Class Hierarchy

Go to the graphical class hierarchy

This inheritance list is sorted roughly, but not completely, alphabetically:

[detail level 1234567891011]

►Cbpp::AncestralStateReconstruction	Interface for ancestral states reconstruction methods
Cbpp::MarginalAncestralReconstruction	Likelihood ancestral states reconstruction: marginal method
Cbpp::AwareNode	A node class aware of its neighbours
Cbpp::BipartitionTools	This class provides tools related to the BipartitionList class
►Cbpp::BppApplication [external]
►Cbpp::BppSequenceApplication [external]
Cbpp::BppPhylogeneticsApplication
►Cbpp::BranchedModelSet
►Cbpp::AbstractSinglePhyloSubstitutionMapping	The AbstractSinglePhyloSubstitutionMapping class: substitution mapping linked with a Single Process PhyloLikelihood
Cbpp::OneProcessSequenceSubstitutionMapping	The OneProcessSequenceSubstitutionMapping class: substitution mapping linked with a OneProcessSequencePhyloLikelihood
Cbpp::SingleProcessSubstitutionMapping	The SingleProcessSubstitutionMapping class: substitution mapping linked with a SingleProcessPhyloLikelihood
►Cbpp::TreeLikelihoodInterface::BranchIterator	An iterator over a set of branches, specified by their node ids
Cbpp::AbstractTreeLikelihood::SimpleBranchIterator	A very simple branch iterator
Cbpp::Context::CachedNodeRef	NodeRef is hashable and comparable as a pointer. CachedNodeRef is hashable and comparable, by comparing the node configuration:
Cbpp::Context::CachedNodeRefHash
►Cbpp::Clonable [external]
Cbpp::BipartitionList	This class deals with the bipartitions defined by trees
Cbpp::DistanceEstimation
►Cbpp::DistanceMethodInterface	General interface for distance-based phylogenetic reconstruction methods
►Cbpp::AgglomerativeDistanceMethodInterface	Interface for agglomerative distance methods
►Cbpp::AbstractAgglomerativeDistanceMethod	Partial implementation of the AgglomerativeDistanceMethod interface
Cbpp::HierarchicalClustering	Hierarchical clustering
►Cbpp::NeighborJoining	The neighbor joining distance method
Cbpp::BioNJ	The BioNJ distance method
Cbpp::PGMA	Compute WPGMA and UPGMA trees from a distance matrix
►Cbpp::GraphObserver [external]
►Cbpp::AssociationGraphObserver< class, class > [external]
►CAssociationGraphImplObserver< N, E, DAGraphImpl > [external]
►Cbpp::AssociationDAGraphImplObserver< class, class, class > [external]
Cbpp::BackwardLikelihoodTree
Cbpp::ForwardLikelihoodTree
Cbpp::ProbabilityDAG
►CAssociationGraphImplObserver< N, E, TreeGraphImpl > [external]
►Cbpp::AssociationTreeGraphImplObserver< class, class, class > [external]
Cbpp::AbstractSinglePhyloSubstitutionMapping	The AbstractSinglePhyloSubstitutionMapping class: substitution mapping linked with a Single Process PhyloLikelihood
Cbpp::ParametrizablePhyloTree	PhyloTree with Parametrizable Phylo Branches. They SHARE their branch length parameters
Cbpp::PhyloTree
Cbpp::ProbabilisticRewardMapping	Data storage class for probabilistic rewards mappings
Cbpp::ProbabilisticSubstitutionMapping	Data storage class for probabilistic substitution mappings
Cbpp::ProcessComputationTree
Cbpp::ProcessTree
►Cbpp::AssociationDAGraphObserver< class, class > [external]
Cbpp::AssociationDAGraphImplObserver< class, class, class > [external]
►Cbpp::AssociationTreeGraphObserver< class, class > [external]
Cbpp::AssociationTreeGraphImplObserver< class, class, class > [external]
►Cbpp::LegacyMappingInterface	General interface for storing mapping data
►Cbpp::LegacyAbstractMapping	Partial implementation of the mapping interface
►Cbpp::LegacyAbstractRewardMapping	Partial implementation of the reward mapping interface
Cbpp::LegacyProbabilisticRewardMapping	Legacy data storage class for probabilistic rewards mappings
►Cbpp::LegacyAbstractSubstitutionMapping	Partial implementation of the substitution mapping interface
Cbpp::LegacyProbabilisticSubstitutionMapping	Legacy data storage class for probabilistic substitution mappings
►Cbpp::LegacyRewardMappingInterface	Legacy interface for storing reward mapping data
Cbpp::LegacyAbstractRewardMapping	Partial implementation of the reward mapping interface
►Cbpp::LegacySubstitutionMappingInterface	Legacy interface for storing mapping data
Cbpp::LegacyAbstractSubstitutionMapping	Partial implementation of the substitution mapping interface
►Cbpp::MappingInterface	General interface for storing mapping data
►Cbpp::AbstractMapping	Partial implementation of the mapping interface
►Cbpp::AbstractRewardMapping	Partial implementation of the substitution mapping interface
Cbpp::ProbabilisticRewardMapping	Data storage class for probabilistic rewards mappings
►Cbpp::AbstractSubstitutionMapping	Partial implementation of the substitution mapping interface
Cbpp::ProbabilisticSubstitutionMapping	Data storage class for probabilistic substitution mappings
►Cbpp::RewardMappingInterface	General interface for storing reward mapping data
Cbpp::AbstractRewardMapping	Partial implementation of the substitution mapping interface
►Cbpp::SubstitutionMapping	General interface for storing mapping data
Cbpp::AbstractSubstitutionMapping	Partial implementation of the substitution mapping interface
►Cbpp::NNISearchable	Interface for Nearest Neighbor Interchanges algorithms
Cbpp::DRTreeParsimonyScore	Double recursive implementation of interface TreeParsimonyScore
Cbpp::NNIHomogeneousTreeLikelihood	This class adds support for NNI topology estimation to the DRHomogeneousTreeLikelihood class
Cbpp::NodeEvent
►Cbpp::OptimizationStopCondition [external]
►Cbpp::AbstractOptimizationStopCondition [external]
Cbpp::PseudoNewtonOptimizer::PNStopCondition
►Cbpp::OptimizerInterface [external]
►Cbpp::AbstractOptimizer [external]
Cbpp::PseudoNewtonOptimizer	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
►Cbpp::Parameter [external]
►Cbpp::ConfiguredParameter	Data flow node representing a parameter
Cbpp::ShiftParameter	Shift param value = n * delta + x
►Cbpp::Parametrizable [external]
►Cbpp::AbstractParametrizable [external]
►Cbpp::AbstractParameterAliasable [external]
Cbpp::AbstractCodonAAFitnessSubstitutionModel	Abstract class for modelling of ratios of substitution rates between codons, whatever they are synonymous or not
Cbpp::AbstractCodonAARateSubstitutionModel	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)
Cbpp::AbstractCodonBGCSubstitutionModel	Abstract class for modelling of non-synonymous and synonymous substitution rates in codon models, with gBGC
Cbpp::AbstractCodonClusterAASubstitutionModel	Abstract class for modelling of non-synonymous and synonymous substitution rates in codon models, with AA clustered
Cbpp::AbstractCodonCpGSubstitutionModel	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
►Cbpp::AbstractCodonDistanceSubstitutionModel	Abstract class for modelling of non-synonymous and synonymous substitution rates in codon models
Cbpp::CodonDistanceFrequenciesSubstitutionModel	Class for asynonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic models
Cbpp::CodonDistancePhaseFrequenciesSubstitutionModel	Class for asynonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic basic models
Cbpp::CodonDistanceSubstitutionModel	Class for substitution models of codons with non-synonymous/synonymous ratios of substitution rates defined through a distance between amino-acids
Cbpp::DFPDistanceFrequenciesSubstitutionModel	Class for non-synonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic models, with allowed multiple substitutions as parameterized in DFP model
Cbpp::KroneckerCodonDistanceFrequenciesSubstitutionModel	Class for non-synonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic models, with allowed multiple substitutions
Cbpp::KroneckerCodonDistanceSubstitutionModel	Class for non-synonymous substitution models on codons with parameterized nucleotidic models, with allowed multiple substitutions
Cbpp::SENCA	Class for non-synonymous and synonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic basic models
►Cbpp::AbstractCodonFitnessSubstitutionModel	Abstract class for modelling of ratios of substitution rates between codons, whatever they are synonymous or not
Cbpp::SENCA	Class for non-synonymous and synonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic basic models
►Cbpp::AbstractCodonFrequenciesSubstitutionModel	Abstract Class for substitution models on codons parametrized by frequencies
Cbpp::CodonDistanceFrequenciesSubstitutionModel	Class for asynonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic models
Cbpp::DFPDistanceFrequenciesSubstitutionModel	Class for non-synonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic models, with allowed multiple substitutions as parameterized in DFP model
Cbpp::KroneckerCodonDistanceFrequenciesSubstitutionModel	Class for non-synonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic models, with allowed multiple substitutions
►Cbpp::AbstractCodonPhaseFrequenciesSubstitutionModel	Abstract Class for substitution models on codons parametrized by a frequency
Cbpp::CodonDistancePhaseFrequenciesSubstitutionModel	Class for asynonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic basic models
►Cbpp::AbstractDiscreteDistribution [external]
►Cbpp::ConstantDistribution [external]
Cbpp::ConstantRateDistribution
►Cbpp::ExponentialDiscreteDistribution [external]
Cbpp::ExponentialDiscreteRateDistribution
►Cbpp::GammaDiscreteDistribution [external]
Cbpp::GammaDiscreteRateDistribution
►Cbpp::GaussianDiscreteDistribution [external]
Cbpp::GaussianDiscreteRateDistribution
►Cbpp::AbstractFrequencySet	Basic implementation of the FrequencySet interface
►Cbpp::AbstractWordFrequencySet
►Cbpp::WordFromIndependentFrequencySet	Frequencies in words are the product of Independent Frequencies in letters
Cbpp::CodonFromIndependentFrequencySet	Frequencies in codons are the product of Independent Frequencies in letters with the frequencies of stop codons set to zero
►Cbpp::WordFromUniqueFrequencySet
Cbpp::CodonFromUniqueFrequencySet	Frequencies in codons are the product of the frequencies for a unique FrequencySet in letters, with the frequencies of stop codons set to zero
Cbpp::FixedCodonFrequencySet	FrequencySet useful for homogeneous and stationary models, codon implementation
►Cbpp::FixedFrequencySet	FrequencySet useful for homogeneous and stationary models
Cbpp::FixedNucleotideFrequencySet	FrequencySet useful for homogeneous and stationary models, nucleotide implementation
Cbpp::FixedProteinFrequencySet	FrequencySet useful for homogeneous and stationary models, protein implementation
Cbpp::FromModelFrequencySet	FrequencySet defined from the equilibrium distribution of a given model
Cbpp::FullCodonFrequencySet	A generic FrequencySet for Full Codon alphabets
►Cbpp::FullFrequencySet	A generic FrequencySet allowing for the estimation of all frequencies
Cbpp::FullProteinFrequencySet	Protein FrequencySet using 19 independent parameters to model the 20 frequencies
Cbpp::FullNucleotideFrequencySet	Nucleotide FrequencySet using three independent parameters (theta, theta1, theta2) to modelize the four frequencies:
Cbpp::FullPerAACodonFrequencySet	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
Cbpp::GCFrequencySet	Nucleotide FrequencySet using only one parameter, the GC content
Cbpp::MarkovModulatedFrequencySet	FrequencySet to be used with a Markov-modulated substitution model
Cbpp::MvaFrequencySet	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
►Cbpp::UserFrequencySet	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)
Cbpp::UserCodonFrequencySet
Cbpp::UserNucleotideFrequencySet	FrequencySet useful for homogeneous and stationary models, nucleotide implementation
Cbpp::UserProteinFrequencySet	FrequencySet from file
►Cbpp::AbstractSubstitutionProcess	A partial implementation of the SubstitutionProcess interface
►Cbpp::AbstractAutonomousSubstitutionProcess	A partial implementation of the SubstitutionProcess interface
Cbpp::NonHomogeneousSubstitutionProcess	Substitution process manager for non-homogeneous / non-reversible models of evolution
Cbpp::RateAcrossSitesSubstitutionProcess
Cbpp::SimpleSubstitutionProcess	Space and time homogeneous substitution process, without mixture
Cbpp::SubstitutionProcessCollectionMember
►Cbpp::AbstractTransitionModel	Partial implementation of the TransitionModel interface
►Cbpp::AbstractMixedTransitionModel	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
►Cbpp::MixtureOfATransitionModel	Transition models defined as a mixture of nested substitution models
Cbpp::MixtureOfASubstitutionModel
►Cbpp::MixtureOfTransitionModels	Transition models defined as a mixture of several substitution models
Cbpp::MixtureOfSubstitutionModels
►Cbpp::AbstractSubstitutionModel
►Cbpp::AbstractDFPSubstitutionModel	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
Cbpp::DFPDistanceFrequenciesSubstitutionModel	Class for non-synonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic models, with allowed multiple substitutions as parameterized in DFP model
►Cbpp::AbstractNucleotideSubstitutionModel	Specialisation abstract class for nucleotide substitution model
Cbpp::L95	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
Cbpp::RN95	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
Cbpp::RN95s	Intersection of models RN95 and L95
Cbpp::gBGC	GBGC model
Cbpp::AbstractProteinSubstitutionModel	Specialisation abstract class for protein substitution model
►Cbpp::AbstractReversibleSubstitutionModel	Partial implementation of the ReversibleSubstitutionModel interface
►Cbpp::AbstractReversibleNucleotideSubstitutionModel	Specialisation abstract class for reversible nucleotide substitution model
Cbpp::F81	The Felsenstein (1981) substitution model for nucleotides
Cbpp::F84	The Felsenstein (1984) substitution model for nucleotides
Cbpp::GTR	The General Time-Reversible substitution model for nucleotides
Cbpp::HKY85	The Hasegawa M, Kishino H and Yano T (1985) substitution model for nucleotides
Cbpp::JCnuc	The Jukes-Cantor substitution model for nucleotides
Cbpp::K80	The Kimura 2-rates substitution model for nucleotides
Cbpp::SSR	The Strand Symmetric Reversible substitution model for nucleotides
Cbpp::T92	The Tamura (1992) substitution model for nucleotides
Cbpp::TN93	The Tamura and Nei (1993) substitution model for nucleotides
►Cbpp::AbstractReversibleProteinSubstitutionModel	Specialisation abstract class for reversible protein substitution model
Cbpp::Coala	The Coala branch-heterogeneous amino-acid substitution model
Cbpp::DSO78	The Dayhoff, Schwartz and Orcutt substitution model for proteins
Cbpp::JCprot	The Jukes-Cantor substitution model for proteins
Cbpp::JTT92	The Jones, Taylor and Thornton substitution model for proteins
Cbpp::LG08	The Le and Gascuel substitution model for proteins
Cbpp::LG10_EX_EHO::EmbeddedModel
Cbpp::LGL08_CAT::EmbeddedModel
Cbpp::LLG08_EHO::EmbeddedModel
Cbpp::LLG08_EX2::EmbeddedModel
Cbpp::LLG08_EX3::EmbeddedModel
Cbpp::LLG08_UL2::EmbeddedModel
Cbpp::LLG08_UL3::EmbeddedModel
Cbpp::UserProteinSubstitutionModel	Build an empirical protein substitution model from a file
Cbpp::WAG01	The Whelan and Goldman substitution model for proteins
Cbpp::BinarySubstitutionModel	The Model on two states
Cbpp::D1WalkSubstitutionModel	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
Cbpp::EquiprobableSubstitutionModel	The EquiprobableSubstitutionModel substitution model for any kind of alphabet. Jukes-Cantor models are specific case of this model, applied to nucleotides or proteins
►Cbpp::RE08	The Rivas-Eddy substitution model with gap characters
Cbpp::RE08Codon	This is a wrapper class of RE08 for codon substitution models
Cbpp::RE08Nucleotide	This is a wrapper class of RE08 for nucleotide substitution models
Cbpp::RE08Protein	This is a wrapper class of RE08 for protein substitution models
Cbpp::TwoParameterBinarySubstitutionModel	The Model on two states
►Cbpp::AbstractWordSubstitutionModel	Abstract Basal class for words of substitution models
►Cbpp::AbstractCodonSubstitutionModel	Abstract class for substitution models on codons
Cbpp::CodonAdHocSubstitutionModel	Class for substitution models of codons with several layers of codon models
Cbpp::CodonDistanceFrequenciesSubstitutionModel	Class for asynonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic models
Cbpp::CodonDistancePhaseFrequenciesSubstitutionModel	Class for asynonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic basic models
Cbpp::CodonDistanceSubstitutionModel	Class for substitution models of codons with non-synonymous/synonymous ratios of substitution rates defined through a distance between amino-acids
Cbpp::SENCA	Class for non-synonymous and synonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic basic models
►Cbpp::AbstractKroneckerWordSubstitutionModel	Abstract Kronecker Word Model
►Cbpp::AbstractKroneckerCodonSubstitutionModel	Abstract class for substitution models on codons allowing multiple substitutions
Cbpp::KroneckerCodonDistanceFrequenciesSubstitutionModel	Class for non-synonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic models, with allowed multiple substitutions
Cbpp::KroneckerCodonDistanceSubstitutionModel	Class for non-synonymous substitution models on codons with parameterized nucleotidic models, with allowed multiple substitutions
Cbpp::KroneckerWordSubstitutionModel	Basal class for words of substitution models with multiple substitutions
►Cbpp::WordSubstitutionModel	Basal class for words of substitution models
Cbpp::TripletSubstitutionModel	Class for neutral substitution models on triplets, which correspond to codons that do not have any significance (whether they are STOP or functional)
Cbpp::AnonymousSubstitutionModel
Cbpp::CodonSameAARateSubstitutionModel	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)
Cbpp::POMO
Cbpp::RegisterRatesSubstitutionModel	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
►Cbpp::YpR	YpR model
Cbpp::YpR_Gen	General YpR model
Cbpp::YpR_Sym	Symmetrical YpR model
►Cbpp::AbstractWrappedModel	Abstract class of Wrapping model class, where all methods are redirected from model()
►Cbpp::AbstractWrappedTransitionModel
►Cbpp::AbstractFromSubstitutionModelTransitionModel	Virtual class of a Transition Model related to a given SubstitutionModel
Cbpp::OneChangeRegisterTransitionModel	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
Cbpp::OneChangeTransitionModel	From a model, compute transition probabilities given there is at least a change in the branch
►Cbpp::AbstractTotallyWrappedTransitionModel
►Cbpp::AbstractBiblioTransitionModel	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
►Cbpp::AbstractBiblioMixedTransitionModel	Abstract class for mixture models based on the bibliography
Cbpp::DFP07	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
Cbpp::LG10_EX_EHO	The Le and Gascuel (2010) EX_EHO substitution model for proteins
Cbpp::LGL08_CAT	The Le et al (2008) CAT substitution model for proteins
Cbpp::LLG08_EHO	The Le et al (2008) EH0 substitution model for proteins
Cbpp::LLG08_EX2	The Le et al (2008) EX2 substitution model for proteins
Cbpp::LLG08_EX3	The Le et al (2008) EX3 substitution model for proteins
Cbpp::LLG08_UL2	The Le et al (2008) UL2 substitution model for proteins
Cbpp::LLG08_UL3	The Le et al (2008) UL3 substitution model for proteins
►Cbpp::YNGP_M	Abstract generic class for The Yang et al (2000) M substitution models for codons. al (2004)
Cbpp::RELAX	The RELAX (2014) branch-site model for codons
Cbpp::YNGP_M1	The Yang et al (2000) M1 substitution model for codons, with the more realistic modification in Wong & al (2004)
Cbpp::YNGP_M10	The Yang et al (2000) M10 substitution model for codons
Cbpp::YNGP_M2	The Yang et al (2000) M2 substitution model for codons, with the more realistic modification in Wong & al (2004)
Cbpp::YNGP_M3	The Yang et al (2000) M3 substitution model for codons
Cbpp::YNGP_M7	The Yang et al (2000) M7 substitution model for codons
Cbpp::YNGP_M8	The Yang et al (2000) M8 substitution model for codons
Cbpp::YNGP_M9	The Yang et al (2000) M9 substitution model for codons
►Cbpp::AbstractBiblioSubstitutionModel
Cbpp::GY94	The Goldman and Yang (1994) substitution model for codons
Cbpp::KCM	The general multiple substitution model for codons, from Zaheri & al, 2014
Cbpp::MG94	The Muse and Gaut (1994) substitution model for codons
Cbpp::YN98	The Yang and Nielsen (1998) substitution model for codons
►Cbpp::AbstractTotallyWrappedSubstitutionModel
Cbpp::AbstractBiblioSubstitutionModel
Cbpp::FromMixtureSubstitutionModel	Model taken from a SubModel of a Mixture of SubstitutionModels
►Cbpp::AbstractWrappedSubstitutionModel
Cbpp::AbstractTotallyWrappedSubstitutionModel
Cbpp::InMixedSubstitutionModel	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
Cbpp::RegisterRatesSubstitutionModel	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
Cbpp::MultinomialFromTransitionModel	From a model, compute the likelihood of counts given an ancestral state
Cbpp::TransitionFromTransitionModel	From a transition model, compute the transition function probabilities
►Cbpp::LikelihoodCalculation
►Cbpp::AlignedLikelihoodCalculation
Cbpp::HmmLikelihood_DF	A simple implementation of hidden Markov models recursion, in DataFlow implementation
Cbpp::LikelihoodCalculationOnABranch
Cbpp::LikelihoodCalculationSingleProcess
►Cbpp::MarkovModulatedSubstitutionModel	Partial implementation of the Markov-modulated class of substitution models
Cbpp::G2001	Galtier's 2001 covarion model
Cbpp::TS98	Tuffley and Steel's 1998 covarion model
►Cbpp::MultiProcessSequenceEvolution	Partial implementation of multiple processes of sequences
Cbpp::AutoCorrelationSequenceEvolution	Sequence evolution framework based on an auto-correlation of substitution processes
Cbpp::HmmSequenceEvolution	Sequence evolution framework based on a hmm
Cbpp::MixtureSequenceEvolution	Sequence evolution framework based on a mixture of substitution processes
Cbpp::PartitionSequenceEvolution	Sequence evolution framework based on a mixture of substitution processes
Cbpp::OneProcessSequenceEvolution	Evolution of a sequence performed by a unique SubstitutionProcess all along the sequence
►Cbpp::SubstitutionModelSet	Substitution models manager for non-homogeneous / non-reversible models of evolution
Cbpp::MixedSubstitutionModelSet	Substitution models manager for Mixed Substitution Models. This class inherits from SubstitutionModelSet
Cbpp::SubstitutionProcessCollection	Collection of Substitution Process, which owns all the necessary objects: Substitution models, frequencies sets, rate distributions and trees
►Cbpp::AbstractParametrizableSequencePhyloLikelihood
►Cbpp::MultiProcessSequencePhyloLikelihood	Partial implementation of the Likelihood interface for multiple processes
Cbpp::AutoCorrelationProcessPhyloLikelihood	Likelihood framework based on an auto-correlation of simple likelihoods
Cbpp::AutoCorrelationProcessPhyloLikelihood	Likelihood framework based on an auto-correlation of simple likelihoods
Cbpp::HmmProcessPhyloLikelihood	Likelihood framework based on a hmm of simple likelihoods
Cbpp::MixtureProcessPhyloLikelihood	Likelihood framework based on a mixture of simple likelihoods
Cbpp::OneProcessSequencePhyloLikelihood	The OneProcessSequencePhyloLikelihood class: phylogenetic likelihood computation with a single process
►Cbpp::AbstractPhyloLikelihoodSet	The PhyloLikelihoodSet class, to manage a subset of PhyloLikelihoods from a given PhyloLikelihoodContainer
►Cbpp::AbstractAlignedPhyloLikelihoodSet	The AlignedPhyloLikelihoodSet abstract class
Cbpp::AlignedPhyloLikelihoodAutoCorrelation	Likelihood framework based on a hmm of simple likelihoods
Cbpp::AlignedPhyloLikelihoodHmm	Likelihood framework based on a hmm of simple likelihoods
Cbpp::AlignedPhyloLikelihoodMixture	Likelihood framework based on a mixture of aligned likelihoods
Cbpp::AlignedPhyloLikelihoodProduct	The AlignedPhyloLikelihoodProduct class, for phylogenetic likelihood on several independent data
Cbpp::PartitionProcessPhyloLikelihood
Cbpp::PhyloLikelihoodFormula	The PhyloLikelihoodFormula class, for phylogenetic likelihood on several independent data
►Cbpp::AbstractTreeLikelihood	Partial implementation of the TreeLikelihood interface
►Cbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	Partial implementation of the DiscreteRatesAcrossSitesTreeLikelihood interface
►Cbpp::AbstractHomogeneousTreeLikelihood	Partial implementation for homogeneous model of the TreeLikelihood interface
►Cbpp::DRHomogeneousTreeLikelihood	This class implements the likelihood computation for a tree using the double-recursive algorithm
Cbpp::DRHomogeneousMixedTreeLikelihood	A class to compute the average of several DRHomogeneousTreeLikelihood defined from a Mixed Substitution Model
Cbpp::NNIHomogeneousTreeLikelihood	This class adds support for NNI topology estimation to the DRHomogeneousTreeLikelihood class
►Cbpp::RHomogeneousTreeLikelihood	This class implement the 'traditional' way of computing likelihood for a tree
Cbpp::RHomogeneousMixedTreeLikelihood
►Cbpp::AbstractNonHomogeneousTreeLikelihood	Partial implementation for branch non-homogeneous models of the TreeLikelihood interface
Cbpp::DRNonHomogeneousTreeLikelihood	This class implements the likelihood computation for a tree using the double-recursive algorithm, allowing for non-homogeneous models of substitutions
►Cbpp::RNonHomogeneousTreeLikelihood	This class implement the 'traditional' way of computing likelihood for a tree, allowing for non-homogeneous models of substitutions
Cbpp::RNonHomogeneousMixedTreeLikelihood
Cbpp::BranchLikelihood	Compute likelihood for a 4-tree
Cbpp::CollectionNodes
Cbpp::ConfiguredDistribution	Data flow node representing a DiscreteDistribution configured with parameter values
Cbpp::ConfiguredFrequencySet	Data flow node representing a Frequencies Set configured with parameter values
Cbpp::ConfiguredModel	Likelihood transition model
Cbpp::ConfiguredSimplex	Data flow node representing a Frequencies Set configured with parameter values
Cbpp::ConfiguredTransitionMatrix	Data flow node representing a TransitionMatrix configured with parameter values
Cbpp::GlobalClockTreeLikelihoodFunctionWrapper
Cbpp::HmmPhyloAlphabet	Hidden states alphabet
Cbpp::HmmPhyloEmissionProbabilities	Emission probabilities in the context of DF phylolikeihoods
Cbpp::HmmProcessAlphabet	Hidden states alphabet
Cbpp::OnABranchPhyloLikelihood	Wraps a dataflow graph as a function: resultNode = f(variableNodes)
Cbpp::ParametrizablePhyloTree	PhyloTree with Parametrizable Phylo Branches. They SHARE their branch length parameters
Cbpp::PhyloBranchParam
Cbpp::SingleProcessPhyloLikelihood	Wraps a dataflow graph as a function: resultNode = f(variableNodes)
►Cbpp::FunctionInterface [external]
Cbpp::BranchLikelihood	Compute likelihood for a 4-tree
►Cbpp::FirstOrderDerivable [external]
►Cbpp::SecondOrderDerivable [external]
Cbpp::GlobalClockTreeLikelihoodFunctionWrapper
►Cbpp::PhyloLikelihoodInterface	The PhyloLikelihood interface, for phylogenetic likelihood
►Cbpp::AbstractPhyloLikelihood
►Cbpp::AbstractAlignedPhyloLikelihood
Cbpp::AbstractAlignedPhyloLikelihoodSet	The AlignedPhyloLikelihoodSet abstract class
►Cbpp::AbstractSingleDataPhyloLikelihood
►Cbpp::AbstractSequencePhyloLikelihood
Cbpp::AbstractParametrizableSequencePhyloLikelihood
Cbpp::PartitionProcessPhyloLikelihood
Cbpp::SingleProcessPhyloLikelihood	Wraps a dataflow graph as a function: resultNode = f(variableNodes)
Cbpp::OnABranchPhyloLikelihood	Wraps a dataflow graph as a function: resultNode = f(variableNodes)
Cbpp::AbstractPhyloLikelihoodSet	The PhyloLikelihoodSet class, to manage a subset of PhyloLikelihoods from a given PhyloLikelihoodContainer
►Cbpp::AlignedPhyloLikelihoodInterface	The AlignedPhyloLikelihood interface, for phylogenetic likelihood
Cbpp::AbstractAlignedPhyloLikelihood
►Cbpp::AlignedPhyloLikelihoodSetInterface	Joint interface SetOf+Aligned PhylLikelihood
Cbpp::AbstractAlignedPhyloLikelihoodSet	The AlignedPhyloLikelihoodSet abstract class
►Cbpp::SingleDataPhyloLikelihoodInterface	The SingleDataPhyloLikelihood interface, for phylogenetic likelihood
Cbpp::AbstractSingleDataPhyloLikelihood
►Cbpp::SequencePhyloLikelihoodInterface	PhyloLikelihoods based on Sequence Evolution class, ie for which there is a (set of) processes able to build a sequence
Cbpp::AbstractSequencePhyloLikelihood
►Cbpp::PhyloLikelihoodSetInterface	The PhyloLikelihoodSet interface, to manage a subset of PhyloLikelihoods from a given PhyloLikelihoodContainer
Cbpp::AbstractPhyloLikelihoodSet	The PhyloLikelihoodSet class, to manage a subset of PhyloLikelihoods from a given PhyloLikelihoodContainer
Cbpp::AlignedPhyloLikelihoodSetInterface	Joint interface SetOf+Aligned PhylLikelihood
►Cbpp::TreeLikelihoodInterface	The TreeLikelihood interface
Cbpp::AbstractTreeLikelihood	Partial implementation of the TreeLikelihood interface
►Cbpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface	Interface for rate across sites (RAS) implementation
Cbpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	Partial implementation of the DiscreteRatesAcrossSitesTreeLikelihood interface
►Cbpp::DRTreeLikelihoodInterface	Interface for double-recursive (DR) implementation of the likelihood computation
Cbpp::DRHomogeneousTreeLikelihood	This class implements the likelihood computation for a tree using the double-recursive algorithm
Cbpp::DRNonHomogeneousTreeLikelihood	This class implements the likelihood computation for a tree using the double-recursive algorithm, allowing for non-homogeneous models of substitutions
►Cbpp::HomogeneousTreeLikelihood	Specialization of the TreeLikelihood interface for the Homogeneous case
Cbpp::AbstractHomogeneousTreeLikelihood	Partial implementation for homogeneous model of the TreeLikelihood interface
►Cbpp::NonHomogeneousTreeLikelihood	Specialization of the TreeLikelihood interface for the branch non-homogeneous and non-stationary models
Cbpp::AbstractNonHomogeneousTreeLikelihood	Partial implementation for branch non-homogeneous models of the TreeLikelihood interface
Cbpp::LegacyOptimizationTools::ScaleFunction
►Cbpp::HmmEmissionProbabilities_Eigen	Interface for computing emission probabilities in a Hidden Markov Model
Cbpp::HmmPhyloEmissionProbabilities	Emission probabilities in the context of DF phylolikeihoods
►Cbpp::HmmStateAlphabet [external]
Cbpp::HmmPhyloAlphabet	Hidden states alphabet
Cbpp::HmmProcessAlphabet	Hidden states alphabet
►Cbpp::ParameterAliasable [external]
Cbpp::AbstractParameterAliasable [external]
►Cbpp::BranchModelInterface	Interface for all Branch models
►Cbpp::TransitionModelInterface	Interface for all transition models
►Cbpp::AbstractLkTransitionModel	Partial implementation of the TransitionModel interface, with function for likelihood computations
Cbpp::AbstractTransitionModel	Partial implementation of the TransitionModel interface
Cbpp::AbstractWrappedTransitionModel
Cbpp::MarkovModulatedSubstitutionModel	Partial implementation of the Markov-modulated class of substitution models
►Cbpp::MixedTransitionModelInterface	Interface for Transition models, defined as a mixture of "simple" transition models
Cbpp::AbstractBiblioMixedTransitionModel	Abstract class for mixture models based on the bibliography
Cbpp::AbstractMixedTransitionModel	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
►Cbpp::SubstitutionModelInterface	Interface for all substitution models
Cbpp::AbstractSubstitutionModel
►Cbpp::CodonSubstitutionModelInterface
Cbpp::AbstractCodonSubstitutionModel	Abstract class for substitution models on codons
Cbpp::AbstractDFPSubstitutionModel	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
Cbpp::AbstractKroneckerCodonSubstitutionModel	Abstract class for substitution models on codons allowing multiple substitutions
►Cbpp::CodonReversibleSubstitutionModelInterface	Interface for reversible codon models
Cbpp::KCM	The general multiple substitution model for codons, from Zaheri & al, 2014
Cbpp::MG94	The Muse and Gaut (1994) substitution model for codons
Cbpp::YN98	The Yang and Nielsen (1998) substitution model for codons
Cbpp::CodonSameAARateSubstitutionModel	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)
Cbpp::RE08Codon	This is a wrapper class of RE08 for codon substitution models
►Cbpp::NucleotideSubstitutionModelInterface	Specialisation interface for nucleotide substitution model
Cbpp::AbstractNucleotideSubstitutionModel	Specialisation abstract class for nucleotide substitution model
►Cbpp::NucleotideReversibleSubstitutionModelInterface	Specialisation interface for rversible nucleotide substitution model
Cbpp::AbstractReversibleNucleotideSubstitutionModel	Specialisation abstract class for reversible nucleotide substitution model
Cbpp::RE08Nucleotide	This is a wrapper class of RE08 for nucleotide substitution models
►Cbpp::ProteinSubstitutionModelInterface	Specialized interface for protein substitution model
Cbpp::AbstractProteinSubstitutionModel	Specialisation abstract class for protein substitution model
►Cbpp::ProteinReversibleSubstitutionModelInterface	Specialized interface for protein reversible substitution model
Cbpp::AbstractReversibleProteinSubstitutionModel	Specialisation abstract class for reversible protein substitution model
Cbpp::RE08Protein	This is a wrapper class of RE08 for protein substitution models
►Cbpp::ReversibleSubstitutionModelInterface	Interface for reversible substitution models
Cbpp::AbstractReversibleSubstitutionModel	Partial implementation of the ReversibleSubstitutionModel interface
Cbpp::CodonReversibleSubstitutionModelInterface	Interface for reversible codon models
Cbpp::GY94	The Goldman and Yang (1994) substitution model for codons
Cbpp::MarkovModulatedSubstitutionModel	Partial implementation of the Markov-modulated class of substitution models
Cbpp::NucleotideReversibleSubstitutionModelInterface	Specialisation interface for rversible nucleotide substitution model
Cbpp::ProteinReversibleSubstitutionModelInterface	Specialized interface for protein reversible substitution model
Cbpp::SENCA	Class for non-synonymous and synonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic basic models
►Cbpp::WrappedSubstitutionModelInterface
Cbpp::AbstractWrappedSubstitutionModel
►Cbpp::WrappedTransitionModelInterface
Cbpp::AbstractWrappedTransitionModel
Cbpp::YNGP_M	Abstract generic class for The Yang et al (2000) M substitution models for codons. al (2004)
►Cbpp::WrappedModelInterface	Wrapping model interface
Cbpp::AbstractWrappedModel	Abstract class of Wrapping model class, where all methods are redirected from model()
Cbpp::WrappedSubstitutionModelInterface
Cbpp::WrappedTransitionModelInterface
►Cbpp::CoreCodonSubstitutionModelInterface	Interface for codon models
Cbpp::AbstractCodonAAFitnessSubstitutionModel	Abstract class for modelling of ratios of substitution rates between codons, whatever they are synonymous or not
Cbpp::AbstractCodonAARateSubstitutionModel	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)
Cbpp::AbstractCodonBGCSubstitutionModel	Abstract class for modelling of non-synonymous and synonymous substitution rates in codon models, with gBGC
Cbpp::AbstractCodonClusterAASubstitutionModel	Abstract class for modelling of non-synonymous and synonymous substitution rates in codon models, with AA clustered
Cbpp::AbstractCodonCpGSubstitutionModel	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
Cbpp::AbstractCodonDistanceSubstitutionModel	Abstract class for modelling of non-synonymous and synonymous substitution rates in codon models
Cbpp::AbstractCodonFitnessSubstitutionModel	Abstract class for modelling of ratios of substitution rates between codons, whatever they are synonymous or not
Cbpp::AbstractCodonFrequenciesSubstitutionModel	Abstract Class for substitution models on codons parametrized by frequencies
Cbpp::AbstractCodonPhaseFrequenciesSubstitutionModel	Abstract Class for substitution models on codons parametrized by a frequency
Cbpp::CodonSubstitutionModelInterface
►Cbpp::DiscreteDistributionInterface [external]
Cbpp::AbstractDiscreteDistribution [external]
►Cbpp::FrequencySetInterface	Parametrize a set of state frequencies
Cbpp::AbstractFrequencySet	Basic implementation of the FrequencySet interface
►Cbpp::CodonFrequencySetInterface	Parametrize a set of state frequencies for codons
Cbpp::CodonFromIndependentFrequencySet	Frequencies in codons are the product of Independent Frequencies in letters with the frequencies of stop codons set to zero
Cbpp::CodonFromUniqueFrequencySet	Frequencies in codons are the product of the frequencies for a unique FrequencySet in letters, with the frequencies of stop codons set to zero
Cbpp::FixedCodonFrequencySet	FrequencySet useful for homogeneous and stationary models, codon implementation
Cbpp::FullCodonFrequencySet	A generic FrequencySet for Full Codon alphabets
Cbpp::FullPerAACodonFrequencySet	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
Cbpp::UserCodonFrequencySet
►Cbpp::NucleotideFrequencySetInterface	Parametrize a set of state frequencies for nucleotides
Cbpp::FixedNucleotideFrequencySet	FrequencySet useful for homogeneous and stationary models, nucleotide implementation
Cbpp::FullNucleotideFrequencySet	Nucleotide FrequencySet using three independent parameters (theta, theta1, theta2) to modelize the four frequencies:
Cbpp::GCFrequencySet	Nucleotide FrequencySet using only one parameter, the GC content
Cbpp::UserNucleotideFrequencySet	FrequencySet useful for homogeneous and stationary models, nucleotide implementation
►Cbpp::ProteinFrequencySetInterface	Parametrize a set of state frequencies for proteins
Cbpp::FixedProteinFrequencySet	FrequencySet useful for homogeneous and stationary models, protein implementation
Cbpp::FullProteinFrequencySet	Protein FrequencySet using 19 independent parameters to model the 20 frequencies
Cbpp::MvaFrequencySet	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
Cbpp::UserProteinFrequencySet	FrequencySet from file
►Cbpp::WordFrequencySetInterface	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
Cbpp::AbstractWordFrequencySet
►Cbpp::SequenceEvolution	This interface describes the evolution process of a sequence
Cbpp::MultiProcessSequenceEvolution	Partial implementation of multiple processes of sequences
Cbpp::OneProcessSequenceEvolution	Evolution of a sequence performed by a unique SubstitutionProcess all along the sequence
►Cbpp::SubstitutionProcessInterface	This interface describes the substitution process along the tree and sites of the alignment
Cbpp::AbstractSubstitutionProcess	A partial implementation of the SubstitutionProcess interface
►Cbpp::AutonomousSubstitutionProcessInterface	Interface for SubstitutionProcess objects that own their own ParametrizablePhyloTree & Scenario
Cbpp::AbstractAutonomousSubstitutionProcess	A partial implementation of the SubstitutionProcess interface
►Cbpp::ParametrizableAdapter [external]
Cbpp::LegacyOptimizationTools::ScaleFunction
Cbpp::PhyloLikelihoodContainer	The PhyloLikelihoodContainer, owns and assigns numbers to Phylolikelihoods
Cbpp::PhyloStatistics	Compute several quantities on a tree simulateously, optimizing the recursions on the tree
►Cbpp::PhyloSubstitutionMapping
Cbpp::AbstractSinglePhyloSubstitutionMapping	The AbstractSinglePhyloSubstitutionMapping class: substitution mapping linked with a Single Process PhyloLikelihood
►Cbpp::Reward	The Reward interface
►Cbpp::AbstractReward	Basic implementation of the the Reward interface
Cbpp::DecompositionReward	Analytical reward using the eigen decomposition method
►Cbpp::SequenceSimulatorInterface	The SequenceSimulator interface. SequenceSimulator classes can simulate whole datasets
Cbpp::GivenDataSubstitutionProcessSequenceSimulator	Sequences simulation under a unique substitution process, but with site specific posterior probabilities
Cbpp::NonHomogeneousSequenceSimulator	(Legacy) Site and sequences simulation under non-homogeneous models
Cbpp::SimpleSubstitutionProcessSequenceSimulator	Sequences simulation under a unique substitution process
►Cbpp::SubstitutionProcessSequenceSimulator	Sequences simulation under position specific substitution process
Cbpp::EvolutionSequenceSimulator
►Cbpp::SitePartition	This is the interface for classes describing a site partition, each partition being intended to have its own substitution model
Cbpp::TrivialSitePartition	Trivial site partition: all sites belong to the same, unique partition
Cbpp::SitePatterns	Data structure for site patterns
►Cbpp::SiteSimulatorInterface	The SiteSimulator interface. SiteSimulator classes can simulate single sites
►Cbpp::DetailedSiteSimulatorInterface	This interface adds the dSimulate method to the SiteSimulator interface
Cbpp::NonHomogeneousSequenceSimulator	(Legacy) Site and sequences simulation under non-homogeneous models
►Cbpp::SimpleSubstitutionProcessSiteSimulator	Site simulation under a unique substitution process
Cbpp::GivenDataSubstitutionProcessSiteSimulator	Site simulation under a unique substitution process, given data
►Cbpp::StateMapInterface	Map the states of a given alphabet which have a model state
►Cbpp::AbstractStateMap	A convenience partial implementation of the StateMap interface
Cbpp::CanonicalStateMap	This class implements a state map where all resolved states are modeled
Cbpp::MarkovModulatedStateMap	This class implements a state map for Markov modulated models
►Cbpp::SubstitutionCountInterface	The SubstitutionsCount interface
►Cbpp::AbstractSubstitutionCount	Partial implementation of the SubstitutionCount interface
Cbpp::DecompositionSubstitutionCount	Analytical substitution count using the eigen decomposition method
Cbpp::LabelSubstitutionCount	Labelling substitution count
Cbpp::LaplaceSubstitutionCount	Laplace estimate of the substitution count
Cbpp::NaiveSubstitutionCount	Naive substitution count
Cbpp::OneJumpSubstitutionCount	Computes the probability that at least one jump occurred on a branch, given the initial and final state
Cbpp::UniformizationSubstitutionCount	Analytical (weighted) substitution count using the uniformization method
►Cbpp::SubstitutionDistance	Interface allowing for using distances between states in substitution counts
►Cbpp::AbstractSubstitutionDistance	Partial implementation of the SubstitutionDistance interface
Cbpp::DecompositionSubstitutionCount	Analytical substitution count using the eigen decomposition method
Cbpp::UniformizationSubstitutionCount	Analytical (weighted) substitution count using the uniformization method
►Cbpp::WeightedSubstitutionCount	Interface allowing for weighting of substitution counts according to state properties
►Cbpp::AbstractWeightedSubstitutionCount	Partial implementation of the WeightedSubstitutionCount interface
Cbpp::DecompositionSubstitutionCount	Analytical substitution count using the eigen decomposition method
Cbpp::NaiveSubstitutionCount	Naive substitution count
Cbpp::UniformizationSubstitutionCount	Analytical (weighted) substitution count using the uniformization method
Cbpp::SubstitutionProcessCollection	Collection of Substitution Process, which owns all the necessary objects: Substitution models, frequencies sets, rate distributions and trees
►Cbpp::SubstitutionRegisterInterface	The SubstitutionRegister interface
►Cbpp::AbstractSubstitutionRegister
►Cbpp::CategorySubstitutionRegister	The CategorySubstitutionRegisters
Cbpp::ComprehensiveSubstitutionRegister	Distinguishes all types of substitutions
Cbpp::GCPositionSubstitutionRegister	Distinguishes AT->GC vs GC->AT on given codon position (0, 1, or 2)
Cbpp::GCSubstitutionRegister	Distinguishes AT<->GC from GC<->AT
Cbpp::GCSynonymousSubstitutionRegister	Distinguishes AT->GC vs GC->AT inside synonymous substitutions on third codon position
Cbpp::CompleteSubstitutionRegister	Completion of a given substitution register to consider all substitutions. The new substitutions are considered in an additional type
Cbpp::DnDsSubstitutionRegister	Distinguishes synonymous from non-synonymous substitutions
►Cbpp::GeneralSubstitutionRegister	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
Cbpp::AAExteriorSubstitutionRegister	Indexes only substitutions between amino-acids. Groups are distinguished by their direction
Cbpp::AAInteriorSubstitutionRegister	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
Cbpp::SelectedSubstitutionRegister	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
Cbpp::KrKcSubstitutionRegister	Count conservative and radical amino-acid substitutions
Cbpp::SWSubstitutionRegister	Distinguishes substitutions given the link between the changed nucleotides : S for strong (GC) and W for weak (AT)
Cbpp::TotalSubstitutionRegister	Count all substitutions
Cbpp::TsTvSubstitutionRegister	Distinguishes transitions from transversions
Cbpp::VectorOfSubstitutionRegisters	Sets a Register based on a vector of Registers. The categories are intersection of categories of those Registers
►Cbpp::TopologyListener	Implement this interface to be notified when the topology of a tree has changed during topology search
Cbpp::NNISearchable	Interface for Nearest Neighbor Interchanges algorithms
Cbpp::NNITopologyListener	Listener used internally by the optimizeTreeNNI method
Cbpp::NNITopologyListener2	Listener used internally by the optimizeTreeNNI2 method
►Cbpp::Tree	Interface for phylogenetic tree objects
Cbpp::TreeTemplate< bpp::Node >
Cbpp::TreeTemplate< bpp::NodeTemplate >
Cbpp::TreeTemplate< N >	The phylogenetic tree class
►Cbpp::TreeDrawing	Basal interface for tree drawing classes
►Cbpp::AbstractTreeDrawing	Partial implementation of the TreeDrawing interface
►Cbpp::AbstractDendrogramPlot	Basic implementation of dendrogram plots
Cbpp::CladogramPlot	Cladogram representation of trees
Cbpp::PhylogramPlot	Phylogram representation of trees
►Cbpp::TreeDrawingListener	Interface allowing to capture drawing events
►Cbpp::TreeDrawingListenerAdapter	An empty implementation of the TreeDrawingListener interface
Cbpp::BootstrapValuesTreeDrawingListener	A TreeDrawingListener implementation that write the bootstrap values of inner nodes
Cbpp::BranchLengthsTreeDrawingListener	A TreeDrawingListener implementation that write the branch lengths of inner nodes
Cbpp::LabelCollapsedNodesTreeDrawingListener	A TreeDrawingListener implementation that label the collapsed nodes
Cbpp::LabelInnerNodesTreeDrawingListener	A TreeDrawingListener implementation that write the names of inner nodes
Cbpp::LeafNamesTreeDrawingListener	A TreeDrawingListener implementation that write leaf names
Cbpp::NodesIdTreeDrawingListener	A TreeDrawingListener implementation that writes nodes id
►Cbpp::TreeLikelihoodData	TreeLikelihood data structure
►Cbpp::AbstractTreeLikelihoodData	Partial implementation of the TreeLikelihoodData interface
Cbpp::DRASDRTreeLikelihoodData	Likelihood data structure for rate across sites models, using a double-recursive algorithm
Cbpp::DRASRTreeLikelihoodData	Discrete Rate Across Sites, (simple) Recursive likelihood data structure
►Cbpp::TreeLikelihoodNodeData	TreeLikelihood partial data structure
Cbpp::DRASDRTreeLikelihoodLeafData	Likelihood data structure for a leaf
Cbpp::DRASDRTreeLikelihoodNodeData	Likelihood data structure for a node
Cbpp::DRASRTreeLikelihoodNodeData	Likelihood data structure for a node
►Cbpp::TreeParsimonyDataInterface	TreeParsimonyScore data structure
►Cbpp::AbstractTreeParsimonyData	Partial implementation of the TreeParsimonyData interface
Cbpp::DRTreeParsimonyData	Parsimony data structure for double-recursive (DR) algorithm
►Cbpp::TreeParsimonyNodeDataInterface	TreeParsimonyScore node data structure
Cbpp::DRTreeParsimonyLeafData	Parsimony data structure for a leaf
Cbpp::DRTreeParsimonyNodeData	Parsimony data structure for a node
►Cbpp::TreeParsimonyScoreInterface	Compute a parsimony score
►Cbpp::AbstractTreeParsimonyScore	Partial implementation of the TreeParsimonyScore interface
Cbpp::DRTreeParsimonyScore	Double recursive implementation of interface TreeParsimonyScore
Cbpp::ClusterInfos
►Cbpp::CoalaCore	This class is the core class inherited by the Coala class. COaLA is a branch-heterogeneous amino-acid substitution model
Cbpp::Coala	The Coala branch-heterogeneous amino-acid substitution model
Cbpp::CWiseCompound< R, ReductionOf< T > >::compound_functor
Cbpp::ConfiguredParametrizable
►Cbpp::TreeLikelihoodInterface::ConstBranchModelDescription	A pair of SubstitutionModel / SiteIterator
Cbpp::AbstractTreeLikelihood::ConstNoPartitionBranchModelDescription
►Cbpp::TreeLikelihoodInterface::ConstBranchModelIterator	Iterates through all models used for all sites on a given branch
Cbpp::AbstractTreeLikelihood::ConstNoPartitionBranchModelIterator
►Cbpp::TreeLikelihoodInterface::ConstSiteModelDescription	A pair of SubstitutionModel / BranchIterator
Cbpp::AbstractTreeLikelihood::ConstNoPartitionSiteModelDescription
Cbpp::TreeLikelihoodInterface::ConstSiteModelIterator	Iterates through all models used for all branches on a given site
►CConstSiteModelIterator
Cbpp::AbstractHomogeneousTreeLikelihood::ConstHomogeneousSiteModelIterator
Cbpp::AbstractNonHomogeneousTreeLikelihood::ConstNonHomogeneousSiteModelIterator
Cbpp::Context	Context for dataflow node construction
Cbpp::Cursor	Data structure describing a plotting direction
Cbpp::CWiseCompound< Result, From >
Cbpp::CWiseDiv< Result, From >
Cbpp::CWiseMatching< Result, From >
Cbpp::CWiseMean< Result, From, Prop >
Cbpp::CWiseMul< Result, From >
Cbpp::CWiseSub< Result, From >
►Cbpp::DecompositionMethods	Methods useful for analytical substitution count and rewards using the eigen decomposition method
Cbpp::DecompositionReward	Analytical reward using the eigen decomposition method
Cbpp::DecompositionSubstitutionCount	Analytical substitution count using the eigen decomposition method
Cbpp::SubstitutionProcessCollectionMember::Deleter
Cbpp::Dimension< T >	Store a dimension for type T
Cbpp::Dimension< Eigen::MatrixXd >
Cbpp::Dimension< F >
Cbpp::Dimension< R >
Cbpp::Dimension< T0 >
►Cbpp::Dimension< VectorLik >
Cbpp::Dimension< TransitionFunction >
►Cbpp::DrawBranchEvent	Event class used by TreeDrawing classes
►Cbpp::DrawIBranchEvent	Event class that uses INode object (more efficient than relying on nodes id, but less generic)
Cbpp::CladogramDrawBranchEvent
Cbpp::PhylogramDrawBranchEvent
►Cbpp::DrawNodeEvent	Event class used by TreeDrawing classes
Cbpp::DrawINodeEvent	Event class that uses INode object (more efficient than relying on nodes id, but less generic)
Cbpp::DrawTreeEvent	Event class used by TreeDrawing classes
Cbpp::IODAG::Element
Cbpp::IOTree::Element
Cbpp::TreeTemplateTools::Element
►Cstd::enable_shared_from_this
Cbpp::MixedSubstitutionModelSet	Substitution models manager for Mixed Substitution Models. This class inherits from SubstitutionModelSet
►Cbpp::Node_DF	Base dataflow Node class
►Cbpp::Value< const HmmTransitionMatrix * >
Cbpp::ConfiguredTransitionMatrix	Data flow node representing a TransitionMatrix configured with parameter values
►Cbpp::Value< Eigen::RowVectorXd >
Cbpp::EquilibriumFrequenciesFromModel
Cbpp::FrequenciesFromFrequencySet
Cbpp::FrequenciesFromSimplex
Cbpp::ProbabilitiesFromDiscreteDistribution
Cbpp::ProbabilitiesFromMixedModel
►Cbpp::Value< Parameter * >
Cbpp::ConfiguredParameter	Data flow node representing a parameter
►Cbpp::Value< const FrequencySetInterface * >
Cbpp::ConfiguredFrequencySet	Data flow node representing a Frequencies Set configured with parameter values
►Cbpp::Value< std::shared_ptr< BranchModelInterface > >
Cbpp::ConfiguredModel	Likelihood transition model
►Cbpp::Value< double >
Cbpp::CategoryFromDiscreteDistribution
Cbpp::ProbabilityFromDiscreteDistribution
Cbpp::ProbabilityFromMixedModel
Cbpp::ValueFromConfiguredParameter
►Cbpp::Value< MatrixLik >
Cbpp::Sequence_DF	Data flow node representing a Sequence as a Value<Eigen::MatrixXd> with a name
►Cbpp::Value< const Simplex * >
Cbpp::ConfiguredSimplex	Data flow node representing a Frequencies Set configured with parameter values
►Cbpp::Value< R >
Cbpp::CWiseAdd< R, T >
Cbpp::CWiseAdd< R, ReductionOf< T > >
Cbpp::CWiseAdd< R, std::tuple< T0, T1 > >
Cbpp::CWiseApply< R, T, F >
Cbpp::CWiseCompound< R, ReductionOf< T > >
Cbpp::CWiseDiv< R, std::tuple< T0, T1 > >
Cbpp::CWiseFill< R, T >
Cbpp::CWiseMatching< R, ReductionOf< T > >
Cbpp::CWiseMean< R, ReductionOf< T >, P >
Cbpp::CWiseMean< R, ReductionOf< T >, ReductionOf< P > >
Cbpp::CWiseMul< R, ReductionOf< T > >
Cbpp::CWiseMul< R, std::tuple< T0, T1 > >
Cbpp::CWisePattern< R >
Cbpp::CWiseSub< R, std::tuple< T0, T1 > >
Cbpp::Convert< R, F >	R = convert(f)
Cbpp::Identity< R >	R = id(f)
Cbpp::LogSumExp< R, T0, T1 >
Cbpp::MatrixProduct< R, T0, T1 >
Cbpp::ScalarProduct< R, T0, T1 >
►Cbpp::Value< RowLik >
Cbpp::ForwardHmmD2Likelihood_DF
Cbpp::ForwardHmmDLikelihood_DF
Cbpp::ForwardHmmLikelihood_DF
►Cbpp::Value< Eigen::MatrixXd >
Cbpp::BackwardHmmLikelihood_DF
Cbpp::CondLikelihood
Cbpp::TransitionMatrixFromModel
Cbpp::TransitionMatrixFromTransitionMatrix
►Cbpp::Value< bpp::TransitionFunction >
Cbpp::TransitionFunctionFromModel
►Cbpp::Value< Eigen::VectorXd >
Cbpp::EquilibriumFrequenciesFromTransitionMatrix
►Cbpp::Value< DataLik >
Cbpp::SumOfLogarithms< F >
►Cbpp::Value< const DiscreteDistributionInterface * >
Cbpp::ConfiguredDistribution	Data flow node representing a DiscreteDistribution configured with parameter values
►Cbpp::Value< T >	Abstract Node storing a value of type T
Cbpp::CWiseConstantPow< T >
Cbpp::CWiseExp< T >
Cbpp::CWiseInverse< T >
Cbpp::CWiseLog< T >
Cbpp::CWiseNegate< T >
Cbpp::CombineDeltaShifted< T >
Cbpp::ConstantOne< T >	R = 1 for each component
Cbpp::ConstantZero< T >	R = 0 for each component
Cbpp::NumericConstant< T >	R = constant_value
Cbpp::NumericMutable< T >	R = variable_value
Cbpp::ShiftDelta< T >
Cbpp::OneProcessSequenceSubstitutionMapping	The OneProcessSequenceSubstitutionMapping class: substitution mapping linked with a OneProcessSequencePhyloLikelihood
Cbpp::SingleProcessSubstitutionMapping	The SingleProcessSubstitutionMapping class: substitution mapping linked with a SingleProcessPhyloLikelihood
►Cbpp::Exception [external]
►Cbpp::NodeException	General exception thrown when something is wrong with a particular node
►Cbpp::NodePException	General exception thrown when something is wrong with a particular node
Cbpp::PropertyNotFoundException	General exception thrown if a property could not be found
Cbpp::NodeNotFoundException	Exception thrown when something is wrong with a particular node
►Cbpp::PhyloBranchException	General exception thrown when something is wrong with a particular branch
►Cbpp::PhyloBranchPException	General exception thrown when something is wrong with a particular branch
Cbpp::PhyloBranchPropertyNotFoundException	General exception thrown if a property could not be found
Cbpp::PhyloBranchNotFoundException	Exception thrown when something is wrong with a particular branch
►Cbpp::PhyloNodeException	General exception thrown when something is wrong with a particular node
►Cbpp::PhyloNodePException	General exception thrown when something is wrong with a particular node
Cbpp::PhyloNodePropertyNotFoundException	General exception thrown if a property could not be found
Cbpp::PhyloNodeNotFoundException	Exception thrown when something is wrong with a particular node
►Cbpp::PhyloTreeException	General exception thrown when something wrong happened in a tree
Cbpp::UnrootedPhyloTreeException	Exception thrown when a tree is expected to be rooted
►Cbpp::TreeException	General exception thrown when something wrong happened in a tree
Cbpp::UnrootedTreeException	Exception thrown when a tree is expected to be rooted
►Cbpp::ExtendedFloat
Cbpp::ExtendedFloatEigen< R, C, EigenType >::OwnedExtendedFloat
Cbpp::ExtendedFloatArrayWrapper< R, C >
►Cbpp::ExtendedFloatEigenCore
►Cbpp::ExtendedFloatEigenBase< ExtendedFloatEigen< R, C, EigenType > >
Cbpp::ExtendedFloatEigen< R, C >
►Cbpp::ExtendedFloatEigen< R, 1, EigenType >
Cbpp::ExtendedFloatCol< R, C, EigenType >
Cbpp::ExtendedFloatEigen< R, C, EigenType >
Cbpp::ExtendedFloatEigenBase< DerivedEF >
Cbpp::ExtendedFloatEigenBase< Derived >
Cbpp::ExtendedFloatNoAlias< DerivedEF >
Cbpp::ExtendedFloatRow< R, C, EigenType >
Cbpp::ExtendedFloatVectorwiseOp< DerivedEF, MatType, Direction >
Cbpp::MixedSubstitutionModelSet::HyperNode
CIntAndInt
►Cbpp::IOFormat [external]
Cbpp::BppOMultiTreeReaderFormat	Tree I/O in BppO format
Cbpp::BppOMultiTreeWriterFormat	Tree I/O in BppO format
Cbpp::BppOTreeReaderFormat	Tree I/O in BppO format
Cbpp::BppOTreeWriterFormat	Tree I/O in BppO format
►Cbpp::IODAG	General interface for DAG I/O
►Cbpp::IMultiPhyloDAG	General interface for multiple trees readers
►Cbpp::AbstractIMultiPhyloDAG	Partial implementation of the IMultiDAG interface
Cbpp::ExtendedNewick	The so-called 'ExtendedNewick' parenthetic format for phylogenetic networks, where hybridization nodes are mandatory tagged and appear several times
►Cbpp::IPhyloDAG	General interface for DAG readers
►Cbpp::AbstractIPhyloDAG	Partial implementation of the IDAG interface
Cbpp::ExtendedNewick	The so-called 'ExtendedNewick' parenthetic format for phylogenetic networks, where hybridization nodes are mandatory tagged and appear several times
►Cbpp::OMultiPhyloDAG	General interface for tree writers
►Cbpp::AbstractOMultiPhyloDAG	Partial implementation of the ODAG interface
Cbpp::ExtendedNewick	The so-called 'ExtendedNewick' parenthetic format for phylogenetic networks, where hybridization nodes are mandatory tagged and appear several times
►Cbpp::OPhyloDAG	General interface for DAG writers
►Cbpp::AbstractOPhyloDAG	Partial implementation of the ODAG interface
Cbpp::ExtendedNewick	The so-called 'ExtendedNewick' parenthetic format for phylogenetic networks, where hybridization nodes are mandatory tagged and appear several times
►Cbpp::IOPairedSiteLikelihoods	Base class for I/O on paired-site likelihoods
Cbpp::IOPhymlPairedSiteLikelihoods	This class provides input for the Phyml paired-site likelihoods format
Cbpp::IOTreepuzzlePairedSiteLikelihoods	This class provides I/O for the Tree-Puzzle/RAxML (phylip-like) paired-site likelihoods format
►Cbpp::IOTree	General interface for tree I/O
►Cbpp::IMultiPhyloTree
►Cbpp::AbstractIMultiPhyloTree	Partial implementation of the IMultiTree interface
Cbpp::Newick	The so-called 'newick' parenthetic format
Cbpp::NexusIOTree	Simple parser for reading trees from a Nexus file
Cbpp::Nhx	The so-called 'Nhx - New Hampshire eXtended' parenthetic format
►Cbpp::IMultiTree	General interface for multiple trees readers
►Cbpp::AbstractIMultiTree	Partial implementation of the IMultiTree interface
Cbpp::Newick	The so-called 'newick' parenthetic format
Cbpp::NexusIOTree	Simple parser for reading trees from a Nexus file
Cbpp::Nhx	The so-called 'Nhx - New Hampshire eXtended' parenthetic format
►Cbpp::IPhyloTree	General interface for tree readers
►Cbpp::AbstractIPhyloTree
Cbpp::Newick	The so-called 'newick' parenthetic format
Cbpp::NexusIOTree	Simple parser for reading trees from a Nexus file
Cbpp::Nhx	The so-called 'Nhx - New Hampshire eXtended' parenthetic format
►Cbpp::ITree	General interface for tree readers
►Cbpp::AbstractITree	Partial implementation of the ITree interface
Cbpp::Newick	The so-called 'newick' parenthetic format
Cbpp::NexusIOTree	Simple parser for reading trees from a Nexus file
Cbpp::Nhx	The so-called 'Nhx - New Hampshire eXtended' parenthetic format
►Cbpp::OMultiPhyloTree	General interface for tree writers
►Cbpp::AbstractOMultiPhyloTree	Partial implementation of the OTree interface
Cbpp::Newick	The so-called 'newick' parenthetic format
Cbpp::NexusIOTree	Simple parser for reading trees from a Nexus file
Cbpp::Nhx	The so-called 'Nhx - New Hampshire eXtended' parenthetic format
►Cbpp::OMultiTree	General interface for tree writers
►Cbpp::AbstractOMultiTree	Partial implementation of the OTree interface
Cbpp::Newick	The so-called 'newick' parenthetic format
Cbpp::NexusIOTree	Simple parser for reading trees from a Nexus file
Cbpp::Nhx	The so-called 'Nhx - New Hampshire eXtended' parenthetic format
►Cbpp::OPhyloTree	General interface for tree writers
►Cbpp::AbstractOPhyloTree	Partial implementation of the OTree interface
Cbpp::Newick	The so-called 'newick' parenthetic format
Cbpp::NexusIOTree	Simple parser for reading trees from a Nexus file
Cbpp::Nhx	The so-called 'Nhx - New Hampshire eXtended' parenthetic format
►Cbpp::OTree	General interface for tree writers
►Cbpp::AbstractOTree	Partial implementation of the OTree interface
Cbpp::Newick	The so-called 'newick' parenthetic format
Cbpp::NexusIOTree	Simple parser for reading trees from a Nexus file
Cbpp::Nhx	The so-called 'Nhx - New Hampshire eXtended' parenthetic format
►Cbpp::IoDiscreteDistribution [external]
►Cbpp::IDiscreteDistribution [external]
►Cbpp::BppODiscreteDistributionFormat [external]
Cbpp::BppORateDistributionFormat	Rate Distribution I/O in BppO format
►Cbpp::ODiscreteDistribution [external]
Cbpp::BppODiscreteDistributionFormat [external]
►Cbpp::IoFrequencySet	General interface for model I/O
►Cbpp::IFrequencySet	General interface for distance matrix readers
Cbpp::BppOFrequencySetFormat	Frequencies set I/O in BppO format
►Cbpp::OFrequencySet	General interface for distance matrix writers
Cbpp::BppOFrequencySetFormat	Frequencies set I/O in BppO format
►Cbpp::IoSubstitutionModel	General interface for model I/O
►Cbpp::ISubstitutionModel	General interface for model readers
►Cbpp::BppOSubstitutionModelFormat	Substitution model I/O in BppO format
►Cbpp::BppOTransitionModelFormat	Transition model I/O in BppO format
Cbpp::BppOBranchModelFormat	Branch model I/O in BppO format
►Cbpp::OSubstitutionModel	General interface for distance matrix writers
Cbpp::BppOSubstitutionModelFormat	Substitution model I/O in BppO format
Cbpp::IOFrequencySetFactory	Utilitary class for creating frequencies set readers and writers
Cbpp::IOSubstitutionModelFactory	Utilitary class for creating substitution model readers and writers
Cbpp::IOTreeFactory	Utilitary class for creating tree readers and writers
►Cbpp::LegacyAncestralStateReconstruction	Interface for ancestral states reconstruction methods
Cbpp::LegacyMarginalAncestralStateReconstruction	Likelihood ancestral states reconstruction: marginal method
Cbpp::LegacyPhylogeneticsApplicationTools	This class provides some common tools for applications
Cbpp::LegacyRewardMappingTools	Provide methods to compute reward mappings
Cbpp::LegacySubstitutionMappingTools	Provide methods to compute substitution mappings
Cbpp::CWiseMatching< R, ReductionOf< T > >::matching_functor
►Cbpp::MatrixDimension	Basic matrix dimension type
Cbpp::Dimension< Eigen::Matrix< T, Rows, Cols > >	Specialisation of Dimension<T> for eigen matrix types
Cbpp::Dimension< ExtendedFloatEigen< R, C, EigenType > >
Cbpp::RowVectorDimension
Cbpp::VectorDimension
Cbpp::ModelBranch
Cbpp::ModelList	A list of models, for building a WordSubstitutionModel
Cbpp::ModelPath	Organization of submodels in mixed substitution models in a path. See class ModelScenario for a thorough description
Cbpp::ModelScenario	Organization of submodels in mixed substitution models as paths
Cbpp::PhyloTreeTools::Moments_
Cbpp::TreeTemplateTools::Moments_	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)
Cbpp::TreeTools::Moments_
Cbpp::MutationPath	This class is used by MutationProcess to store detailed results of simulations
►Cbpp::MutationProcess	Interface for simulations
►Cbpp::AbstractMutationProcess	Partial implementation of the MutationProcess interface
Cbpp::SelfMutationProcess	This class is mainly for testing purpose. It allow "self" mutation of the kind i->i;
Cbpp::SimpleMutationProcess	Generally used mutation process model
Cbpp::MixedSubstitutionModelSet::HyperNode::Node
►Cbpp::Node	The phylogenetic node class
Cbpp::NodeTemplate< NodeInfos >	The NodeTemplate class
►Cbpp::NoDimension	Empty type representing no dimensions
Cbpp::Dimension< ExtendedFloat >
Cbpp::Dimension< Parameter >
Cbpp::Dimension< char >
Cbpp::Dimension< double >	Specialisation of Dimension<T> for floating point types
Cbpp::Dimension< float >
Cbpp::Dimension< size_t >
Cbpp::Dimension< std::string >
Cbpp::Dimension< uint >
Cbpp::NumericalDependencyTransform< T >	Template struct used to describe a dependency transformation before compute()
Cbpp::NumericalDependencyTransform< Transposed< T > >	Implementation for a dependency transposition
Cbpp::NumericalDerivativeConfiguration	Configuration for a numerical derivation: what delta to use, and type of derivation
►CNumTraits
CEigen::NumTraits< bpp::ExtendedFloat >
►Cbpp::OptimizationListener [external]
Cbpp::NaNListener	A listener which capture NaN function values and throw an exception in case this happens
Cbpp::OptimizationTools::OptimizationOptions
►Cbpp::OptimizationTools	Optimization methods for phylogenetic inference
Cbpp::LegacyOptimizationTools	Optimization methods for phylogenetic inference
Cbpp::TreeTemplateTools::OrderTreeData_
Cbpp::PairedSiteLikelihoods	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)
Cbpp::CWisePattern< R >::pattern_functor
Cbpp::PatternTools	Utilitary methods to compute site patterns
Cbpp::PGMAInfos	Inner data structure for WPGMA and UPGMA distance methods
►Cbpp::PhyloBranch
Cbpp::PhyloBranchMapping
Cbpp::PhyloBranchReward
Cbpp::PhylogeneticsApplicationTools	This class provides some common tools for applications
►Cbpp::PhyloNode
►Cbpp::ProcessComputationNode	Tree Organization of Computing Nodes
Cbpp::SimProcessNode
Cbpp::PhyloTreeTools	Generic utilitary methods dealing with trees
►Cbpp::ProcessComputationEdge
Cbpp::SimProcessEdge
Cbpp::ProcessEdge
Cbpp::LikelihoodCalculationSingleProcess::ProcessNodes	DF Nodes used in the process. ProcessTree is used without any rate multiplier
Cbpp::ProcPos	Likelihood framework based on a partition of a sequence in simple likelihoods
Cbpp::Nhx::Property
Cbpp::RASTools	Tools to deal with Rates Across Sites (RAS) models
Cbpp::LikelihoodCalculationOnABranch::RateCategoryEdge
Cbpp::LikelihoodCalculationSingleProcess::RateCategoryTrees
Cbpp::ReductionOf< T >
Cbpp::RewardMappingTools	Provide methods to compute reward mappings
CEigen::ScalarBinaryOpTraits< bpp::ExtendedFloat, double, BinaryOp >
CEigen::ScalarBinaryOpTraits< double, bpp::ExtendedFloat, BinaryOp >
Cbpp::SequenceSimulationTools	Tools for sites and sequences simulation
Cbpp::SimData
►Cbpp::TreeLikelihoodInterface::SiteIterator	An iterator over a set of sites, specified by their position
Cbpp::AbstractTreeLikelihood::SimpleSiteIterator	A very simple site iterator
►Cbpp::SiteSimulationResult	Data structure to store the result of a DetailedSiteSimulator
Cbpp::RASiteSimulationResult	Data structure to store the result of a DetailedSiteSimulator
Cbpp::SitePatterns::SortableSite	Class used for site pattern sorting
Cbpp::StochasticMapping
CStringAndInt
Cbpp::AbstractPhyloLikelihood::StringPairHash
Cbpp::SubstitutionMappingTools	Provide methods to compute substitution mappings
Cbpp::SubstitutionModelSetTools	Tools for automatically creating SubstitutionModelSet objects
Cbpp::TopologyChangeEvent	Class for notifying new toplogy change events
►Cbpp::TopologySearch	Interface for topology search methods
Cbpp::NNITopologySearch	NNI topology search method
►CTransitionFunction
Cbpp::ConstantTransitionFunction
Cbpp::Transposed< T >	The T dependency should be transposed before computation
►Cbpp::TreeDrawingDisplayControler	Easy tune of tree drawings display
Cbpp::BasicTreeDrawingDisplayControler	Easy tune of tree drawings display, a basic implementation:
Cbpp::TreeDrawingNodeInfo
Cbpp::TreeDrawingSettings	A set of options to tune the display of a TreeDrawing object
►Cbpp::TreeIterator
Cbpp::InOrderTreeIterator
Cbpp::PostOrderTreeIterator
Cbpp::PreOrderTreeIterator
►CTreeLikelihood
Cbpp::SitePartitionHomogeneousTreeLikelihood	Specialization of the TreeLikelihood interface for partition models, homogeneous case
►Cbpp::TreeLikelihoodTools	Utilitary methods that work with TreeLikelihood objects
Cbpp::DRTreeLikelihoodTools	Utilitary methods dealing with objects implementing the DRTreeLikelihood interface
Cbpp::TreeTemplateTools	Utilitary methods working with TreeTemplate and Node objects
Cbpp::TreeTools	Generic utilitary methods dealing with trees
►Cstd::vector< unsigned int >
Cbpp::ModelPath::PathNode	A vector<int> where all elements are different and in INCREASING ORDER. So inclusion should be done through dedicated methods