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

[detail level 123456789]

bpp::AncestralStateReconstruction	Interface for ancestral states reconstruction methods
bpp::MarginalAncestralStateReconstruction	Likelihood ancestral states reconstruction: marginal method
bpp::BipartitionTools	This class provides tools related to the BipartitionList class
bpp::TreeLikelihood::BranchIterator	An iterator over a set of branches, specified by their node ids
bpp::AbstractTreeLikelihood::SimpleBranchIterator	A very simple branch iterator
bpp::Clonable [external]
bpp::BipartitionList	This class deals with the bipartitions defined by trees
bpp::DistanceEstimation	Estimate a distance matrix from sequence data, according to a given model
bpp::DistanceMethod	General interface for distance-based phylogenetic reconstruction methods
bpp::AgglomerativeDistanceMethod	Interface for agglomerative distance methods
bpp::AbstractAgglomerativeDistanceMethod	Partial implementation of the AgglomerativeDistanceMethod interface
bpp::HierarchicalClustering	Hierarchical clustering
bpp::NeighborJoining	The neighbor joining distance method
bpp::BioNJ	The BioNJ distance method
bpp::PGMA	Compute WPGMA and UPGMA trees from a distance matrix
bpp::NNISearchable	Interface for Nearest Neighbor Interchanges algorithms
bpp::DRTreeParsimonyScore	Double recursive implementation of interface TreeParsimonyScore
bpp::NNIHomogeneousTreeLikelihood	This class adds support for NNI topology estimation to the DRHomogeneousTreeLikelihood class
bpp::OptimizationStopCondition [external]
bpp::AbstractOptimizationStopCondition [external]
bpp::PseudoNewtonOptimizer::PNStopCondition
bpp::Optimizer [external]
bpp::AbstractOptimizer [external]
bpp::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
bpp::Parametrizable [external]
bpp::AbstractParametrizable [external]
bpp::AbstractFrequenciesSet	Basic implementation of the FrequenciesSet interface
bpp::AbstractWordFrequenciesSet
bpp::WordFromIndependentFrequenciesSet	Frequencies in words are the product of Independent Frequencies in letters
bpp::CodonFromIndependentFrequenciesSet	Frequencies in codons are the product of Independent Frequencies in letters with the frequencies of stop codons set to zero
bpp::WordFromUniqueFrequenciesSet
bpp::CodonFromUniqueFrequenciesSet	Frequencies in codons are the product of the frequencies for a unique FrequenciesSet in letters, with the frequencies of stop codons set to zero
bpp::FixedCodonFrequenciesSet	FrequenciesSet useful for homogeneous and stationary models, codon implementation
bpp::FixedFrequenciesSet	FrequenciesSet useful for homogeneous and stationary models
bpp::FixedNucleotideFrequenciesSet	FrequenciesSet useful for homogeneous and stationary models, nucleotide implementation
bpp::FixedProteinFrequenciesSet	FrequenciesSet useful for homogeneous and stationary models, protein implementation
bpp::FullCodonFrequenciesSet	A generic FrequenciesSet for Full Codon alphabets
bpp::FullFrequenciesSet	A generic FrequenciesSet allowing for the estimation of all frequencies
bpp::FullProteinFrequenciesSet	Protein FrequenciesSet using 19 independent parameters to modelize the 20 frequencies
bpp::FullNucleotideFrequenciesSet	Nucleotide FrequenciesSet using three independent parameters (theta, theta1, theta2) to modelize the four frequencies:
bpp::FullPerAACodonFrequenciesSet	FrequenciesSet integrating ProteinFrequenciesSet inside CodonFrequenciesSet. In this case, FrequencieSet defined inside each amino acid is parametrized as a FullFrequenciesSet. Hence there are 61-20=41 parameters in addition of the parameters of the ProteinFrequenciesSet
bpp::GCFrequenciesSet	Nucleotide FrequenciesSet using only one parameter, the GC content
bpp::MarkovModulatedFrequenciesSet	FrequenciesSet to be used with a Markov-modulated substitution model
bpp::MvaFrequenciesSet	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
bpp::AbstractParameterAliasable [external]
bpp::AbstractBiblioSubstitutionModel	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
bpp::AbstractBiblioMixedSubstitutionModel	Abstract class for mixture models based on the bibliography
bpp::LGL08_CAT	The Le et al (2008) CAT substitution model for proteins
bpp::LLG08_EHO	The Le et al (2008) EH0 substitution model for proteins
bpp::LLG08_EX2	The Le et al (2008) EX2 substitution model for proteins
bpp::LLG08_EX3	The Le et al (2008) EX3 substitution model for proteins
bpp::LLG08_UL2	The Le et al (2008) UL2 substitution model for proteins
bpp::LLG08_UL3	The Le et al (2008) UL3 substitution model for proteins
bpp::YNGKP_M1	The Yang et al (2000) M1 substitution model for codons, with the more realistic modification in Wong & al (2004)
bpp::YNGKP_M2	The Yang et al (2000) M2 substitution model for codons, with the more realistic modification in Wong & al (2004)
bpp::YNGKP_M3	The Yang et al (2000) M3 substitution model for codons
bpp::YNGKP_M7	The Yang et al (2000) M7 substitution model for codons
bpp::YNGKP_M8	The Yang et al (2000) M8 substitution model for codons
bpp::GY94	The Goldman and Yang (1994) substitution model for codons
bpp::MG94	The Muse and Gaut (1994) substitution model for codons
bpp::YN98	The Yang and Nielsen (1998) substitution model for codons
bpp::AbstractCodonDistanceSubstitutionModel	Abstract class for modelling of non-synonymous abd synonymous substitution rates in codon models
bpp::CodonDistanceFitnessPhaseFrequenciesSubstitutionModel	Class for asynonymous and synonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic basic models
bpp::CodonDistanceFrequenciesSubstitutionModel	Class for asynonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic models
bpp::CodonDistancePhaseFrequenciesSubstitutionModel	Class for asynonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic basic models
bpp::CodonDistanceSubstitutionModel	Class for substitution models of codons with non-synonymous/synonymous ratios of substitution rates defined through a distance between amino-acids
bpp::AbstractCodonFitnessSubstitutionModel	Abstract class for modelling of ratios of substitution rates between codons, whatever they are synonymous or not
bpp::CodonDistanceFitnessPhaseFrequenciesSubstitutionModel	Class for asynonymous and synonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic basic models
bpp::AbstractCodonFrequenciesSubstitutionModel	Abstract Class for substitution models on codons parametrized by frequencies
bpp::CodonDistanceFrequenciesSubstitutionModel	Class for asynonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic models
bpp::CodonRateFrequenciesSubstitutionModel	Class for substitution models on non stop codons, with different parametrized rates on the models, depending on their phase and defined through a specific equilibrium distribution
bpp::AbstractCodonPhaseFrequenciesSubstitutionModel	Abstract Class for substitution models on codons parametrized by a frequency
bpp::CodonDistanceFitnessPhaseFrequenciesSubstitutionModel	Class for asynonymous and synonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic basic models
bpp::CodonDistancePhaseFrequenciesSubstitutionModel	Class for asynonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic basic models
bpp::AbstractDiscreteDistribution [external]
bpp::ConstantDistribution [external]
bpp::ConstantRateDistribution
bpp::ExponentialDiscreteDistribution [external]
bpp::ExponentialDiscreteRateDistribution
bpp::GammaDiscreteDistribution [external]
bpp::GammaDiscreteRateDistribution
bpp::GaussianDiscreteDistribution [external]
bpp::GaussianDiscreteRateDistribution
bpp::AbstractSubstitutionModel	Partial implementation of the SubstitutionModel interface
bpp::AbstractMixedSubstitutionModel	Partial implementation for Mixed Substitution 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
bpp::MixtureOfASubstitutionModel	Substitution models defined as a mixture of nested substitution models
bpp::MixtureOfSubstitutionModels	Substitution models defined as a mixture of several substitution models
bpp::AbstractReversibleSubstitutionModel	Partial implementation of the ReversibleSubstitutionModel interface
bpp::BinarySubstitutionModel	The Model on two states
bpp::Coala	The Coala branch-heterogeneous amino-acid substitution model
bpp::DSO78	The Dayhoff, Schwartz and Orcutt substitution model for proteins
bpp::F84	The Felsenstein (1984) substitution model for nucleotides
bpp::GTR	The General Time-Reversible substitution model for nucleotides
bpp::HKY85	The Hasegawa M, Kishino H and Yano T (1985) substitution model for nucleotides
bpp::JCnuc	The Jukes-Cantor substitution model for nucleotides
bpp::JCprot	The Jukes-Cantor substitution model for proteins
bpp::JTT92	The Jones, Taylor and Thornton substitution model for proteins
bpp::K80	The Kimura 2-rates substitution model for nucleotides
bpp::LG08	The Le and Gascuel substitution model for proteins
bpp::LGL08_CAT::EmbeddedModel
bpp::LLG08_EHO::EmbeddedModel
bpp::LLG08_EX2::EmbeddedModel
bpp::LLG08_EX3::EmbeddedModel
bpp::LLG08_UL2::EmbeddedModel
bpp::LLG08_UL3::EmbeddedModel
bpp::RE08	The Rivas-Eddy substitution model with gap characters
bpp::SSR	The Strand Symmetric Reversible substitution model for nucleotides
bpp::T92	The Tamura (1992) substitution model for nucleotides
bpp::TN93	The Tamura and Nei (1993) substitution model for nucleotides
bpp::UserProteinSubstitutionModel	Build an empirical protein substitution model from a file
bpp::WAG01	The Whelan and Goldman substitution model for proteins
bpp::AbstractWordSubstitutionModel	Abstract Basal class for words of substitution models
bpp::AbstractCodonSubstitutionModel	Abstract class for substitution models on codons
bpp::CodonDistanceFitnessPhaseFrequenciesSubstitutionModel	Class for asynonymous and synonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic basic models
bpp::CodonDistanceFrequenciesSubstitutionModel	Class for asynonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic models
bpp::CodonDistancePhaseFrequenciesSubstitutionModel	Class for asynonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic basic models
bpp::CodonDistanceSubstitutionModel	Class for substitution models of codons with non-synonymous/synonymous ratios of substitution rates defined through a distance between amino-acids
bpp::CodonRateFrequenciesSubstitutionModel	Class for substitution models on non stop codons, with different parametrized rates on the models, depending on their phase and defined through a specific equilibrium distribution
bpp::CodonRateSubstitutionModel	Class for substitution models on non stop codons, with different rates on the models, depending on their phase
bpp::WordSubstitutionModel	Basal class for words of reversible substitution models
bpp::TripletSubstitutionModel	Class for neutral substitution models on triplets, which correspond to codons that do not have any significance (whether they are STOP or functional)
bpp::gBGC	GBGC model
bpp::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
bpp::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
bpp::RN95s	Intersection of models RN95 and L95
bpp::YpR	YpR model
bpp::YpR_Gen	General YpR model
bpp::YpR_Sym	Symetrical YpR model
bpp::MarkovModulatedSubstitutionModel	Partial implementation of the Markov-modulated class of substitution models
bpp::G2001	Galtier's 2001 covarion model
bpp::TS98	Tuffley and Steel's 1998 covarion model
bpp::SubstitutionModelSet	Substitution models manager for non-homogeneous / non-reversible models of evolution
bpp::MixedSubstitutionModelSet	Substitution models manager for Mixed Substitution Models. This class inherits from SubstitutionModelSet
bpp::AbstractTreeLikelihood	Partial implementation of the TreeLikelihood interface
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	Partial implementation of the DiscreteRatesAcrossSitesTreeLikelihood interface
bpp::AbstractHomogeneousTreeLikelihood	Partial implementation for homogeneous model of the TreeLikelihood interface
bpp::DRHomogeneousTreeLikelihood	This class implements the likelihood computation for a tree using the double-recursive algorithm
bpp::DRHomogeneousMixedTreeLikelihood	A class to compute the average of several DRHomogeneousTreeLikelihood defined from a Mixed Substitution Model
bpp::NNIHomogeneousTreeLikelihood	This class adds support for NNI topology estimation to the DRHomogeneousTreeLikelihood class
bpp::RHomogeneousTreeLikelihood	This class implement the 'traditional' way of computing likelihood for a tree
bpp::RHomogeneousClockTreeLikelihood	Likelihood computation with a global clock
bpp::RHomogeneousMixedTreeLikelihood
bpp::AbstractNonHomogeneousTreeLikelihood	Partial implementation for branch non-homogeneous models of the TreeLikelihood interface
bpp::DRNonHomogeneousTreeLikelihood	This class implements the likelihood computation for a tree using the double-recursive algorithm, allowing for non-homogeneous models of substitutions
bpp::RNonHomogeneousTreeLikelihood	This class implement the 'traditional' way of computing likelihood for a tree, allowing for non-homogeneous models of substitutions
bpp::RNonHomogeneousMixedTreeLikelihood
bpp::TwoTreeLikelihood	This class is a simplified version of DRHomogeneousTreeLikelihood for 2-Trees
bpp::BranchLikelihood	Compute likelihood for a 4-tree
bpp::GlobalClockTreeLikelihoodFunctionWrapper
bpp::FrequenciesSet	Parametrize a set of state frequencies
bpp::AbstractFrequenciesSet	Basic implementation of the FrequenciesSet interface
bpp::CodonFrequenciesSet	Parametrize a set of state frequencies for codons
bpp::CodonFromIndependentFrequenciesSet	Frequencies in codons are the product of Independent Frequencies in letters with the frequencies of stop codons set to zero
bpp::CodonFromUniqueFrequenciesSet	Frequencies in codons are the product of the frequencies for a unique FrequenciesSet in letters, with the frequencies of stop codons set to zero
bpp::FixedCodonFrequenciesSet	FrequenciesSet useful for homogeneous and stationary models, codon implementation
bpp::FullCodonFrequenciesSet	A generic FrequenciesSet for Full Codon alphabets
bpp::FullPerAACodonFrequenciesSet	FrequenciesSet integrating ProteinFrequenciesSet inside CodonFrequenciesSet. In this case, FrequencieSet defined inside each amino acid is parametrized as a FullFrequenciesSet. Hence there are 61-20=41 parameters in addition of the parameters of the ProteinFrequenciesSet
bpp::NucleotideFrequenciesSet	Parametrize a set of state frequencies for nucleotides
bpp::FixedNucleotideFrequenciesSet	FrequenciesSet useful for homogeneous and stationary models, nucleotide implementation
bpp::FullNucleotideFrequenciesSet	Nucleotide FrequenciesSet using three independent parameters (theta, theta1, theta2) to modelize the four frequencies:
bpp::GCFrequenciesSet	Nucleotide FrequenciesSet using only one parameter, the GC content
bpp::ProteinFrequenciesSet	Parametrize a set of state frequencies for proteins
bpp::FixedProteinFrequenciesSet	FrequenciesSet useful for homogeneous and stationary models, protein implementation
bpp::FullProteinFrequenciesSet	Protein FrequenciesSet using 19 independent parameters to modelize the 20 frequencies
bpp::MvaFrequenciesSet	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
bpp::WordFrequenciesSet	Frequencies in words computed from the frequencies on letters. The parameters are the parameters of the Frequencies on letters. The WordFrequenciesSet owns the FrequenciesSet* it is built on. Interface class
bpp::AbstractWordFrequenciesSet
bpp::Function [external]
bpp::BranchLikelihood	Compute likelihood for a 4-tree
bpp::DerivableFirstOrder [external]
bpp::DerivableSecondOrder [external]
bpp::GlobalClockTreeLikelihoodFunctionWrapper
bpp::TreeLikelihood	The TreeLikelihood interface
bpp::AbstractTreeLikelihood	Partial implementation of the TreeLikelihood interface
bpp::ClockTreeLikelihood	Interface for likelihood computation with a global clock
bpp::DiscreteRatesAcrossSitesClockTreeLikelihood	Interface for likelihood computation with a global clock and rate across sites variation
bpp::RHomogeneousClockTreeLikelihood	Likelihood computation with a global clock
bpp::DiscreteRatesAcrossSitesTreeLikelihood	Interface for rate across sites (RAS) implementation
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	Partial implementation of the DiscreteRatesAcrossSitesTreeLikelihood interface
bpp::DiscreteRatesAcrossSitesClockTreeLikelihood	Interface for likelihood computation with a global clock and rate across sites variation
bpp::DRTreeLikelihood	Interface for double-recursive (DR) implementation of the likelihood computation
bpp::DRHomogeneousTreeLikelihood	This class implements the likelihood computation for a tree using the double-recursive algorithm
bpp::DRNonHomogeneousTreeLikelihood	This class implements the likelihood computation for a tree using the double-recursive algorithm, allowing for non-homogeneous models of substitutions
bpp::HomogeneousTreeLikelihood	Specialization of the TreeLikelihood interface for the Homogeneous case
bpp::AbstractHomogeneousTreeLikelihood	Partial implementation for homogeneous model of the TreeLikelihood interface
bpp::NonHomogeneousTreeLikelihood	Specialization of the TreeLikelihood interface for the branch non-homogeneous and non-stationary models
bpp::AbstractNonHomogeneousTreeLikelihood	Partial implementation for branch non-homogeneous models of the TreeLikelihood interface
bpp::SitePartitionHomogeneousTreeLikelihood	Specialization of the TreeLikelihood interface for partition models, homogeneous case
bpp::OptimizationTools::ScaleFunction
bpp::ParameterAliasable [external]
bpp::AbstractParameterAliasable [external]
bpp::DiscreteDistribution [external]
bpp::AbstractDiscreteDistribution [external]
bpp::SubstitutionModel	Interface for all substitution models
bpp::AbstractBiblioSubstitutionModel	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
bpp::AbstractSubstitutionModel	Partial implementation of the SubstitutionModel interface
bpp::CodonSubstitutionModel	Abstract class for codon models
bpp::AbstractCodonDistanceSubstitutionModel	Abstract class for modelling of non-synonymous abd synonymous substitution rates in codon models
bpp::AbstractCodonFitnessSubstitutionModel	Abstract class for modelling of ratios of substitution rates between codons, whatever they are synonymous or not
bpp::AbstractCodonFrequenciesSubstitutionModel	Abstract Class for substitution models on codons parametrized by frequencies
bpp::AbstractCodonPhaseFrequenciesSubstitutionModel	Abstract Class for substitution models on codons parametrized by a frequency
bpp::AbstractCodonSubstitutionModel	Abstract class for substitution models on codons
bpp::MixedSubstitutionModel	Interface for Substitution models, defined as a mixture of "simple" substitution models
bpp::AbstractBiblioMixedSubstitutionModel	Abstract class for mixture models based on the bibliography
bpp::AbstractMixedSubstitutionModel	Partial implementation for Mixed Substitution 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
bpp::NucleotideSubstitutionModel	Specialisation interface for nucleotide substitution model
bpp::F84	The Felsenstein (1984) substitution model for nucleotides
bpp::gBGC	GBGC model
bpp::GTR	The General Time-Reversible substitution model for nucleotides
bpp::HKY85	The Hasegawa M, Kishino H and Yano T (1985) substitution model for nucleotides
bpp::JCnuc	The Jukes-Cantor substitution model for nucleotides
bpp::K80	The Kimura 2-rates substitution model for nucleotides
bpp::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
bpp::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
bpp::RN95s	Intersection of models RN95 and L95
bpp::SSR	The Strand Symmetric Reversible substitution model for nucleotides
bpp::T92	The Tamura (1992) substitution model for nucleotides
bpp::TN93	The Tamura and Nei (1993) substitution model for nucleotides
bpp::ProteinSubstitutionModel	Specialized interface for protein substitution model
bpp::Coala	The Coala branch-heterogeneous amino-acid substitution model
bpp::DSO78	The Dayhoff, Schwartz and Orcutt substitution model for proteins
bpp::JCprot	The Jukes-Cantor substitution model for proteins
bpp::JTT92	The Jones, Taylor and Thornton substitution model for proteins
bpp::LG08	The Le and Gascuel substitution model for proteins
bpp::LGL08_CAT::EmbeddedModel
bpp::LLG08_EHO::EmbeddedModel
bpp::LLG08_EX2::EmbeddedModel
bpp::LLG08_EX3::EmbeddedModel
bpp::LLG08_UL2::EmbeddedModel
bpp::LLG08_UL3::EmbeddedModel
bpp::UserProteinSubstitutionModel	Build an empirical protein substitution model from a file
bpp::WAG01	The Whelan and Goldman substitution model for proteins
bpp::ReversibleSubstitutionModel	Interface for reversible substitution models
bpp::AbstractReversibleSubstitutionModel	Partial implementation of the ReversibleSubstitutionModel interface
bpp::GY94	The Goldman and Yang (1994) substitution model for codons
bpp::MarkovModulatedSubstitutionModel	Partial implementation of the Markov-modulated class of substitution models
bpp::MG94	The Muse and Gaut (1994) substitution model for codons
bpp::YN98	The Yang and Nielsen (1998) substitution model for codons
bpp::YNGKP_M1	The Yang et al (2000) M1 substitution model for codons, with the more realistic modification in Wong & al (2004)
bpp::YNGKP_M2	The Yang et al (2000) M2 substitution model for codons, with the more realistic modification in Wong & al (2004)
bpp::YNGKP_M3	The Yang et al (2000) M3 substitution model for codons
bpp::YNGKP_M7	The Yang et al (2000) M7 substitution model for codons
bpp::YNGKP_M8	The Yang et al (2000) M8 substitution model for codons
bpp::ParametrizableAdapter [external]
bpp::OptimizationTools::ScaleFunction
bpp::PhyloStatistics	Compute several quantities on a tree simulateously, optimizing the recursions on the tree
bpp::SequenceSimulator	The SequenceSimulator interface. SequenceSimulator classes can simulate whole datasets
bpp::NonHomogeneousSequenceSimulator	Site and sequences simulation under non-homogeneous models
bpp::HomogeneousSequenceSimulator	Site and sequences simulation under homogeneous models
bpp::SitePatterns	Data structure for site patterns
bpp::StateMap	Map the states of a given alphabet which have a model state
bpp::AbstractStateMap	A convenience partial implementation of the StateMap interface
bpp::CanonicalStateMap	This class implements a state map where all resolved states are modeled
bpp::SubstitutionCount	The SubstitutionsCount interface
bpp::AbstractSubstitutionCount	Basic implementation of the the SubstitutionCount interface
bpp::DecompositionSubstitutionCount	Analytical substitution count using the eigen decomposition method
bpp::LabelSubstitutionCount	Labelling substitution count
bpp::LaplaceSubstitutionCount	Laplace estimate of the substitution count
bpp::NaiveSubstitutionCount	Naive substitution count
bpp::OneJumpSubstitutionCount	Computes the probability that at least one jump occured on a branch, given the initial and final state
bpp::UniformizationSubstitutionCount	Analytical (weighted) substitution count using the uniformization method
bpp::WeightedSubstitutionCount	Interface allowing for weighting of substitution counts according to state properties
bpp::AbstractWeightedSubstitutionCount	Partial implementation of the WeightedSubstitutionCount interface
bpp::DecompositionSubstitutionCount	Analytical substitution count using the eigen decomposition method
bpp::NaiveSubstitutionCount	Naive substitution count
bpp::UniformizationSubstitutionCount	Analytical (weighted) substitution count using the uniformization method
bpp::SubstitutionMapping	General interface for storing mapping data
bpp::AbstractSubstitutionMapping	Partial implementation of the substitution mapping interface
bpp::ProbabilisticSubstitutionMapping	Data storage class for probabilistic substitution mappings
bpp::SubstitutionRegister	The SubstitutionRegister interface
bpp::AbstractSubstitutionRegister
bpp::CategorySubstitutionRegister	Gather states into defined categories, and count the changes between categories
bpp::ComprehensiveSubstitutionRegister	Distinguishes all types of substitutions
bpp::GCSubstitutionRegister	Distinguishes AT<->GC from GC<->AT
bpp::GCSynonymousSubstitutionRegister	Distinguishes AT->GC vs GC->AT inside synonymous substitutions on third codon position
bpp::DnDsSubstitutionRegister	Distinguishes synonymous from non-synonymous substitutions
bpp::TotalSubstitutionRegister	Count all substitutions
bpp::TsTvSubstitutionRegister	Distinguishes transitions from transversions
bpp::TopologyListener	Implement this interface to be notified when the topology of a tree has changed during topology search
bpp::NNISearchable	Interface for Nearest Neighbor Interchanges algorithms
bpp::NNITopologyListener	Listener used internally by the optimizeTreeNNI method
bpp::NNITopologyListener2	Listener used internally by the optimizeTreeNNI2 method
bpp::Tree	Interface for phylogenetic tree objects
bpp::TreeTemplate< N >	The phylogenetic tree class
bpp::TreeTemplate< bpp::Node >
bpp::TreeTemplate< bpp::NodeTemplate >
bpp::TreeDrawing	Basal interface for tree drawing classes
bpp::AbstractTreeDrawing	Partial implementation of the TreeDrawing interface
bpp::AbstractDendrogramPlot	Basic implementation of dendrogram plots
bpp::CladogramPlot	Cladogram representation of trees
bpp::PhylogramPlot	Phylogram representation of trees
bpp::TreeDrawingListener	Interface allowing to capture drawing events
bpp::TreeDrawingListenerAdapter	An empty implementation of the TreeDrawingListener interface
bpp::BootstrapValuesTreeDrawingListener	A TreeDrawingListener implementation that write the bootstrap values of inner nodes
bpp::BranchLengthsTreeDrawingListener	A TreeDrawingListener implementation that write the branch lengths of inner nodes
bpp::LabelCollapsedNodesTreeDrawingListener	A TreeDrawingListener implementation that label the collapsed nodes
bpp::LabelInnerNodesTreeDrawingListener	A TreeDrawingListener implementation that write the names of inner nodes
bpp::LeafNamesTreeDrawingListener	A TreeDrawingListener implementation that write leaf names
bpp::NodesIdTreeDrawingListener	A TreeDrawingListener implementation that writes nodes id
bpp::TreeLikelihoodData	TreeLikelihood data structure
bpp::AbstractTreeLikelihoodData	Partial implementation of the TreeLikelihoodData interface
bpp::DRASDRTreeLikelihoodData	Likelihood data structure for rate across sites models, using a double-recursive algorithm
bpp::DRASRTreeLikelihoodData	Discrete Rate Across Sites, (simple) Recursive likelihood data structure
bpp::TreeLikelihoodNodeData	TreeLikelihood partial data structure
bpp::DRASDRTreeLikelihoodLeafData	Likelihood data structure for a leaf
bpp::DRASDRTreeLikelihoodNodeData	Likelihood data structure for a node
bpp::DRASRTreeLikelihoodNodeData	Likelihood data structure for a node
bpp::TreeParsimonyData	TreeParsimonyScore data structure
bpp::AbstractTreeParsimonyData	Partial implementation of the TreeParsimonyData interface
bpp::DRTreeParsimonyData	Parsimony data structure for double-recursive (DR) algorithm
bpp::TreeParsimonyNodeData	TreeParsimonyScore node data structure
bpp::DRTreeParsimonyLeafData	Parsimony data structure for a leaf
bpp::DRTreeParsimonyNodeData	Parsimony data structure for a node
bpp::TreeParsimonyScore	Compute a parsimony score
bpp::AbstractTreeParsimonyScore	Partial implementation of the TreeParsimonyScore interface
bpp::DRTreeParsimonyScore	Double recursive implementation of interface TreeParsimonyScore
bpp::ClusterInfos
bpp::CoalaCore	This class is the core class inherited by the Coala class. COaLA is a branch-heterogeneous amino-acid substitution model
bpp::Coala	The Coala branch-heterogeneous amino-acid substitution model
bpp::TreeLikelihood::ConstBranchModelDescription	A pair of SubstitutionModel / SiteIterator
bpp::AbstractTreeLikelihood::ConstNoPartitionBranchModelDescription
bpp::TreeLikelihood::ConstBranchModelIterator	Iterates through all models used for all sites on a given branch
bpp::AbstractTreeLikelihood::ConstNoPartitionBranchModelIterator
bpp::TreeLikelihood::ConstSiteModelDescription	A pair of SubstitutionModel / BranchIterator
bpp::AbstractTreeLikelihood::ConstNoPartitionSiteModelDescription
bpp::TreeLikelihood::ConstSiteModelIterator	Iterates through all models used for all branches on a given site
bpp::AbstractNonHomogeneousTreeLikelihood::ConstNonHomogeneousSiteModelIterator
ConstSiteModelIterator
bpp::AbstractHomogeneousTreeLikelihood::ConstHomogeneousSiteModelIterator
bpp::Cursor	Data structure describing a plotting direction
bpp::DrawBranchEvent	Event class used by TreeDrawing classes
bpp::DrawIBranchEvent	Event class that uses INode object (more efficient than relying on nodes id, but less generic)
bpp::CladogramDrawBranchEvent
bpp::PhylogramDrawBranchEvent
bpp::DrawNodeEvent	Event class used by TreeDrawing classes
bpp::DrawINodeEvent	Event class that uses INode object (more efficient than relying on nodes id, but less generic)
bpp::DrawTreeEvent	Event class used by TreeDrawing classes
bpp::Nhx::Element
bpp::TreeTemplateTools::Element
bpp::Exception [external]
bpp::NodeException	General exception thrown when something is wrong with a particular node
bpp::NodePException	General exception thrown when something is wrong with a particular node
bpp::PropertyNotFoundException	General exception thrown if a property could not be found
bpp::NodeNotFoundException	Exception thrown when something is wrong with a particular node
bpp::SubstitutionModelException	Exception that may be thrown by susbstitution models
bpp::TreeException	General exception thrown when something wrong happened in a tree
bpp::UnrootedTreeException	Exception thrown when a tree is expected to be rooted
bpp::MixedSubstitutionModelSet::HyperNode
IntAndInt
bpp::IODistanceMatrixFactory	Utilitary class for creating distance matrix readers and writers
bpp::IOFormat [external]
bpp::IoDiscreteDistribution [external]
bpp::IDiscreteDistribution [external]
bpp::BppODiscreteDistributionFormat [external]
bpp::BppORateDistributionFormat	Rate Distribution I/O in BppO format
bpp::ODiscreteDistribution [external]
bpp::BppODiscreteDistributionFormat [external]
bpp::IODistanceMatrix	General interface for distance matrix I/O
bpp::IDistanceMatrix	General interface for distance matrix readers
bpp::AbstractIDistanceMatrix	Partial implementation of the IDistanceMatrix interface
bpp::PhylipDistanceMatrixFormat	Distance matrix I/O in Phylip format
bpp::ODistanceMatrix	General interface for distance matrix writers
bpp::AbstractODistanceMatrix	Partial implementation of the ODistanceMatrix interface
bpp::PhylipDistanceMatrixFormat	Distance matrix I/O in Phylip format
bpp::IoFrequenciesSet	General interface for model I/O
bpp::IFrequenciesSet	General interface for distance matrix readers
bpp::BppOFrequenciesSetFormat	Substitution model I/O in BppO format
bpp::OFrequenciesSet	General interface for distance matrix writers
bpp::BppOFrequenciesSetFormat	Substitution model I/O in BppO format
bpp::IOPairedSiteLikelihoods	Base class for I/O on paired-site likelihoods
bpp::IOPhymlPairedSiteLikelihoods	This class provides input for the Phyml paired-site likelihoods format
bpp::IOTreepuzzlePairedSiteLikelihoods	This class provides I/O for the Tree-Puzzle/RAxML (phylip-like) paired-site likelihoods format
bpp::IoSubstitutionModel	General interface for model I/O
bpp::ISubstitutionModel	General interface for distance matrix readers
bpp::BppOSubstitutionModelFormat	Substitution model I/O in BppO format
bpp::OSubstitutionModel	General interface for distance matrix writers
bpp::BppOSubstitutionModelFormat	Substitution model I/O in BppO format
bpp::IOTree	General interface for tree I/O
bpp::IMultiTree	General interface for multiple trees readers
bpp::AbstractIMultiTree	Partial implementation of the IMultiTree interface
bpp::Newick	The so-called 'newick' parenthetic format
bpp::NexusIOTree	Simple parser for reading trees from a Nexus file
bpp::Nhx	The so-called 'Nhx - New Hampshire eXtended' parenthetic format
bpp::ITree	General interface for tree readers
bpp::AbstractITree	Partial implementation of the ITree interface
bpp::Newick	The so-called 'newick' parenthetic format
bpp::NexusIOTree	Simple parser for reading trees from a Nexus file
bpp::Nhx	The so-called 'Nhx - New Hampshire eXtended' parenthetic format
bpp::OMultiTree	General interface for tree writers
bpp::AbstractOMultiTree	Partial implementation of the OTree interface
bpp::Newick	The so-called 'newick' parenthetic format
bpp::NexusIOTree	Simple parser for reading trees from a Nexus file
bpp::Nhx	The so-called 'Nhx - New Hampshire eXtended' parenthetic format
bpp::OTree	General interface for tree writers
bpp::AbstractOTree	Partial implementation of the OTree interface
bpp::Newick	The so-called 'newick' parenthetic format
bpp::NexusIOTree	Simple parser for reading trees from a Nexus file
bpp::Nhx	The so-called 'Nhx - New Hampshire eXtended' parenthetic format
bpp::IOFrequenciesSetFactory	Utilitary class for creating frequencies set readers and writers
bpp::IOSubstitutionModelFactory	Utilitary class for creating substitution model readers and writers
bpp::IOTreeFactory	Utilitary class for creating tree readers and writers
bpp::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)
bpp::TreeTools::Moments_
bpp::MutationPath	This class is used by MutationProcess to store detailed results of simulations
bpp::MutationProcess	Interface for simulations
bpp::AbstractMutationProcess	Partial implmentation of the MutationProcess interface
bpp::SelfMutationProcess	This class is mainly for testing purpose. It allow "self" mutation of the kind i->i;
bpp::SimpleMutationProcess	Generally used mutation process model
bpp::MixedSubstitutionModelSet::HyperNode::Node
bpp::Node	The phylogenetic node class
bpp::NodeTemplate< NodeInfos >	The NodeTemplate class
bpp::OptimizationListener [external]
bpp::NaNListener	A listener which capture NaN function values and throw an exception in case this happens
bpp::OptimizationTools	Optimization methods for phylogenetic inference
bpp::TreeTemplateTools::OrderTreeData_
bpp::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)
bpp::PatternTools	Utilitary methods to compute site patterns
bpp::PGMAInfos	Inner data structure for WPGMA and UPGMA distance methods
bpp::PhylogeneticsApplicationTools	This class provides some common tools for applications
bpp::Nhx::Property
bpp::RASTools	Tools to deal with Rates Across Sites (RAS) models
bpp::RateDistributionFactory	Utilitary class for creating rate distributions
bpp::SequenceSimulationTools	Tools for sites and sequences simulation
bpp::SimData
bpp::TreeLikelihood::SiteIterator	An iterator over a set of sites, speicfied by their position
bpp::AbstractTreeLikelihood::SimpleSiteIterator	A very simple site iterator
bpp::SiteSimulationResult	Data structure to store the result of a DetailedSiteSimulator
bpp::RASiteSimulationResult	Data structure to store the result of a DetailedSiteSimulator
bpp::SiteSimulator	The SiteSimulator interface. SiteSimulator classes can simulate single sites
bpp::DetailedSiteSimulator	This interface adds the dSimulate method to the SiteSimulator interface
bpp::NonHomogeneousSequenceSimulator	Site and sequences simulation under non-homogeneous models
bpp::SitePatterns::SortableSite	Class used for site pattern sorting
StringAndInt
bpp::SubstitutionMappingTools	Provide methods to compute substitution mappings
bpp::SubstitutionModelFactory	Utilitary class for creating substitution models
bpp::SubstitutionModelSetTools	Tools for automatically creating SubstitutionModelSet objects
bpp::TopologyChangeEvent	Class for notifying new toplogy change events
bpp::TopologySearch	Interface for topology search methods
bpp::NNITopologySearch	NNI topology search method
bpp::TreeDrawingDisplayControler	Easy tune of tree drawings display
bpp::BasicTreeDrawingDisplayControler	Easy tune of tree drawings display, a basic implementation:
bpp::TreeDrawingNodeInfo
bpp::TreeDrawingSettings	A set of options to tune the display of a TreeDrawing object
bpp::TreeLikelihoodTools	Utilitary methods that work with TreeLikelihood objects
bpp::DRTreeLikelihoodTools	Utilitary methods dealing with objects implementing the DRTreeLikelihood interface
bpp::TreeTemplateTools	Utilitary methods working with TreeTemplate and Node objects
bpp::TreeTools	Generic utilitary methods dealing with trees