| ►Nbpp | Defines the basic types of data flow nodes |
| CAAExteriorSubstitutionRegister | Indexes only substitutions between amino-acids. Groups are distinguished by their direction |
| CAAInteriorSubstitutionRegister | Indexes only intra amino-acid substitutions. Every group represents a substitutions for the same amino acid. Met and Trp are not taken into account due their non-degenerescence |
| CAbstractAgglomerativeDistanceMethod | Partial implementation of the AgglomerativeDistanceMethod interface |
| CAbstractAlignedPhyloLikelihood | |
| CAbstractAlignedPhyloLikelihoodSet | The AlignedPhyloLikelihoodSet abstract class |
| CAbstractAutonomousSubstitutionProcess | A partial implementation of the SubstitutionProcess interface |
| CAbstractBiblioMixedTransitionModel | Abstract class for mixture models based on the bibliography |
| CAbstractBiblioSubstitutionModel | |
| CAbstractBiblioTransitionModel | Partial implementation of the SubstitutionModel interface for models that are set for matching the bibliography, and are only defined through a link to a "real" model |
| CAbstractCodonAAFitnessSubstitutionModel | Abstract class for modelling of ratios of substitution rates between codons, whatever they are synonymous or not |
| CAbstractCodonAARateSubstitutionModel | Abstract class for modelling of non-synonymous and synonymous substitution rates in codon models, given an amino acid rate matrix (from a shared_ptr model) |
| CAbstractCodonBGCSubstitutionModel | Abstract class for modelling of non-synonymous and synonymous substitution rates in codon models, with gBGC |
| CAbstractCodonClusterAASubstitutionModel | Abstract class for modelling of non-synonymous and synonymous substitution rates in codon models, with AA clustered |
| CAbstractCodonCpGSubstitutionModel | Abstract class for modelling of CpG -> CpA or TpG (symmetric) hypermutability substitution rate inside codons. Note that the neihbouring effects between codons are not considered |
| CAbstractCodonDistanceSubstitutionModel | Abstract class for modelling of non-synonymous and synonymous substitution rates in codon models |
| CAbstractCodonFitnessSubstitutionModel | Abstract class for modelling of ratios of substitution rates between codons, whatever they are synonymous or not |
| CAbstractCodonFrequenciesSubstitutionModel | Abstract Class for substitution models on codons parametrized by frequencies |
| CAbstractCodonPhaseFrequenciesSubstitutionModel | Abstract Class for substitution models on codons parametrized by a frequency |
| CAbstractCodonSubstitutionModel | Abstract class for substitution models on codons |
| CAbstractDendrogramPlot | Basic implementation of dendrogram plots |
| CAbstractDFPSubstitutionModel | Class for neutral substitution models on triplets, following the mutation process proposed in Doron-Fagenboim & Pupko, 2006, but without equilibrium frequencies. This model is an extension of Kimura 2-rates substitution model to codons |
| CAbstractDiscreteRatesAcrossSitesTreeLikelihood | Partial implementation of the DiscreteRatesAcrossSitesTreeLikelihood interface |
| CAbstractFrequencySet | Basic implementation of the FrequencySet interface |
| CAbstractFromSubstitutionModelTransitionModel | Virtual class of a Transition Model related to a given SubstitutionModel |
| ►CAbstractHomogeneousTreeLikelihood | Partial implementation for homogeneous model of the TreeLikelihood interface |
| CConstHomogeneousSiteModelIterator | |
| CAbstractIMultiPhyloDAG | Partial implementation of the IMultiDAG interface |
| CAbstractIMultiPhyloTree | Partial implementation of the IMultiTree interface |
| CAbstractIMultiTree | Partial implementation of the IMultiTree interface |
| CAbstractIPhyloDAG | Partial implementation of the IDAG interface |
| CAbstractIPhyloTree | |
| CAbstractITree | Partial implementation of the ITree interface |
| CAbstractKroneckerCodonSubstitutionModel | Abstract class for substitution models on codons allowing multiple substitutions |
| CAbstractKroneckerWordSubstitutionModel | Abstract Kronecker Word Model |
| CAbstractLkTransitionModel | Partial implementation of the TransitionModel interface, with function for likelihood computations |
| CAbstractMapping | Partial implementation of the mapping interface |
| CAbstractMixedTransitionModel | Partial implementation for Mixed Transition models, defined as a mixture of "simple" substitution models. Each model has a specific probability and rate, with the constraint that the expectation (on the distribution of the models) of the rate of all the models equals one |
| CAbstractMutationProcess | Partial implementation of the MutationProcess interface |
| ►CAbstractNonHomogeneousTreeLikelihood | Partial implementation for branch non-homogeneous models of the TreeLikelihood interface |
| CConstNonHomogeneousSiteModelIterator | |
| CAbstractNucleotideSubstitutionModel | Specialisation abstract class for nucleotide substitution model |
| CAbstractOMultiPhyloDAG | Partial implementation of the ODAG interface |
| CAbstractOMultiPhyloTree | Partial implementation of the OTree interface |
| CAbstractOMultiTree | Partial implementation of the OTree interface |
| CAbstractOPhyloDAG | Partial implementation of the ODAG interface |
| CAbstractOPhyloTree | Partial implementation of the OTree interface |
| CAbstractOTree | Partial implementation of the OTree interface |
| CAbstractParametrizableSequencePhyloLikelihood | |
| ►CAbstractPhyloLikelihood | |
| CStringPairHash | |
| CAbstractPhyloLikelihoodSet | The PhyloLikelihoodSet class, to manage a subset of PhyloLikelihoods from a given PhyloLikelihoodContainer |
| CAbstractProteinSubstitutionModel | Specialisation abstract class for protein substitution model |
| CAbstractReversibleNucleotideSubstitutionModel | Specialisation abstract class for reversible nucleotide substitution model |
| CAbstractReversibleProteinSubstitutionModel | Specialisation abstract class for reversible protein substitution model |
| CAbstractReversibleSubstitutionModel | Partial implementation of the ReversibleSubstitutionModel interface |
| CAbstractReward | Basic implementation of the the Reward interface |
| CAbstractRewardMapping | Partial implementation of the substitution mapping interface |
| CAbstractSequencePhyloLikelihood | |
| CAbstractSingleDataPhyloLikelihood | |
| CAbstractSinglePhyloSubstitutionMapping | The AbstractSinglePhyloSubstitutionMapping class: substitution mapping linked with a Single Process PhyloLikelihood |
| CAbstractStateMap | A convenience partial implementation of the StateMap interface |
| CAbstractSubstitutionCount | Partial implementation of the SubstitutionCount interface |
| CAbstractSubstitutionDistance | Partial implementation of the SubstitutionDistance interface |
| CAbstractSubstitutionMapping | Partial implementation of the substitution mapping interface |
| CAbstractSubstitutionModel | |
| CAbstractSubstitutionProcess | A partial implementation of the SubstitutionProcess interface |
| CAbstractSubstitutionRegister | |
| CAbstractTotallyWrappedSubstitutionModel | |
| CAbstractTotallyWrappedTransitionModel | |
| CAbstractTransitionModel | Partial implementation of the TransitionModel interface |
| CAbstractTreeDrawing | Partial implementation of the TreeDrawing interface |
| ►CAbstractTreeLikelihood | Partial implementation of the TreeLikelihood interface |
| CConstNoPartitionBranchModelDescription | |
| CConstNoPartitionBranchModelIterator | |
| CConstNoPartitionSiteModelDescription | |
| CSimpleBranchIterator | A very simple branch iterator |
| CSimpleSiteIterator | A very simple site iterator |
| CAbstractTreeLikelihoodData | Partial implementation of the TreeLikelihoodData interface |
| CAbstractTreeParsimonyData | Partial implementation of the TreeParsimonyData interface |
| CAbstractTreeParsimonyScore | Partial implementation of the TreeParsimonyScore interface |
| CAbstractWeightedSubstitutionCount | Partial implementation of the WeightedSubstitutionCount interface |
| CAbstractWordFrequencySet | |
| CAbstractWordSubstitutionModel | Abstract Basal class for words of substitution models |
| CAbstractWrappedModel | Abstract class of Wrapping model class, where all methods are redirected from model() |
| CAbstractWrappedSubstitutionModel | |
| CAbstractWrappedTransitionModel | |
| CAgglomerativeDistanceMethodInterface | Interface for agglomerative distance methods |
| CAlignedLikelihoodCalculation | |
| CAlignedPhyloLikelihoodAutoCorrelation | Likelihood framework based on a hmm of simple likelihoods |
| CAlignedPhyloLikelihoodHmm | Likelihood framework based on a hmm of simple likelihoods |
| CAlignedPhyloLikelihoodInterface | The AlignedPhyloLikelihood interface, for phylogenetic likelihood |
| CAlignedPhyloLikelihoodMixture | Likelihood framework based on a mixture of aligned likelihoods |
| CAlignedPhyloLikelihoodProduct | The AlignedPhyloLikelihoodProduct class, for phylogenetic likelihood on several independent data |
| CAlignedPhyloLikelihoodSetInterface | Joint interface SetOf+Aligned PhylLikelihood |
| CAncestralStateReconstruction | Interface for ancestral states reconstruction methods |
| CAnonymousSubstitutionModel | |
| CAutoCorrelationProcessPhyloLikelihood | Likelihood framework based on an auto-correlation of simple likelihoods |
| CAutoCorrelationSequenceEvolution | Sequence evolution framework based on an auto-correlation of substitution processes |
| CAutonomousSubstitutionProcessInterface | Interface for SubstitutionProcess objects that own their own ParametrizablePhyloTree & Scenario |
| CAwareNode | A node class aware of its neighbours |
| CBackwardHmmLikelihood_DF | |
| CBackwardLikelihoodTree | |
| CBasicTreeDrawingDisplayControler | Easy tune of tree drawings display, a basic implementation: |
| CBinarySubstitutionModel | The Model on two states |
| CBioNJ | The BioNJ distance method |
| CBipartitionList | This class deals with the bipartitions defined by trees |
| CBipartitionTools | This class provides tools related to the BipartitionList class |
| CBootstrapValuesTreeDrawingListener | A TreeDrawingListener implementation that write the bootstrap values of inner nodes |
| CBppOBranchModelFormat | Branch model I/O in BppO format |
| CBppOFrequencySetFormat | Frequencies set I/O in BppO format |
| CBppOMultiTreeReaderFormat | Tree I/O in BppO format |
| CBppOMultiTreeWriterFormat | Tree I/O in BppO format |
| CBppORateDistributionFormat | Rate Distribution I/O in BppO format |
| CBppOSubstitutionModelFormat | Substitution model I/O in BppO format |
| CBppOTransitionModelFormat | Transition model I/O in BppO format |
| CBppOTreeReaderFormat | Tree I/O in BppO format |
| CBppOTreeWriterFormat | Tree I/O in BppO format |
| CBppPhylogeneticsApplication | |
| CBranchedModelSet | |
| CBranchLengthsTreeDrawingListener | A TreeDrawingListener implementation that write the branch lengths of inner nodes |
| CBranchLikelihood | Compute likelihood for a 4-tree |
| CBranchModelInterface | Interface for all Branch models |
| CCanonicalStateMap | This class implements a state map where all resolved states are modeled |
| CCategoryFromDiscreteDistribution | |
| CCategorySubstitutionRegister | The CategorySubstitutionRegisters |
| CCladogramDrawBranchEvent | |
| CCladogramPlot | Cladogram representation of trees |
| CClusterInfos | |
| CCoala | The Coala branch-heterogeneous amino-acid substitution model |
| CCoalaCore | This class is the core class inherited by the Coala class. COaLA is a branch-heterogeneous amino-acid substitution model |
| CCodonAdHocSubstitutionModel | Class for substitution models of codons with several layers of codon models |
| CCodonDistanceFrequenciesSubstitutionModel | Class for asynonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic models |
| CCodonDistancePhaseFrequenciesSubstitutionModel | Class for asynonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic basic models |
| CCodonDistanceSubstitutionModel | Class for substitution models of codons with non-synonymous/synonymous ratios of substitution rates defined through a distance between amino-acids |
| CCodonFrequencySetInterface | Parametrize a set of state frequencies for codons |
| CCodonFromIndependentFrequencySet | Frequencies in codons are the product of Independent Frequencies in letters with the frequencies of stop codons set to zero |
| CCodonFromUniqueFrequencySet | Frequencies in codons are the product of the frequencies for a unique FrequencySet in letters, with the frequencies of |
| CCodonReversibleSubstitutionModelInterface | Interface for reversible codon models |
| CCodonSameAARateSubstitutionModel | Class for modelling of non-synonymous rates in codon models, such that the substitution rates between amino acids are similar to the ones in an amino acid rate matrix (from a shared_ptr model) |
| CCodonSubstitutionModelInterface | |
| CCollectionNodes | |
| CCombineDeltaShifted | |
| CCompleteSubstitutionRegister | Completion of a given substitution register to consider all substitutions. The new substitutions are considered in an additional type |
| CComprehensiveSubstitutionRegister | Distinguishes all types of substitutions |
| CCondLikelihood | |
| CConfiguredDistribution | Data flow node representing a DiscreteDistribution configured with parameter values |
| CConfiguredFrequencySet | Data flow node representing a Frequencies Set configured with parameter values |
| CConfiguredModel | Likelihood transition model |
| CConfiguredParameter | Data flow node representing a parameter |
| CConfiguredParametrizable | |
| CConfiguredSimplex | Data flow node representing a Frequencies Set configured with parameter values |
| CConfiguredTransitionMatrix | Data flow node representing a TransitionMatrix configured with parameter values |
| CConstantOne | R = 1 for each component |
| CConstantRateDistribution | |
| CConstantTransitionFunction | |
| CConstantZero | R = 0 for each component |
| ►CContext | Context for dataflow node construction |
| CCachedNodeRef | NodeRef is hashable and comparable as a pointer. CachedNodeRef is hashable and comparable, by comparing the node configuration: |
| CCachedNodeRefHash | |
| CConvert | R = convert(f) |
| CCoreCodonSubstitutionModelInterface | Interface for codon models |
| CCursor | Data structure describing a plotting direction |
| CCWiseAdd | |
| CCWiseAdd< R, ReductionOf< T > > | |
| CCWiseAdd< R, std::tuple< T0, T1 > > | |
| CCWiseApply | |
| CCWiseCompound | |
| ►CCWiseCompound< R, ReductionOf< T > > | |
| Ccompound_functor | |
| CCWiseConstantPow | |
| CCWiseDiv | |
| CCWiseDiv< R, std::tuple< T0, T1 > > | |
| CCWiseExp | |
| CCWiseFill | |
| CCWiseInverse | |
| CCWiseLog | |
| CCWiseMatching | |
| ►CCWiseMatching< R, ReductionOf< T > > | |
| Cmatching_functor | |
| CCWiseMean | |
| CCWiseMean< R, ReductionOf< T >, P > | |
| CCWiseMean< R, ReductionOf< T >, ReductionOf< P > > | |
| CCWiseMul | |
| CCWiseMul< R, ReductionOf< T > > | |
| CCWiseMul< R, std::tuple< T0, T1 > > | |
| CCWiseNegate | |
| ►CCWisePattern | |
| Cpattern_functor | |
| CCWiseSub | |
| CCWiseSub< R, std::tuple< T0, T1 > > | |
| CD1WalkSubstitutionModel | The D1Walk substitution model for Integer alphabet [0;N-1]. In this model, substitutions are possible between adjacent states only. The model is defined through an equilibrium distribution, and rates towards a state are proportional to its frequency at equilibrium |
| CDecompositionMethods | Methods useful for analytical substitution count and rewards using the eigen decomposition method |
| CDecompositionReward | Analytical reward using the eigen decomposition method |
| CDecompositionSubstitutionCount | Analytical substitution count using the eigen decomposition method |
| CDetailedSiteSimulatorInterface | This interface adds the dSimulate method to the SiteSimulator interface |
| CDFP07 | Class for non-synonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic models, with allowed multiple substitutions as parameterized in DFP model, with correction to mimic AA substitution rates from a given protein substitution model |
| CDFPDistanceFrequenciesSubstitutionModel | Class for non-synonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic models, with allowed multiple substitutions as parameterized in DFP model |
| CDimension | Store a dimension for type T |
| CDimension< char > | |
| CDimension< double > | Specialisation of Dimension<T> for floating point types |
| CDimension< Eigen::Matrix< T, Rows, Cols > > | Specialisation of Dimension<T> for eigen matrix types |
| CDimension< ExtendedFloat > | |
| CDimension< ExtendedFloatEigen< R, C, EigenType > > | |
| CDimension< float > | |
| CDimension< Parameter > | |
| CDimension< size_t > | |
| CDimension< std::string > | |
| CDimension< TransitionFunction > | |
| CDimension< uint > | |
| CDiscreteRatesAcrossSitesTreeLikelihoodInterface | Interface for rate across sites (RAS) implementation |
| CDistanceEstimation | |
| CDistanceMethodInterface | General interface for distance-based phylogenetic reconstruction methods |
| CDnDsSubstitutionRegister | Distinguishes synonymous from non-synonymous substitutions |
| CDRASDRTreeLikelihoodData | Likelihood data structure for rate across sites models, using a double-recursive algorithm |
| CDRASDRTreeLikelihoodLeafData | Likelihood data structure for a leaf |
| CDRASDRTreeLikelihoodNodeData | Likelihood data structure for a node |
| CDRASRTreeLikelihoodData | Discrete Rate Across Sites, (simple) Recursive likelihood data structure |
| CDRASRTreeLikelihoodNodeData | Likelihood data structure for a node |
| CDrawBranchEvent | Event class used by TreeDrawing classes |
| CDrawIBranchEvent | Event class that uses INode object (more efficient than relying on nodes id, but less generic) |
| CDrawINodeEvent | Event class that uses INode object (more efficient than relying on nodes id, but less generic) |
| CDrawNodeEvent | Event class used by TreeDrawing classes |
| CDrawTreeEvent | Event class used by TreeDrawing classes |
| CDRHomogeneousMixedTreeLikelihood | A class to compute the average of several DRHomogeneousTreeLikelihood defined from a Mixed Substitution Model |
| CDRHomogeneousTreeLikelihood | This class implements the likelihood computation for a tree using the double-recursive algorithm |
| CDRNonHomogeneousTreeLikelihood | This class implements the likelihood computation for a tree using the double-recursive algorithm, allowing for non-homogeneous models of substitutions |
| CDRTreeLikelihoodInterface | Interface for double-recursive (DR) implementation of the likelihood computation |
| CDRTreeLikelihoodTools | Utilitary methods dealing with objects implementing the DRTreeLikelihood interface |
| CDRTreeParsimonyData | Parsimony data structure for double-recursive (DR) algorithm |
| CDRTreeParsimonyLeafData | Parsimony data structure for a leaf |
| CDRTreeParsimonyNodeData | Parsimony data structure for a node |
| CDRTreeParsimonyScore | Double recursive implementation of interface TreeParsimonyScore |
| CDSO78 | The Dayhoff, Schwartz and Orcutt substitution model for proteins |
| CEquilibriumFrequenciesFromModel | |
| CEquilibriumFrequenciesFromTransitionMatrix | |
| CEquiprobableSubstitutionModel | The EquiprobableSubstitutionModel substitution model for any kind of alphabet. Jukes-Cantor models are specific case of this model, applied to nucleotides or proteins |
| CEvolutionSequenceSimulator | |
| CExponentialDiscreteRateDistribution | |
| CExtendedFloat | |
| CExtendedFloatArrayWrapper | |
| CExtendedFloatCol | |
| ►CExtendedFloatEigen | |
| COwnedExtendedFloat | |
| CExtendedFloatEigenBase | |
| CExtendedFloatEigenCore | |
| CExtendedFloatNoAlias | |
| CExtendedFloatRow | |
| CExtendedFloatVectorwiseOp | |
| CExtendedNewick | The so-called 'ExtendedNewick' parenthetic format for phylogenetic networks, where hybridization nodes are mandatory tagged and appear several times |
| CF81 | The Felsenstein (1981) substitution model for nucleotides |
| CF84 | The Felsenstein (1984) substitution model for nucleotides |
| CFixedCodonFrequencySet | FrequencySet for codons, with no parameter |
| CFixedFrequencySet | FrequencySet useful for homogeneous and stationary models |
| CFixedNucleotideFrequencySet | FrequencySet useful for homogeneous and stationary models, nucleotide implementation |
| CFixedProteinFrequencySet | FrequencySet useful for homogeneous and stationary models, protein implementation |
| CForwardHmmD2Likelihood_DF | |
| CForwardHmmDLikelihood_DF | |
| CForwardHmmLikelihood_DF | |
| CForwardLikelihoodTree | |
| CFrequenciesFromFrequencySet | |
| CFrequenciesFromSimplex | |
| CFrequencySetInterface | Parametrize a set of state frequencies |
| CFromMixtureSubstitutionModel | Model taken from a SubModel of a Mixture of SubstitutionModels |
| CFromModelFrequencySet | FrequencySet defined from the equilibrium distribution of a given model |
| CFullCodonFrequencySet | A generic FrequencySet for Full Codon alphabets |
| CFullFrequencySet | A generic FrequencySet allowing for the estimation of all frequencies |
| CFullNucleotideFrequencySet | Nucleotide FrequencySet using three independent parameters (theta, theta1, theta2) to modelize the four frequencies: |
| CFullPerAACodonFrequencySet | FrequencySet integrating ProteinFrequencySet inside CodonFrequencySet. In this case, FrequencieSet defined inside each amino acid is parametrized as a FullFrequencySet. Hence there are 61-20=41 parameters in addition of the parameters of the ProteinFrequencySet |
| CFullProteinFrequencySet | Protein FrequencySet using 19 independent parameters to model the 20 frequencies |
| CG2001 | Galtier's 2001 covarion model |
| CGammaDiscreteRateDistribution | |
| CGaussianDiscreteRateDistribution | |
| CgBGC | GBGC model |
| CGCFrequencySet | Nucleotide FrequencySet using only one parameter, the GC content (denoted as 'GC.theta') |
| CGCPositionSubstitutionRegister | Distinguishes AT->GC vs GC->AT on given codon position (0, 1, or 2) |
| CGCSubstitutionRegister | Distinguishes AT<->GC from GC<->AT |
| CGCSynonymousSubstitutionRegister | Distinguishes AT->GC vs GC->AT inside synonymous substitutions on third codon position |
| CGeneralSubstitutionRegister | Sets a Register based on a matrix of integers. If M is the matrix, M[i,j] is the number of the substitution type from i to j, or 0 if there is no substitution type from i to j |
| CGivenDataSubstitutionProcessSequenceSimulator | Sequences simulation under a unique substitution process, but with site specific posterior probabilities |
| CGivenDataSubstitutionProcessSiteSimulator | Site simulation under a unique substitution process, given data |
| CGlobalClockTreeLikelihoodFunctionWrapper | |
| CGTR | The General Time-Reversible substitution model for nucleotides |
| CGY94 | The Goldman and Yang (1994) substitution model for codons |
| CHierarchicalClustering | Hierarchical clustering |
| CHKY85 | The Hasegawa M, Kishino H and Yano T (1985) substitution model for nucleotides |
| CHmmEmissionProbabilities_Eigen | Interface for computing emission probabilities in a Hidden Markov Model |
| CHmmLikelihood_DF | A simple implementation of hidden Markov models recursion, in DataFlow implementation |
| CHmmPhyloAlphabet | Hidden states alphabet |
| CHmmPhyloEmissionProbabilities | Emission probabilities in the context of DF phylolikeihoods |
| CHmmProcessAlphabet | Hidden states alphabet |
| CHmmProcessPhyloLikelihood | Likelihood framework based on a hmm of simple likelihoods |
| CHmmSequenceEvolution | Sequence evolution framework based on a hmm |
| CHomogeneousTreeLikelihood | Specialization of the TreeLikelihood interface for the Homogeneous case |
| CIdentity | R = id(f) |
| CIFrequencySet | General interface for distance matrix readers |
| CIMultiPhyloDAG | General interface for multiple trees readers |
| CIMultiPhyloTree | |
| CIMultiTree | General interface for multiple trees readers |
| CInMixedSubstitutionModel | SubModel taken from a MixedTransitionModel, kept in the context of the MixedTransitionModel (see FromMixtureSubstitutionModel for an out of context subModel). So "rate" and "scale" are set for the MixedTransitionModel |
| CInOrderTreeIterator | |
| ►CIODAG | General interface for DAG I/O |
| CElement | |
| CIoFrequencySet | General interface for model I/O |
| CIOFrequencySetFactory | Utilitary class for creating frequencies set readers and writers |
| CIOPairedSiteLikelihoods | Base class for I/O on paired-site likelihoods |
| CIOPhymlPairedSiteLikelihoods | This class provides input for the Phyml paired-site likelihoods format |
| CIoSubstitutionModel | General interface for model I/O |
| CIOSubstitutionModelFactory | Utilitary class for creating substitution model readers and writers |
| ►CIOTree | General interface for tree I/O |
| CElement | |
| CIOTreeFactory | Utilitary class for creating tree readers and writers |
| CIOTreepuzzlePairedSiteLikelihoods | This class provides I/O for the Tree-Puzzle/RAxML (phylip-like) paired-site likelihoods format |
| CIPhyloDAG | General interface for DAG readers |
| CIPhyloTree | General interface for tree readers |
| CISubstitutionModel | General interface for model readers |
| CITree | General interface for tree readers |
| CJCnuc | The Jukes-Cantor substitution model for nucleotides |
| CJCprot | The Jukes-Cantor substitution model for proteins |
| CJTT92 | The Jones, Taylor and Thornton substitution model for proteins |
| CK80 | The Kimura 2-rates substitution model for nucleotides |
| CKCM | The general multiple substitution model for codons, from Zaheri & al, 2014 |
| CKrKcSubstitutionRegister | Count conservative and radical amino-acid substitutions |
| CKroneckerCodonDistanceFrequenciesSubstitutionModel | Class for non-synonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic models, with allowed multiple substitutions |
| CKroneckerCodonDistanceSubstitutionModel | Class for non-synonymous substitution models on codons with parameterized nucleotidic models, with allowed multiple substitutions |
| CKroneckerWordSubstitutionModel | Basal class for words of substitution models with multiple substitutions |
| CL95 | The no-strand bias substitution model for nucleotides, from Lobry 1995. The point of this model is that the substitution rate from a nucleotide N towards another M is the same as the rate from the complement of N towards the complement of M. Note that this model is not reversible |
| CLabelCollapsedNodesTreeDrawingListener | A TreeDrawingListener implementation that label the collapsed nodes |
| CLabelInnerNodesTreeDrawingListener | A TreeDrawingListener implementation that write the names of inner nodes |
| CLabelSubstitutionCount | Labelling substitution count |
| CLaplaceSubstitutionCount | Laplace estimate of the substitution count |
| CLeafNamesTreeDrawingListener | A TreeDrawingListener implementation that write leaf names |
| CLegacyAbstractMapping | Partial implementation of the mapping interface |
| CLegacyAbstractRewardMapping | Partial implementation of the reward mapping interface |
| CLegacyAbstractSubstitutionMapping | Partial implementation of the substitution mapping interface |
| CLegacyAncestralStateReconstruction | Interface for ancestral states reconstruction methods |
| CLegacyMappingInterface | General interface for storing mapping data |
| CLegacyMarginalAncestralStateReconstruction | Likelihood ancestral states reconstruction: marginal method |
| ►CLegacyOptimizationTools | Optimization methods for phylogenetic inference |
| CScaleFunction | |
| CLegacyPhylogeneticsApplicationTools | This class provides some common tools for applications |
| CLegacyProbabilisticRewardMapping | Legacy data storage class for probabilistic rewards mappings |
| CLegacyProbabilisticSubstitutionMapping | Legacy data storage class for probabilistic substitution mappings |
| CLegacyRewardMappingInterface | Legacy interface for storing reward mapping data |
| CLegacyRewardMappingTools | Provide methods to compute reward mappings |
| CLegacySubstitutionMappingInterface | Legacy interface for storing mapping data |
| CLegacySubstitutionMappingTools | Provide methods to compute substitution mappings |
| CLG08 | The Le and Gascuel substitution model for proteins |
| ►CLG10_EX_EHO | The Le and Gascuel (2010) EX_EHO substitution model for proteins |
| CEmbeddedModel | |
| ►CLGL08_CAT | The Le et al (2008) CAT substitution model for proteins |
| CEmbeddedModel | |
| CLikelihoodCalculation | |
| ►CLikelihoodCalculationOnABranch | |
| CRateCategoryEdge | |
| ►CLikelihoodCalculationSingleProcess | |
| CProcessNodes | DF Nodes used in the process. ProcessTree is used without any rate multiplier |
| CRateCategoryTrees | |
| ►CLLG08_EHO | The Le et al (2008) EH0 substitution model for proteins |
| CEmbeddedModel | |
| ►CLLG08_EX2 | The Le et al (2008) EX2 substitution model for proteins |
| CEmbeddedModel | |
| ►CLLG08_EX3 | The Le et al (2008) EX3 substitution model for proteins |
| CEmbeddedModel | |
| ►CLLG08_UL2 | The Le et al (2008) UL2 substitution model for proteins |
| CEmbeddedModel | |
| ►CLLG08_UL3 | The Le et al (2008) UL3 substitution model for proteins |
| CEmbeddedModel | |
| CLogSumExp | |
| CMappingInterface | General interface for storing mapping data |
| CMarginalAncestralReconstruction | Likelihood ancestral states reconstruction: marginal method |
| CMarkovModulatedFrequencySet | FrequencySet to be used with a Markov-modulated substitution model |
| CMarkovModulatedStateMap | This class implements a state map for Markov modulated models |
| CMarkovModulatedSubstitutionModel | Partial implementation of the Markov-modulated class of substitution models |
| CMatrixDimension | Basic matrix dimension type |
| CMatrixProduct | |
| CMG94 | The Muse and Gaut (1994) substitution model for codons |
| ►CMixedSubstitutionModelSet | Substitution models manager for Mixed Substitution Models. This class inherits from SubstitutionModelSet |
| ►CHyperNode | |
| CNode | |
| CMixedTransitionModelInterface | Interface for Transition models, defined as a mixture of "simple" transition models |
| CMixtureOfASubstitutionModel | |
| CMixtureOfATransitionModel | Transition models defined as a mixture of nested substitution models |
| CMixtureOfSubstitutionModels | |
| CMixtureOfTransitionModels | Transition models defined as a mixture of several substitution models |
| CMixtureProcessPhyloLikelihood | Likelihood framework based on a mixture of simple likelihoods |
| CMixtureSequenceEvolution | Sequence evolution framework based on a mixture of substitution processes |
| CModelBranch | |
| CModelList | A list of models, for building a WordSubstitutionModel |
| ►CModelPath | Organization of submodels in mixed substitution models in a path. See class ModelScenario for a thorough description |
| CPathNode | A vector<int> where all elements are different and in INCREASING ORDER. So inclusion should be done through dedicated methods |
| CModelScenario | Organization of submodels in mixed substitution models as paths |
| CMultinomialFromTransitionModel | From a model, compute the likelihood of counts given an ancestral state |
| CMultiProcessSequenceEvolution | Partial implementation of multiple processes of sequences |
| CMultiProcessSequencePhyloLikelihood | Partial implementation of the Likelihood interface for multiple processes |
| CMutationPath | This class is used by MutationProcess to store detailed results of simulations |
| CMutationProcess | Interface for simulations |
| CMvaFrequencySet | A frequencies set used to estimate frequencies at the root with the COaLA model. Frequencies at the root are optimized in the same way than the equlibrium frequencies on branches. Hyperparameters are used, which represent positions along the principal axes obtained from a preliminary Correspondence Analysis. From the optimized positions, the 20 frequencies are calculated |
| CNaiveSubstitutionCount | Naive substitution count |
| CNaNListener | A listener which capture NaN function values and throw an exception in case this happens |
| CNeighborJoining | The neighbor joining distance method |
| CNewick | The so-called 'newick' parenthetic format |
| CNexusIOTree | Simple parser for reading trees from a Nexus file |
| ►CNhx | The so-called 'Nhx - New Hampshire eXtended' parenthetic format |
| CProperty | |
| CNNIHomogeneousTreeLikelihood | This class adds support for NNI topology estimation to the DRHomogeneousTreeLikelihood class |
| CNNISearchable | Interface for Nearest Neighbor Interchanges algorithms |
| CNNITopologyListener | Listener used internally by the optimizeTreeNNI method |
| CNNITopologyListener2 | Listener used internally by the optimizeTreeNNI2 method |
| CNNITopologySearch | NNI topology search method |
| CNode | The phylogenetic node class |
| CNode_DF | Base dataflow Node class |
| CNodeEvent | |
| CNodeException | General exception thrown when something is wrong with a particular node |
| CNodeNotFoundException | Exception thrown when something is wrong with a particular node |
| CNodePException | General exception thrown when something is wrong with a particular node |
| CNodesIdTreeDrawingListener | A TreeDrawingListener implementation that writes nodes id |
| CNodeTemplate | The NodeTemplate class |
| CNoDimension | Empty type representing no dimensions |
| CNonHomogeneousSequenceSimulator | (Legacy) Site and sequences simulation under non-homogeneous models |
| CNonHomogeneousSubstitutionProcess | Substitution process manager for non-homogeneous / non-reversible models of evolution |
| CNonHomogeneousTreeLikelihood | Specialization of the TreeLikelihood interface for the branch non-homogeneous and non-stationary models |
| CNucleotideFrequencySetInterface | Parametrize a set of state frequencies for nucleotides |
| CNucleotideReversibleSubstitutionModelInterface | Specialisation interface for rversible nucleotide substitution model |
| CNucleotideSubstitutionModelInterface | Specialisation interface for nucleotide substitution model |
| CNumericalDependencyTransform | Template struct used to describe a dependency transformation before compute() |
| CNumericalDependencyTransform< Transposed< T > > | Implementation for a dependency transposition |
| CNumericalDerivativeConfiguration | Configuration for a numerical derivation: what delta to use, and type of derivation |
| CNumericConstant | R = constant_value |
| CNumericMutable | R = variable_value |
| COFrequencySet | General interface for distance matrix writers |
| COMultiPhyloDAG | General interface for tree writers |
| COMultiPhyloTree | General interface for tree writers |
| COMultiTree | General interface for tree writers |
| COnABranchPhyloLikelihood | Wraps a dataflow graph as a function: resultNode = f(variableNodes) |
| COneChangeRegisterTransitionModel | From a model, compute transition probabilities given there is at least a change of a category (ie a non null number in a register) in the branch |
| COneChangeTransitionModel | From a model, compute transition probabilities given there is at least a change in the branch |
| COneJumpSubstitutionCount | Computes the probability that at least one jump occurred on a branch, given the initial and final state |
| COneProcessSequenceEvolution | Evolution of a sequence performed by a unique SubstitutionProcess all along the sequence |
| COneProcessSequencePhyloLikelihood | The OneProcessSequencePhyloLikelihood class: phylogenetic likelihood computation with a single process |
| COneProcessSequenceSubstitutionMapping | The OneProcessSequenceSubstitutionMapping class: substitution mapping linked with a OneProcessSequencePhyloLikelihood |
| COPhyloDAG | General interface for DAG writers |
| COPhyloTree | General interface for tree writers |
| ►COptimizationTools | Optimization methods for phylogenetic inference |
| COptimizationOptions | |
| COSubstitutionModel | General interface for distance matrix writers |
| COTree | General interface for tree writers |
| CPairedSiteLikelihoods | A container for paired-site likelihoods (likelihoods over the same sites for different models, especially topologies). An instance of this class is, roughly, a list of models, each of them having a name (stored in the modelNames attribute) and a set of site likelihoods (stored in the logLikelihoods attribute) |
| CParametrizablePhyloTree | PhyloTree with Parametrizable Phylo Branches. They SHARE their branch length parameters |
| CPartitionProcessPhyloLikelihood | |
| CPartitionSequenceEvolution | Sequence evolution framework based on a mixture of substitution processes |
| CPatternTools | Utilitary methods to compute site patterns |
| CPGMA | Compute WPGMA and UPGMA trees from a distance matrix |
| CPGMAInfos | Inner data structure for WPGMA and UPGMA distance methods |
| CPhyloBranch | |
| CPhyloBranchException | General exception thrown when something is wrong with a particular branch |
| CPhyloBranchMapping | |
| CPhyloBranchNotFoundException | Exception thrown when something is wrong with a particular branch |
| CPhyloBranchParam | |
| CPhyloBranchPException | General exception thrown when something is wrong with a particular branch |
| CPhyloBranchPropertyNotFoundException | General exception thrown if a property could not be found |
| CPhyloBranchReward | |
| CPhyloDAG | |
| CPhylogeneticsApplicationTools | This class provides some common tools for applications |
| CPhylogramDrawBranchEvent | |
| CPhylogramPlot | Phylogram representation of trees |
| CPhyloLikelihoodContainer | The PhyloLikelihoodContainer, owns and assigns numbers to Phylolikelihoods |
| CPhyloLikelihoodFormula | The PhyloLikelihoodFormula class, for phylogenetic likelihood on several independent data |
| CPhyloLikelihoodInterface | The PhyloLikelihood interface, for phylogenetic likelihood |
| CPhyloLikelihoodSetInterface | The PhyloLikelihoodSet interface, to manage a subset of PhyloLikelihoods from a given PhyloLikelihoodContainer |
| CPhyloNode | |
| CPhyloNodeException | General exception thrown when something is wrong with a particular node |
| CPhyloNodeNotFoundException | Exception thrown when something is wrong with a particular node |
| CPhyloNodePException | General exception thrown when something is wrong with a particular node |
| CPhyloNodePropertyNotFoundException | General exception thrown if a property could not be found |
| CPhyloStatistics | Compute several quantities on a tree simulateously, optimizing the recursions on the tree |
| CPhyloSubstitutionMapping | |
| CPhyloTree | |
| CPhyloTreeException | General exception thrown when something wrong happened in a tree |
| ►CPhyloTreeTools | Generic utilitary methods dealing with trees |
| CMoments_ | |
| CPOMO | |
| CPostOrderTreeIterator | |
| CPreOrderTreeIterator | |
| CProbabilisticRewardMapping | Data storage class for probabilistic rewards mappings |
| CProbabilisticSubstitutionMapping | Data storage class for probabilistic substitution mappings |
| CProbabilitiesFromDiscreteDistribution | |
| CProbabilitiesFromMixedModel | |
| CProbabilityDAG | |
| CProbabilityFromDiscreteDistribution | |
| CProbabilityFromMixedModel | |
| CProcessComputationEdge | |
| CProcessComputationNode | Tree Organization of Computing Nodes |
| CProcessComputationTree | |
| CProcessEdge | |
| CProcessTree | |
| CProcPos | Likelihood framework based on a partition of a sequence in simple likelihoods |
| CPropertyNotFoundException | General exception thrown if a property could not be found |
| CProteinFrequencySetInterface | Parametrize a set of state frequencies for proteins |
| CProteinReversibleSubstitutionModelInterface | Specialized interface for protein reversible substitution model |
| CProteinSubstitutionModelInterface | Specialized interface for protein substitution model |
| ►CPseudoNewtonOptimizer | This Optimizer implements Newton's algorithm for finding a minimum of a function. This is in fact a modified version of the algorithm, as suggested by Nicolas Galtier, for the purpose of optimizing phylogenetic likelihoods |
| CPNStopCondition | |
| CRASiteSimulationResult | Data structure to store the result of a DetailedSiteSimulator |
| CRASTools | Tools to deal with Rates Across Sites (RAS) models |
| CRateAcrossSitesSubstitutionProcess | |
| CRE08 | The Rivas-Eddy substitution model with gap characters |
| CRE08Codon | This is a wrapper class of RE08 for codon substitution models |
| CRE08Nucleotide | This is a wrapper class of RE08 for nucleotide substitution models |
| CRE08Protein | This is a wrapper class of RE08 for protein substitution models |
| CReductionOf | |
| CRegisterRatesSubstitutionModel | From a model, substitution rates are set into categories following a given register. Each substitution of a category is then multiplied by a rate parameter specific to this category |
| CRELAX | The RELAX (2014) branch-site model for codons |
| CReversibleSubstitutionModelInterface | Interface for reversible substitution models |
| CReward | The Reward interface |
| CRewardMappingInterface | General interface for storing reward mapping data |
| CRewardMappingTools | Provide methods to compute reward mappings |
| CRHomogeneousMixedTreeLikelihood | |
| CRHomogeneousTreeLikelihood | This class implement the 'traditional' way of computing likelihood for a tree |
| CRN95 | The model described by Rhetsky & Nei, where the only hypothesis is that the transversion rates are only dependent of the target nucleotide. This model is not reversible |
| CRN95s | Intersection of models RN95 and L95 |
| CRNonHomogeneousMixedTreeLikelihood | |
| CRNonHomogeneousTreeLikelihood | This class implement the 'traditional' way of computing likelihood for a tree, allowing for non-homogeneous models of substitutions |
| CRowVectorDimension | |
| CScalarProduct | |
| CSelectedSubstitutionRegister | Class inheriting from GeneralSubstitutionRegister, this one uses a special constructor which allows it to build a substitution matrix from string input specifying a desired substitutions |
| CSelfMutationProcess | This class is mainly for testing purpose. It allow "self" mutation of the kind i->i; |
| CSENCA | Class for non-synonymous and synonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic basic models |
| CSequence_DF | Data flow node representing a Sequence as a Value<Eigen::MatrixXd> with a name |
| CSequenceEvolution | This interface describes the evolution process of a sequence |
| CSequencePhyloLikelihoodInterface | PhyloLikelihoods based on Sequence Evolution class, ie for which there is a (set of) processes able to build a sequence |
| CSequenceSimulationTools | Tools for sites and sequences simulation |
| CSequenceSimulatorInterface | The SequenceSimulator interface. SequenceSimulator classes can simulate whole datasets |
| CShiftDelta | |
| CShiftParameter | Shift param value = n * delta + x |
| CSimData | |
| CSimpleMutationProcess | Generally used mutation process model |
| CSimpleSubstitutionProcess | Space and time homogeneous substitution process, without mixture |
| CSimpleSubstitutionProcessSequenceSimulator | Sequences simulation under a unique substitution process |
| CSimpleSubstitutionProcessSiteSimulator | Site simulation under a unique substitution process |
| CSimProcessEdge | |
| CSimProcessNode | |
| CSingleDataPhyloLikelihoodInterface | The SingleDataPhyloLikelihood interface, for phylogenetic likelihood |
| CSingleProcessPhyloLikelihood | Wraps a dataflow graph as a function: resultNode = f(variableNodes) |
| CSingleProcessSubstitutionMapping | The SingleProcessSubstitutionMapping class: substitution mapping linked with a SingleProcessPhyloLikelihood |
| CSitePartition | This is the interface for classes describing a site partition, each partition being intended to have its own substitution model |
| CSitePartitionHomogeneousTreeLikelihood | Specialization of the TreeLikelihood interface for partition models, homogeneous case |
| ►CSitePatterns | Data structure for site patterns |
| CSortableSite | Class used for site pattern sorting |
| CSiteSimulationResult | Data structure to store the result of a DetailedSiteSimulator |
| CSiteSimulatorInterface | The SiteSimulator interface. SiteSimulator classes can simulate single sites |
| CSSR | The Strand Symmetric Reversible substitution model for nucleotides |
| CStateMapInterface | Map the states of a given alphabet which have a model state |
| CStochasticMapping | |
| CSubstitutionCountInterface | The SubstitutionsCount interface |
| CSubstitutionDistance | Interface allowing for using distances between states in substitution counts |
| CSubstitutionMapping | General interface for storing mapping data |
| CSubstitutionMappingTools | Provide methods to compute substitution mappings |
| CSubstitutionModelInterface | Interface for all substitution models |
| CSubstitutionModelSet | Substitution models manager for non-homogeneous / non-reversible models of evolution |
| CSubstitutionModelSetTools | Tools for automatically creating SubstitutionModelSet objects |
| CSubstitutionProcessCollection | Collection of Substitution Process, which owns all the necessary objects: Substitution models, frequencies sets, rate distributions and trees |
| ►CSubstitutionProcessCollectionMember | |
| CDeleter | |
| CSubstitutionProcessInterface | This interface describes the substitution process along the tree and sites of the alignment |
| CSubstitutionProcessSequenceSimulator | Sequences simulation under position specific substitution process |
| CSubstitutionRegisterInterface | The SubstitutionRegister interface |
| CSumOfLogarithms | |
| CSWSubstitutionRegister | Distinguishes substitutions given the link between the changed nucleotides : S for strong (GC) and W for weak (AT) |
| CT92 | The Tamura (1992) substitution model for nucleotides |
| CTN93 | The Tamura and Nei (1993) substitution model for nucleotides |
| CTopologyChangeEvent | Class for notifying new toplogy change events |
| CTopologyListener | Implement this interface to be notified when the topology of a tree has changed during topology search |
| CTopologySearch | Interface for topology search methods |
| CTotalSubstitutionRegister | Count all substitutions |
| CTransitionFromTransitionModel | From a transition model, compute the transition function probabilities |
| CTransitionFunctionFromModel | |
| CTransitionMatrixFromModel | |
| CTransitionMatrixFromTransitionMatrix | |
| CTransitionModelInterface | Interface for all transition models |
| CTransposed | The T dependency should be transposed before computation |
| CTree | Interface for phylogenetic tree objects |
| CTreeDrawing | Basal interface for tree drawing classes |
| CTreeDrawingDisplayControler | Easy tune of tree drawings display |
| CTreeDrawingListener | Interface allowing to capture drawing events |
| CTreeDrawingListenerAdapter | An empty implementation of the TreeDrawingListener interface |
| CTreeDrawingNodeInfo | |
| CTreeDrawingSettings | A set of options to tune the display of a TreeDrawing object |
| CTreeException | General exception thrown when something wrong happened in a tree |
| CTreeIterator | |
| CTreeLikelihoodData | TreeLikelihood data structure |
| ►CTreeLikelihoodInterface | The TreeLikelihood interface |
| CBranchIterator | An iterator over a set of branches, specified by their node ids |
| CConstBranchModelDescription | A pair of SubstitutionModel / SiteIterator |
| CConstBranchModelIterator | Iterates through all models used for all sites on a given branch |
| CConstSiteModelDescription | A pair of SubstitutionModel / BranchIterator |
| CConstSiteModelIterator | Iterates through all models used for all branches on a given site |
| CSiteIterator | An iterator over a set of sites, specified by their position |
| CTreeLikelihoodNodeData | TreeLikelihood partial data structure |
| CTreeLikelihoodTools | Utilitary methods that work with TreeLikelihood objects |
| CTreeParsimonyDataInterface | TreeParsimonyScore data structure |
| CTreeParsimonyNodeDataInterface | TreeParsimonyScore node data structure |
| CTreeParsimonyScoreInterface | Compute a parsimony score |
| CTreeTemplate | The phylogenetic tree class |
| ►CTreeTemplateTools | Utilitary methods working with TreeTemplate and Node objects |
| CElement | |
| CMoments_ | A structure recording, for a subtree, the sum of root-leaf distances, the sum of their squares, and the number of elements in these sums (ie. the number of leaves) |
| COrderTreeData_ | |
| ►CTreeTools | Generic utilitary methods dealing with trees |
| CMoments_ | |
| CTripletSubstitutionModel | Class for neutral substitution models on triplets, which correspond to codons that do not have any significance (whether they are STOP or functional) |
| CTrivialSitePartition | Trivial site partition: all sites belong to the same, unique partition |
| CTS98 | Tuffley and Steel's 1998 covarion model |
| CTsTvSubstitutionRegister | Distinguishes transitions from transversions |
| CTwoParameterBinarySubstitutionModel | The Model on two states |
| CUniformizationSubstitutionCount | Analytical (weighted) substitution count using the uniformization method |
| CUnrootedPhyloTreeException | Exception thrown when a tree is expected to be rooted |
| CUnrootedTreeException | Exception thrown when a tree is expected to be rooted |
| CUserCodonFrequencySet | |
| CUserFrequencySet | FrequencySet to be read in a file. More specifically, a frequency set is read in a column of a given file, which column number is given in argument (default: 1) |
| CUserNucleotideFrequencySet | FrequencySet useful for homogeneous and stationary models, nucleotide implementation |
| CUserProteinFrequencySet | FrequencySet from file |
| CUserProteinSubstitutionModel | Build an empirical protein substitution model from a file |
| CValue | Abstract Node storing a value of type T |
| CValueFromConfiguredParameter | |
| CVectorDimension | |
| CVectorOfSubstitutionRegisters | Sets a Register based on a vector of Registers. The categories are intersection of categories of those Registers |
| CWAG01 | The Whelan and Goldman substitution model for proteins |
| CWeightedSubstitutionCount | Interface allowing for weighting of substitution counts according to state properties |
| CWordFrequencySetInterface | Frequencies in words computed from the frequencies on letters. The parameters are the parameters of the Frequencies on letters. The WordFrequencySet owns the std::shared_ptr<FrequencySet> it is built on. Interface class |
| CWordFromIndependentFrequencySet | Frequencies in words are the product of Independent Frequencies in letters |
| CWordFromUniqueFrequencySet | |
| CWordSubstitutionModel | Basal class for words of substitution models |
| CWrappedModelInterface | Wrapping model interface |
| CWrappedSubstitutionModelInterface | |
| CWrappedTransitionModelInterface | |
| CYN98 | The Yang and Nielsen (1998) substitution model for codons |
| CYNGP_M | Abstract generic class for The Yang et al (2000) M substitution models for codons. al (2004) |
| CYNGP_M1 | The Yang et al (2000) M1 substitution model for codons, with the more realistic modification in Wong & al (2004) |
| CYNGP_M10 | The Yang et al (2000) M10 substitution model for codons |
| CYNGP_M2 | The Yang et al (2000) M2 substitution model for codons, with the more realistic modification in Wong & al (2004) |
| CYNGP_M3 | The Yang et al (2000) M3 substitution model for codons |
| CYNGP_M7 | The Yang et al (2000) M7 substitution model for codons |
| CYNGP_M8 | The Yang et al (2000) M8 substitution model for codons |
| CYNGP_M9 | The Yang et al (2000) M9 substitution model for codons |
| CYpR | YpR model |
| CYpR_Gen | General YpR model |
| CYpR_Sym | Symmetrical YpR model |
| ►NEigen | |
| CNumTraits< bpp::ExtendedFloat > | |
| CScalarBinaryOpTraits< bpp::ExtendedFloat, double, BinaryOp > | |
| CScalarBinaryOpTraits< double, bpp::ExtendedFloat, BinaryOp > | |
| CIntAndInt | |
| CStringAndInt | |
1.9.4 
