeddedModel , bpp::LLG08_EX3::EmbeddedModel , bpp::LLG08_EX3 , bpp::LLG08_UL2::EmbeddedModel , bpp::LLG08_UL3::EmbeddedModel , bpp::LLG08_UL3 , bpp::UserProteinSubstitutionModel , bpp::WAG01 , bpp::RE08 , bpp::SubstitutionModel , bpp::TS98 , bpp::Node , bpp::Tree , bpp::TreeTemplate< N >
• getNbrOfAxes() : bpp::CoalaCore
• getNeighbors() : bpp::NodeTemplate< NodeInfos > , bpp::Node , bpp::NodeTemplate< NodeInfos >
• getNestedModel() : bpp::MarkovModulatedSubstitutionModel , bpp::YpR , bpp::RE08
• getNestedPrefix() : bpp::YpR
• getNewBranchIterator() : bpp::AbstractTreeLikelihood::ConstNoPartitionSiteModelDescription , bpp::TreeLikelihood::ConstSiteModelDescription
• getNewBranchModelIterator() : bpp::AbstractHomogeneousTreeLikelihood , bpp::TwoTreeLikelihood , bpp::AbstractNonHomogeneousTreeLikelihood , bpp::TreeLikelihood
• getNewSiteIterator() : bpp::TreeLikelihood::ConstBranchModelDescription , bpp::AbstractTreeLikelihood::ConstNoPartitionBranchModelDescription
• getNewSiteModelIterator() : bpp::TwoTreeLikelihood , bpp::AbstractHomogeneousTreeLikelihood , bpp::AbstractNonHomogeneousTreeLikelihood , bpp::TreeLikelihood
• getNextId() : bpp::Tree , bpp::TreeTemplate< N >
• getNModel() : bpp::AbstractBiblioMixedSubstitutionModel , bpp::AbstractMixedSubstitutionModel , bpp::AbstractWordSubstitutionModel , bpp::MixedSubstitutionModel
• getNode() : bpp::DRASDRTreeLikelihoodLeafData , bpp::DRASDRTreeLikelihoodNodeData , bpp::TreeLikelihoodNodeData , bpp::AbstractSubstitutionMapping , bpp::MixedSubstitutionModelSet::HyperNode , bpp::DRTreeParsimonyLeafData , bpp::TreeParsimonyNodeData , bpp::NodePException , bpp::TreeTemplate< N > , bpp::DRTreeParsimonyNodeData , bpp::DRASRTreeLikelihoodNodeData
• getNodeAt() : bpp::TreeDrawing , bpp::AbstractTreeDrawing
• getNodeData() : bpp::DRASDRTreeLikelihoodData , bpp::DRASRTreeLikelihoodData , bpp::TreeLikelihoodData , bpp::DRTreeParsimonyData , bpp::TreeParsimonyData , bpp::DRTreeParsimonyData , bpp::DRASRTreeLikelihoodData
• getNodeDepths() : bpp::PhyloStatistics
• getNodeHeights() : bpp::PhyloStatistics
• getNodeId() : bpp::DrawNodeEvent , bpp::DrawBranchEvent , bpp::NodePException , bpp::NodeException
• getNodeIds() : bpp::PhyloStatistics
• getNodeIndex() : bpp::SubstitutionMapping , bpp::AbstractSubstitutionMapping
• getNodeName() : bpp::Tree , bpp::TreeTemplate< N >
• getNodeNumberOfSons() : bpp::PhyloStatistics
• getNodeParameters() : bpp::SubstitutionModelSet
• getNodePosition() : bpp::AbstractTreeDrawing , bpp::TreeDrawing
• getNodeProperties() : bpp::TreeTemplateTools
• getNodeProperty() : bpp::Node , bpp::Tree , bpp::TreeTemplate< N > , bpp::Tree
• getNodePropertyNames() : bpp::Node , bpp::TreeTemplate< N > , bpp::TreeTemplateTools , bpp::Tree
• getNodes() : bpp::TreeTemplate< N > , bpp::TreeTemplateTools , bpp::TreeTemplate< N >
• getNodesId() : bpp::Tree , bpp::TreeTemplate< N > , bpp::TreeTemplateTools , bpp::TreeTools
• getNodesWithModel() : bpp::SubstitutionModelSet
• getNodesWithParameter() : bpp::SubstitutionModelSet
• getNonDerivableParameters() : bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood , bpp::TreeLikelihood , bpp::RHomogeneousClockTreeLikelihood
• getNProbability() : bpp::AbstractBiblioMixedSubstitutionModel , bpp::AbstractMixedSubstitutionModel , bpp::MixedSubstitutionModel
• getNRate() : bpp::AbstractBiblioMixedSubstitutionModel , bpp::AbstractMixedSubstitutionModel , bpp::MixedSubstitutionModel
• getNumberOfAncestors() : bpp::PhyloStatistics
• getNumberOfBipartitions() : bpp::BipartitionList
• getNumberOfBranches() : bpp::SubstitutionMapping , bpp::AbstractSubstitutionMapping
• getNumberOfCategories() : bpp::CategorySubstitutionRegister
• getNumberOfClasses() : bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood , bpp::DiscreteRatesAcrossSitesTreeLikelihood , bpp::DRASDRTreeLikelihoodData , bpp::DRASRTreeLikelihoodData
• getNumberOfDistinctSites() : bpp::DRTreeParsimonyData , bpp::DRASDRTreeLikelihoodData , bpp::DRASRTreeLikelihoodData , bpp::TreeLikelihoodData
• getNumberOfElements() : bpp::BipartitionList
• getNumberOfEvents() : bpp::MutationPath
• getNumberOfFrequencies() : bpp::FrequenciesSet , bpp::AbstractFrequenciesSet
• getNumberOfHyperNodes() : bpp::MixedSubstitutionModelSet
• getNumberOfIndependentParameters() : bpp::OptimizationTools::ScaleFunction
• getNumberOfLeaves() : bpp::PhyloStatistics , bpp::TreeTemplate< N > , bpp::TreeTemplateTools , bpp::TreeTools , bpp::Tree
• getNumberOfModels() : bpp::AbstractBiblioMixedSubstitutionModel , bpp::AbstractMixedSubstitutionModel , bpp::AbstractWordSubstitutionModel , bpp::SubstitutionModelSet , bpp::MixedSubstitutionModel , bpp::PairedSiteLikelihoods
• getNumberOfNodes() : bpp::Tree , bpp::TreeTemplate< N > , bpp::TreeTemplateTools
• getNumberOfParameters() : bpp::OptimizationTools::ScaleFunction
• getNumberOfSites() : bpp::DRTreeParsimonyData , bpp::TreeLikelihood , bpp::DRASDRTreeLikelihoodData , bpp::PairedSiteLikelihoods , bpp::AbstractTreeLikelihood , bpp::TreeLikelihoodData , bpp::AbstractSubstitutionMapping , bpp::DRASRTreeLikelihoodData , bpp::SubstitutionMapping
• getNumberOfSons() : bpp::Node
• getNumberOfStates() : bpp::AbstractTreeLikelihood , bpp::RE08 , bpp::MarkovModulatedSubstitutionModel , bpp::ProteinSubstitutionModel , bpp::AbstractMixedSubstitutionModel , bpp::AbstractBiblioSubstitutionModel , bpp::TreeLikelihood , bpp::DRASDRTreeLikelihoodData , bpp::DRASRTreeLikelihoodData , bpp::SubstitutionCount , bpp::BinarySubstitutionModel , bpp::gBGC , bpp::YpR , bpp::AbstractStateMap , bpp::SubstitutionModel , bpp::SubstitutionModelSet , bpp::TreeLikelihoodData , bpp::AbstractWordSubstitutionModel , bpp::NucleotideSubstitutionModel , bpp::StateMap , bpp::DRTreeParsimonyData
• getNumberOfSubstitutions() : bpp::ProbabilisticSubstitutionMapping , bpp::LaplaceSubstitutionCount , bpp::NaiveSubstitutionCount , bpp::DecompositionSubstitutionCount , bpp::OneJumpSubstitutionCount , bpp::ProbabilisticSubstitutionMapping , bpp::UniformizationSubstitutionCount , bpp::LabelSubstitutionCount , bpp::SubstitutionCount
• getNumberOfSubstitutionsForEachType() : bpp::NaiveSubstitutionCount , bpp::LaplaceSubstitutionCount , bpp::DecompositionSubstitutionCount , bpp::LabelSubstitutionCount , bpp::OneJumpSubstitutionCount , bpp::SubstitutionCount , bpp::UniformizationSubstitutionCount
• getNumberOfSubstitutionTypes() : bpp::DnDsSubstitutionRegister , bpp::TotalSubstitutionRegister , bpp::SubstitutionMapping , bpp::SubstitutionCount , bpp::ProbabilisticSubstitutionMapping , bpp::CategorySubstitutionRegister , bpp::TsTvSubstitutionRegister , bpp::GCSynonymousSubstitutionRegister , bpp::SubstitutionRegister
• getOptimizer() : bpp::DistanceEstimation
• getParameter() : bpp::OptimizationTools::ScaleFunction
• getParameters() : bpp::OptimizationTools::ScaleFunction
• getParameterValue() : bpp::OptimizationTools::ScaleFunction
• getParentNode() : bpp::HierarchicalClustering , bpp::AbstractAgglomerativeDistanceMethod , bpp::PGMA
• getPartitionSize() : bpp::BipartitionList
• getPath() : bpp::UserProteinSubstitutionModel
• getPathBetweenAnyTwoNodes() : bpp::TreeTemplateTools , bpp::TreeTools , bpp::TreeTemplateTools
• getPij_t() : bpp::MarkovModulatedSubstitutionModel , bpp::AbstractMixedSubstitutionModel , bpp::RN95 , bpp::JCprot , bpp::F84 , bpp::SubstitutionModel , bpp::TN93 , bpp::T92 , bpp::BinarySubstitutionModel , bpp::K80 , bpp::AbstractBiblioSubstitutionModel , bpp::AbstractSubstitutionModel , bpp::HKY85 , bpp::JCnuc , bpp::RN95s , bpp::RE08 , bpp::WordSubstitutionModel
• getPosition() : bpp::TreeDrawingNodeInfo
• getPosteriorProbabilitiesForEachStateForEachRate() : bpp::DRTreeLikelihoodTools
• getPosteriorProbabilitiesOfEachRate() : bpp::DiscreteRatesAcrossSitesTreeLikelihood , bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood
• getPosteriorRateDistribution() : bpp::RASTools
• getPosteriorRateOfEachSite() : bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood , bpp::DiscreteRatesAcrossSitesTreeLikelihood
• getPosteriorStateFrequencies() : bpp::DRTreeLikelihoodTools
• getProbabilities() : bpp::AbstractMixedSubstitutionModel , bpp::MixedSubstitutionModel , bpp::AbstractBiblioMixedSubstitutionModel
• getProbability() : bpp::RNonHomogeneousMixedTreeLikelihood , bpp::MixedSubstitutionModelSet::HyperNode
• getPropertyName() : bpp::PropertyNotFoundException
• getProportion() : bpp::LLG08_UL3::EmbeddedModel , bpp::LLG08_UL2::EmbeddedModel , bpp::LLG08_EX3::EmbeddedModel , bpp::LLG08_EHO::EmbeddedModel , bpp::LGL08_CAT::EmbeddedModel , bpp::LLG08_EX2::EmbeddedModel
• getProteinFrequenciesSet() : bpp::FullPerAACodonFrequenciesSet
• getRadius() : bpp::TreeTemplateTools
• getRandomTree() : bpp::TreeTemplateTools
• getRate() : bpp::TS98 , bpp::MarkovModulatedSubstitutionModel , bpp::G2001 , bpp::AbstractBiblioSubstitutionModel , bpp::AbstractSubstitutionModel , bpp::SubstitutionModel , bpp::RASiteSimulationResult
• getRateClassWithMaxPostProbOfEachSite() : bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood , bpp::DiscreteRatesAcrossSitesTreeLikelihood
• getRateDistribution() : bpp::G2001 , bpp::DistanceEstimation , bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood , bpp::PhylogeneticsApplicationTools , bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood , bpp::DiscreteRatesAcrossSitesTreeLikelihood , bpp::NonHomogeneousSequenceSimulator
• getRateDistributionParameters() : bpp::AbstractNonHomogeneousTreeLikelihood , bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood , bpp::AbstractHomogeneousTreeLikelihood , bpp::DiscreteRatesAcrossSitesTreeLikelihood
• getRateWithMaxPostProbOfEachSite() : bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood , bpp::DiscreteRatesAcrossSitesTreeLikelihood
• getRemainingNeighbors() : bpp::TreeTemplateTools
• getRootArrayPosition() : bpp::TreeLikelihoodData , bpp::DRASRTreeLikelihoodData , bpp::AbstractTreeLikelihoodData , bpp::TreeParsimonyData , bpp::AbstractTreeParsimonyData
• getRootArrayPositions() : bpp::AbstractTreeLikelihoodData
• getRootBitset() : bpp::DRTreeParsimonyData
• getRootBitsets() : bpp::DRTreeParsimonyData
• getRootFrequencies() : bpp::AbstractNonHomogeneousTreeLikelihood , bpp::SubstitutionModelSet , bpp::TreeLikelihood , bpp::TwoTreeLikelihood , bpp::AbstractHomogeneousTreeLikelihood
• getRootFrequenciesParameters() : bpp::NonHomogeneousTreeLikelihood , bpp::SubstitutionModelSet , bpp::AbstractNonHomogeneousTreeLikelihood
• getRootFrequenciesSet() : bpp::SubstitutionModelSet , bpp::PhylogeneticsApplicationTools
• getRootId() : bpp::Tree , bpp::TreeTemplate< N >
• getRootLikelihoodArray() : bpp::DRASDRTreeLikelihoodData
• getRootNode() : bpp::TreeTemplate< N >
• getRootRateSiteLikelihoodArray() : bpp::DRASDRTreeLikelihoodData
• getRootScore() : bpp::DRTreeParsimonyData
• getRootScores() : bpp::DRTreeParsimonyData
• getRootSiteLikelihoodArray() : bpp::DRASDRTreeLikelihoodData
• getRowCoordinates() : bpp::CoalaCore
• getRowLeftEigenVectors() : bpp::SubstitutionModel , bpp::AbstractSubstitutionModel , bpp::AbstractBiblioSubstitutionModel , bpp::MarkovModulatedSubstitutionModel
• getScale() : bpp::SubstitutionModel , bpp::AbstractSubstitutionModel , bpp::AbstractBiblioSubstitutionModel , bpp::MarkovModulatedSubstitutionModel
• getScore() : bpp::TreeParsimonyScore , bpp::DRTreeParsimonyScore
• getScoreForEachSite() : bpp::AbstractTreeParsimonyScore , bpp::TreeParsimonyScore
• getScoreForSite() : bpp::DRTreeParsimonyScore , bpp::TreeParsimonyScore
• getScoresArray() : bpp::DRTreeParsimonyData
• getScoresArrayForNeighbor() : bpp::DRTreeParsimonyNodeData
• getSearchableObject() : bpp::NNITopologySearch
• getSecondOrderDerivative() : bpp::RHomogeneousClockTreeLikelihood , bpp::TwoTreeLikelihood , bpp::RHomogeneousTreeLikelihood , bpp::DRNonHomogeneousTreeLikelihood , bpp::RNonHomogeneousTreeLikelihood , bpp::DRHomogeneousTreeLikelihood , bpp::DRNonHomogeneousTreeLikelihood , bpp::DRHomogeneousTreeLikelihood , bpp::RHomogeneousClockTreeLikelihood , bpp::DRHomogeneousMixedTreeLikelihood , bpp::GlobalClockTreeLikelihoodFunctionWrapper , bpp::TwoTreeLikelihood , bpp::DRHomogeneousMixedTreeLikelihood , bpp::RNonHomogeneousTreeLikelihood
• getSequencesNames() : bpp::NonHomogeneousSequenceSimulator , bpp::SiteSimulator
• getSequenceSubset() : bpp::PatternTools
• getShrunkData() : bpp::DRASDRTreeLikelihoodData
• getSite() : bpp::SiteSimulationResult
• getSiteIndex() : bpp::TwoTreeLikelihood , bpp::TreeLikelihood , bpp::DRHomogeneousTreeLikelihood , bpp::DRNonHomogeneousTreeLikelihood , bpp::RNonHomogeneousTreeLikelihood , bpp::RHomogeneousTreeLikelihood
• getSitePosition() : bpp::AbstractSubstitutionMapping , bpp::SubstitutionMapping
• getSites() : bpp::SitePatterns
• getSizeFromVector() : bpp::WordFrequenciesSet , bpp::AbstractWordFrequenciesSet
• getSon() : bpp::Node , bpp::NodeTemplate< NodeInfos > , bpp::Node
• getSonPosition() : bpp::Node
• getSons() : bpp::Node
• getSonsId() : bpp::TreeTemplate< N > , bpp::Node , bpp::Tree
• getStateMap() : bpp::AbstractTreeParsimonyScore
• getStatesFrequenciesSet() : bpp::MarkovModulatedFrequenciesSet
• getSubmodelNumbers() : bpp::MixtureOfSubstitutionModels , bpp::MixedSubstitutionModel , bpp::MixtureOfASubstitutionModel , bpp::AbstractBiblioMixedSubstitutionModel
• getSubstitutionCount() : bpp::PhylogeneticsApplicationTools , bpp::SiteSimulationResult
• getSubstitutionModel() : bpp::SubstitutionModelException , bpp::HomogeneousTreeLikelihood , bpp::MutationProcess , bpp::SitePartitionHomogeneousTreeLikelihood , bpp::HomogeneousSequenceSimulator , bpp::TreeLikelihood , bpp::SitePartitionHomogeneousTreeLikelihood , bpp::NonHomogeneousTreeLikelihood , bpp::HomogeneousTreeLikelihood , bpp::AbstractHomogeneousTreeLikelihood , bpp::TwoTreeLikelihood , bpp::PhylogeneticsApplicationTools , bpp::AbstractHomogeneousTreeLikelihood , bpp::DistanceEstimation , bpp::HomogeneousTreeLikelihood , bpp::TwoTreeLikelihood , bpp::NonHomogeneousTreeLikelihood , bpp::AbstractMutationProcess , bpp::TreeLikelihood , bpp::HomogeneousTreeLikelihood
• getSubstitutionModelForNode() : bpp::NonHomogeneousTreeLikelihood , bpp::AbstractNonHomogeneousTreeLikelihood , bpp::NonHomogeneousTreeLikelihood
• getSubstitutionModelForSite() : bpp::SitePartitionHomogeneousTreeLikelihood
• getSubstitutionModelParameters() : bpp::AbstractNonHomogeneousTreeLikelihood , bpp::AbstractHomogeneousTreeLikelihood , bpp::TwoTreeLikelihood , bpp::TreeLikelihood
• getSubstitutionModelSet() : bpp::NonHomogeneousSequenceSimulator , bpp::NonHomogeneousTreeLikelihood , bpp::AbstractNonHomogeneousTreeLikelihood , bpp::NonHomogeneousTreeLikelihood , bpp::AbstractNonHomogeneousTreeLikelihood , bpp::PhylogeneticsApplicationTools
• getSubstitutionRegister() : bpp::SubstitutionCount , bpp::AbstractSubstitutionCount , bpp::SubstitutionCount , bpp::AbstractSubstitutionCount
• getSubstitutionVector() : bpp::SiteSimulationResult
• getSubtreeMoments() : bpp::TreeTemplateTools
• getTimeBeforeNextMutationEvent() : bpp::AbstractMutationProcess , bpp::MutationProcess
• getTopology() : bpp::NNIHomogeneousTreeLikelihood , bpp::DRTreeParsimonyScore , bpp::NNITopologySearch , bpp::NNISearchable
• getTopologyValue() : bpp::NNISearchable , bpp::NNIHomogeneousTreeLikelihood , bpp::DRTreeParsimonyScore
• getTotalLength() : bpp::TreeTemplateTools , bpp::TreeTools , bpp::Tree , bpp::TreeTemplate< N >
• getTotalTime() : bpp::MutationPath
• getTppalAxesMatrix() : bpp::CoalaCore
• getTransitionProbabilities() : bpp::TreeLikelihood , bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood
• getTransitionProbabilitiesPerRateClass() : bpp::DiscreteRatesAcrossSitesTreeLikelihood , bpp::AbstractHomogeneousTreeLikelihood , bpp::TwoTreeLikelihood , bpp::AbstractNonHomogeneousTreeLikelihood
• getTranslation() : bpp::Cursor
• getTree() : bpp::PhylogeneticsApplicationTools , bpp::AbstractTreeParsimonyScore , bpp::TreeDrawing , bpp::DistanceMethod , bpp::SubstitutionMapping , bpp::TreeParsimonyScore , bpp::TreeLikelihoodData , bpp::AbstractTreeLikelihood , bpp::AbstractTreeLikelihoodData , bpp::NonHomogeneousSequenceSimulator , bpp::AbstractTreeDrawing , bpp::AbstractTreeParsimonyData , bpp::AbstractAgglomerativeDistanceMethod , bpp::TreeParsimonyData , bpp::TreeException , bpp::TreeLikelihood , bpp::HierarchicalClustering , bpp::AbstractSubstitutionMapping , bpp::PGMA
• getTree_() : bpp::AbstractTreeDrawing
• getTreeDrawing() : bpp::DrawBranchEvent , bpp::DrawTreeEvent , bpp::DrawNodeEvent
• getTreeP_() : bpp::AbstractTreeParsimonyScore , bpp::AbstractTreeParsimonyData
• getTrees() : bpp::PhylogeneticsApplicationTools
• getType() : bpp::TotalSubstitutionRegister , bpp::CategorySubstitutionRegister , bpp::SubstitutionRegister , bpp::DnDsSubstitutionRegister , bpp::GCSynonymousSubstitutionRegister , bpp::TsTvSubstitutionRegister
• getTypeName() : bpp::DnDsSubstitutionRegister , bpp::GCSynonymousSubstitutionRegister , bpp::CategorySubstitutionRegister , bpp::TsTvSubstitutionRegister , bpp::TotalSubstitutionRegister , bpp::SubstitutionRegister
• getUnparsedArguments() : bpp::ISubstitutionModel , bpp::BppOSubstitutionModelFormat , bpp::IFrequenciesSet , bpp::BppOFrequenciesSetFormat
• getValue() : bpp::DRNonHomogeneousTreeLikelihood , bpp::DRHomogeneousTreeLikelihood , bpp::GlobalClockTreeLikelihoodFunctionWrapper , bpp::BranchLikelihood , bpp::RHomogeneousTreeLikelihood , bpp::RNonHomogeneousTreeLikelihood , bpp::OptimizationTools::ScaleFunction , bpp::TwoTreeLikelihood
• getVerbose() : bpp::DistanceEstimation
• getVerticalOrientation() : bpp::AbstractDendrogramPlot
• getVPos() : bpp::Cursor
• getVRates() : bpp::AbstractBiblioMixedSubstitutionModel , bpp::AbstractMixedSubstitutionModel , bpp::MixedSubstitutionModel
• getWeight() : bpp::AbstractTreeParsimonyData , bpp::TreeLikelihoodData , bpp::AbstractTreeLikelihoodData
• getWeights() : bpp::SitePatterns , bpp::AbstractWeightedSubstitutionCount , bpp::WeightedSubstitutionCount , bpp::TreeLikelihoodData , bpp::AbstractTreeLikelihoodData
• getWidth() : bpp::PhylogramPlot , bpp::TreeDrawing , bpp::CladogramPlot
• getX() : bpp::TreeDrawingNodeInfo , bpp::Cursor
• getXUnit() : bpp::AbstractTreeDrawing , bpp::TreeDrawing
• getY() : bpp::Cursor , bpp::TreeDrawingNodeInfo
• getYUnit() : bpp::TreeDrawing , bpp::AbstractTreeDrawing
• GlobalClockTreeLikelihoodFunctionWrapper() : bpp::GlobalClockTreeLikelihoodFunctionWrapper
• GTR() : bpp::GTR
• GY94() : bpp::GY94