| bpp::AbstractAgglomerativeDistanceMethod | Partial implementation of the AgglomerativeDistanceMethod interface |
| bpp::AbstractBiblioMixedSubstitutionModel | Abstract class for mixture models based on the bibliography |
| 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::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::AbstractDendrogramPlot | Basic implementation of dendrogram plots |
| bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood | Partial implementation of the DiscreteRatesAcrossSitesTreeLikelihood interface |
| bpp::AbstractFrequenciesSet | Basic implementation of the FrequenciesSet interface |
| bpp::AbstractHomogeneousTreeLikelihood | Partial implementation for homogeneous model of the TreeLikelihood interface |
| bpp::AbstractIDistanceMatrix | Partial implementation of the IDistanceMatrix interface |
| bpp::AbstractIMultiTree | Partial implementation of the IMultiTree interface |
| bpp::AbstractITree | Partial implementation of the ITree 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::AbstractMutationProcess | Partial implmentation of the MutationProcess interface |
| bpp::AbstractNonHomogeneousTreeLikelihood | Partial implementation for branch non-homogeneous models of the TreeLikelihood interface |
| bpp::AbstractODistanceMatrix | Partial implementation of the ODistanceMatrix interface |
| bpp::AbstractOMultiTree | Partial implementation of the OTree interface |
| bpp::AbstractOTree | Partial implementation of the OTree interface |
| bpp::AbstractReversibleSubstitutionModel | Partial implementation of the ReversibleSubstitutionModel interface |
| bpp::AbstractStateMap | A convenience partial implementation of the StateMap interface |
| bpp::AbstractSubstitutionCount | Basic implementation of the the SubstitutionCount interface |
| bpp::AbstractSubstitutionMapping | Partial implementation of the substitution mapping interface |
| bpp::AbstractSubstitutionModel | Partial implementation of the SubstitutionModel interface |
| bpp::AbstractSubstitutionRegister | |
| bpp::AbstractTreeDrawing | Partial implementation of the TreeDrawing interface |
| bpp::AbstractTreeLikelihood | Partial implementation of the TreeLikelihood interface |
| bpp::AbstractTreeLikelihoodData | Partial implementation of the TreeLikelihoodData interface |
| bpp::AbstractTreeParsimonyData | Partial implementation of the TreeParsimonyData interface |
| bpp::AbstractTreeParsimonyScore | Partial implementation of the TreeParsimonyScore interface |
| bpp::AbstractWeightedSubstitutionCount | Partial implementation of the WeightedSubstitutionCount interface |
| bpp::AbstractWordFrequenciesSet | |
| bpp::AbstractWordSubstitutionModel | Abstract Basal class for words of substitution models |
| bpp::AgglomerativeDistanceMethod | Interface for agglomerative distance methods |
| bpp::AncestralStateReconstruction | Interface for ancestral states reconstruction methods |
| bpp::BasicTreeDrawingDisplayControler | Easy tune of tree drawings display, a basic implementation: |
| bpp::BinarySubstitutionModel | The Model on two states |
| bpp::BioNJ | The BioNJ distance method |
| bpp::BipartitionList | This class deals with the bipartitions defined by trees |
| bpp::BipartitionTools | This class provides tools related to the BipartitionList class |
| bpp::BootstrapValuesTreeDrawingListener | A TreeDrawingListener implementation that write the bootstrap values of inner nodes |
| bpp::BppOFrequenciesSetFormat | Frequencies set I/O in BppO format |
| bpp::BppORateDistributionFormat | Rate Distribution I/O in BppO format |
| bpp::BppOSubstitutionModelFormat | Substitution model I/O in BppO format |
| bpp::TreeLikelihood::BranchIterator | An iterator over a set of branches, specified by their node ids |
| bpp::BranchLengthsTreeDrawingListener | A TreeDrawingListener implementation that write the branch lengths of inner nodes |
| bpp::BranchLikelihood | Compute likelihood for a 4-tree |
| bpp::CanonicalStateMap | This class implements a state map where all resolved states are modeled |
| bpp::CategorySubstitutionRegister | Gather states into defined categories, and count the changes between categories |
| bpp::CladogramDrawBranchEvent | |
| bpp::CladogramPlot | Cladogram representation of trees |
| bpp::ClockTreeLikelihood | Interface for likelihood computation with a global clock |
| bpp::ClusterInfos | |
| bpp::Coala | The Coala branch-heterogeneous amino-acid substitution model |
| bpp::CoalaCore | This class is the core class inherited by the Coala class. COaLA is a branch-heterogeneous amino-acid substitution model |
| 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::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::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::CodonSubstitutionModel | Abstract class for codon models |
| bpp::ComprehensiveSubstitutionRegister | Distinguishes all types of substitutions |
| bpp::ConstantRateDistribution | |
| bpp::TreeLikelihood::ConstBranchModelDescription | A pair of SubstitutionModel / SiteIterator |
| bpp::TreeLikelihood::ConstBranchModelIterator | Iterates through all models used for all sites on a given branch |
| bpp::AbstractHomogeneousTreeLikelihood::ConstHomogeneousSiteModelIterator | |
| bpp::AbstractNonHomogeneousTreeLikelihood::ConstNonHomogeneousSiteModelIterator | |
| bpp::AbstractTreeLikelihood::ConstNoPartitionBranchModelDescription | |
| bpp::AbstractTreeLikelihood::ConstNoPartitionBranchModelIterator | |
| bpp::AbstractTreeLikelihood::ConstNoPartitionSiteModelDescription | |
| bpp::TreeLikelihood::ConstSiteModelDescription | A pair of SubstitutionModel / BranchIterator |
| bpp::TreeLikelihood::ConstSiteModelIterator | Iterates through all models used for all branches on a given site |
| bpp::Cursor | Data structure describing a plotting direction |
| bpp::DecompositionSubstitutionCount | Analytical substitution count using the eigen decomposition method |
| bpp::DetailedSiteSimulator | This interface adds the dSimulate method to the SiteSimulator interface |
| bpp::DiscreteRatesAcrossSitesClockTreeLikelihood | Interface for likelihood computation with a global clock and rate across sites variation |
| bpp::DiscreteRatesAcrossSitesTreeLikelihood | Interface for rate across sites (RAS) implementation |
| 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::DnDsSubstitutionRegister | Distinguishes synonymous from non-synonymous substitutions |
| bpp::DRASDRTreeLikelihoodData | Likelihood data structure for rate across sites models, using a double-recursive algorithm |
| bpp::DRASDRTreeLikelihoodLeafData | Likelihood data structure for a leaf |
| bpp::DRASDRTreeLikelihoodNodeData | Likelihood data structure for a node |
| bpp::DRASRTreeLikelihoodData | Discrete Rate Across Sites, (simple) Recursive likelihood data structure |
| bpp::DRASRTreeLikelihoodNodeData | Likelihood data structure for a node |
| 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::DrawINodeEvent | Event class that uses INode object (more efficient than relying on nodes id, but less generic) |
| bpp::DrawNodeEvent | Event class used by TreeDrawing classes |
| bpp::DrawTreeEvent | Event class used by TreeDrawing classes |
| bpp::DRHomogeneousMixedTreeLikelihood | A class to compute the average of several DRHomogeneousTreeLikelihood defined from a Mixed Substitution Model |
| 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::DRTreeLikelihood | Interface for double-recursive (DR) implementation of the likelihood computation |
| bpp::DRTreeLikelihoodTools | Utilitary methods dealing with objects implementing the DRTreeLikelihood interface |
| bpp::DRTreeParsimonyData | Parsimony data structure for double-recursive (DR) algorithm |
| bpp::DRTreeParsimonyLeafData | Parsimony data structure for a leaf |
| bpp::DRTreeParsimonyNodeData | Parsimony data structure for a node |
| bpp::DRTreeParsimonyScore | Double recursive implementation of interface TreeParsimonyScore |
| bpp::DSO78 | The Dayhoff, Schwartz and Orcutt substitution model for proteins |
| bpp::Nhx::Element | |
| bpp::TreeTemplateTools::Element | |
| bpp::LG10_EX_EHO::EmbeddedModel | |
| 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::ExponentialDiscreteRateDistribution | |
| bpp::F84 | The Felsenstein (1984) substitution model for nucleotides |
| 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::FrequenciesSet | Parametrize a set of state frequencies |
| bpp::FullCodonFrequenciesSet | A generic FrequenciesSet for Full Codon alphabets |
| bpp::FullFrequenciesSet | A generic FrequenciesSet allowing for the estimation of all 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::FullProteinFrequenciesSet | Protein FrequenciesSet using 19 independent parameters to modelize the 20 frequencies |
| bpp::G2001 | Galtier's 2001 covarion model |
| bpp::GammaDiscreteRateDistribution | |
| bpp::GaussianDiscreteRateDistribution | |
| bpp::gBGC | GBGC model |
| bpp::GCFrequenciesSet | Nucleotide FrequenciesSet using only one parameter, the GC content |
| bpp::GCSubstitutionRegister | Distinguishes AT<->GC from GC<->AT |
| bpp::GCSynonymousSubstitutionRegister | Distinguishes AT->GC vs GC->AT inside synonymous substitutions on third codon position |
| bpp::GlobalClockTreeLikelihoodFunctionWrapper | |
| bpp::GTR | The General Time-Reversible substitution model for nucleotides |
| bpp::GY94 | The Goldman and Yang (1994) substitution model for codons |
| bpp::HierarchicalClustering | Hierarchical clustering |
| bpp::HKY85 | The Hasegawa M, Kishino H and Yano T (1985) substitution model for nucleotides |
| bpp::HomogeneousSequenceSimulator | Site and sequences simulation under homogeneous models |
| bpp::HomogeneousTreeLikelihood | Specialization of the TreeLikelihood interface for the Homogeneous case |
| bpp::MixedSubstitutionModelSet::HyperNode | |
| bpp::IDistanceMatrix | General interface for distance matrix readers |
| bpp::IFrequenciesSet | General interface for distance matrix readers |
| bpp::IMultiTree | General interface for multiple trees readers |
| IntAndInt | |
| bpp::IODistanceMatrix | General interface for distance matrix I/O |
| bpp::IODistanceMatrixFactory | Utilitary class for creating distance matrix readers and writers |
| bpp::IoFrequenciesSet | General interface for model I/O |
| bpp::IOFrequenciesSetFactory | Utilitary class for creating frequencies set readers and writers |
| 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::IoSubstitutionModel | General interface for model I/O |
| bpp::IOSubstitutionModelFactory | Utilitary class for creating substitution model readers and writers |
| bpp::IOTree | General interface for tree I/O |
| bpp::IOTreeFactory | Utilitary class for creating tree readers and writers |
| bpp::IOTreepuzzlePairedSiteLikelihoods | This class provides I/O for the Tree-Puzzle/RAxML (phylip-like) paired-site likelihoods format |
| bpp::ISubstitutionModel | General interface for distance matrix readers |
| bpp::ITree | General interface for tree readers |
| 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::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::LabelCollapsedNodesTreeDrawingListener | A TreeDrawingListener implementation that label the collapsed nodes |
| bpp::LabelInnerNodesTreeDrawingListener | A TreeDrawingListener implementation that write the names of inner nodes |
| bpp::LabelSubstitutionCount | Labelling substitution count |
| bpp::LaplaceSubstitutionCount | Laplace estimate of the substitution count |
| bpp::LeafNamesTreeDrawingListener | A TreeDrawingListener implementation that write leaf names |
| bpp::LG08 | The Le and Gascuel substitution model for proteins |
| bpp::LG10_EX_EHO | The Le and Gascuel (2010) EX_EHO substitution model for proteins |
| 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::MarginalAncestralStateReconstruction | Likelihood ancestral states reconstruction: marginal method |
| bpp::MarkovModulatedFrequenciesSet | FrequenciesSet to be used with a Markov-modulated substitution model |
| bpp::MarkovModulatedSubstitutionModel | Partial implementation of the Markov-modulated class of substitution models |
| bpp::MG94 | The Muse and Gaut (1994) substitution model for codons |
| bpp::MixedSubstitutionModel | Interface for Substitution models, defined as a mixture of "simple" substitution models |
| bpp::MixedSubstitutionModelSet | Substitution models manager for Mixed Substitution Models. This class inherits from SubstitutionModelSet |
| 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::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::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::NaiveSubstitutionCount | Naive substitution count |
| bpp::NaNListener | A listener which capture NaN function values and throw an exception in case this happens |
| bpp::NeighborJoining | The neighbor joining distance method |
| 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::NNIHomogeneousTreeLikelihood | This class adds support for NNI topology estimation to the DRHomogeneousTreeLikelihood class |
| 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::NNITopologySearch | NNI topology search method |
| bpp::Node | The phylogenetic node class |
| bpp::MixedSubstitutionModelSet::HyperNode::Node | |
| bpp::NodeException | General exception thrown when something is wrong with a particular node |
| bpp::NodeNotFoundException | Exception thrown when something is wrong with a particular node |
| bpp::NodePException | General exception thrown when something is wrong with a particular node |
| bpp::NodesIdTreeDrawingListener | A TreeDrawingListener implementation that writes nodes id |
| bpp::NodeTemplate< NodeInfos > | The NodeTemplate class |
| bpp::NonHomogeneousSequenceSimulator | Site and sequences simulation under non-homogeneous models |
| bpp::NonHomogeneousTreeLikelihood | Specialization of the TreeLikelihood interface for the branch non-homogeneous and non-stationary models |
| bpp::NucleotideFrequenciesSet | Parametrize a set of state frequencies for nucleotides |
| bpp::NucleotideSubstitutionModel | Specialisation interface for nucleotide substitution model |
| bpp::ODistanceMatrix | General interface for distance matrix writers |
| bpp::OFrequenciesSet | General interface for distance matrix writers |
| bpp::OMultiTree | General interface for tree writers |
| bpp::OneJumpSubstitutionCount | Computes the probability that at least one jump occured on a branch, given the initial and final state |
| bpp::OptimizationTools | Optimization methods for phylogenetic inference |
| bpp::TreeTemplateTools::OrderTreeData_ | |
| bpp::OSubstitutionModel | General interface for distance matrix writers |
| bpp::OTree | General interface for tree writers |
| 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::PGMA | Compute WPGMA and UPGMA trees from a distance matrix |
| bpp::PGMAInfos | Inner data structure for WPGMA and UPGMA distance methods |
| bpp::PhylipDistanceMatrixFormat | Distance matrix I/O in Phylip format |
| bpp::PhylogeneticsApplicationTools | This class provides some common tools for applications |
| bpp::PhylogramDrawBranchEvent | |
| bpp::PhylogramPlot | Phylogram representation of trees |
| bpp::PhyloStatistics | Compute several quantities on a tree simulateously, optimizing the recursions on the tree |
| bpp::PseudoNewtonOptimizer::PNStopCondition | |
| bpp::ProbabilisticSubstitutionMapping | Data storage class for probabilistic substitution mappings |
| bpp::Nhx::Property | |
| bpp::PropertyNotFoundException | General exception thrown if a property could not be found |
| bpp::ProteinFrequenciesSet | Parametrize a set of state frequencies for proteins |
| bpp::ProteinSubstitutionModel | Specialized interface for protein substitution model |
| 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::RASiteSimulationResult | Data structure to store the result of a DetailedSiteSimulator |
| bpp::RASTools | Tools to deal with Rates Across Sites (RAS) models |
| bpp::RateDistributionFactory | Utilitary class for creating rate distributions |
| bpp::RE08 | The Rivas-Eddy substitution model with gap characters |
| bpp::ReversibleSubstitutionModel | Interface for reversible substitution models |
| bpp::RHomogeneousClockTreeLikelihood | Likelihood computation with a global clock |
| bpp::RHomogeneousMixedTreeLikelihood | |
| bpp::RHomogeneousTreeLikelihood | This class implement the 'traditional' way of computing likelihood for a tree |
| 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::RNonHomogeneousMixedTreeLikelihood | |
| bpp::RNonHomogeneousTreeLikelihood | This class implement the 'traditional' way of computing likelihood for a tree, allowing for non-homogeneous models of substitutions |
| bpp::OptimizationTools::ScaleFunction | |
| bpp::SelfMutationProcess | This class is mainly for testing purpose. It allow "self" mutation of the kind i->i; |
| bpp::SequenceSimulationTools | Tools for sites and sequences simulation |
| bpp::SequenceSimulator | The SequenceSimulator interface. SequenceSimulator classes can simulate whole datasets |
| bpp::SimData | |
| bpp::AbstractTreeLikelihood::SimpleBranchIterator | A very simple branch iterator |
| bpp::SimpleMutationProcess | Generally used mutation process model |
| bpp::AbstractTreeLikelihood::SimpleSiteIterator | A very simple site iterator |
| bpp::TreeLikelihood::SiteIterator | An iterator over a set of sites, speicfied by their position |
| bpp::SitePartitionHomogeneousTreeLikelihood | Specialization of the TreeLikelihood interface for partition models, homogeneous case |
| bpp::SitePatterns | Data structure for site patterns |
| bpp::SiteSimulationResult | Data structure to store the result of a DetailedSiteSimulator |
| bpp::SiteSimulator | The SiteSimulator interface. SiteSimulator classes can simulate single sites |
| bpp::SitePatterns::SortableSite | Class used for site pattern sorting |
| bpp::SSR | The Strand Symmetric Reversible substitution model for nucleotides |
| bpp::StateMap | Map the states of a given alphabet which have a model state |
| StringAndInt | |
| bpp::SubstitutionCount | The SubstitutionsCount interface |
| bpp::SubstitutionMapping | General interface for storing mapping data |
| bpp::SubstitutionMappingTools | Provide methods to compute substitution mappings |
| bpp::SubstitutionModel | Interface for all substitution models |
| bpp::SubstitutionModelException | Exception that may be thrown by susbstitution models |
| bpp::SubstitutionModelFactory | Utilitary class for creating substitution models |
| bpp::SubstitutionModelSet | Substitution models manager for non-homogeneous / non-reversible models of evolution |
| bpp::SubstitutionModelSetTools | Tools for automatically creating SubstitutionModelSet objects |
| bpp::SubstitutionRegister | The SubstitutionRegister interface |
| bpp::T92 | The Tamura (1992) substitution model for nucleotides |
| bpp::TN93 | The Tamura and Nei (1993) substitution model for nucleotides |
| bpp::TopologyChangeEvent | Class for notifying new toplogy change events |
| bpp::TopologyListener | Implement this interface to be notified when the topology of a tree has changed during topology search |
| bpp::TopologySearch | Interface for topology search methods |
| bpp::TotalSubstitutionRegister | Count all substitutions |
| bpp::Tree | Interface for phylogenetic tree objects |
| bpp::TreeDrawing | Basal interface for tree drawing classes |
| bpp::TreeDrawingDisplayControler | Easy tune of tree drawings display |
| bpp::TreeDrawingListener | Interface allowing to capture drawing events |
| bpp::TreeDrawingListenerAdapter | An empty implementation of the TreeDrawingListener interface |
| bpp::TreeDrawingNodeInfo | |
| bpp::TreeDrawingSettings | A set of options to tune the display of a TreeDrawing object |
| bpp::TreeException | General exception thrown when something wrong happened in a tree |
| bpp::TreeLikelihood | The TreeLikelihood interface |
| bpp::TreeLikelihoodData | TreeLikelihood data structure |
| bpp::TreeLikelihoodNodeData | TreeLikelihood partial data structure |
| bpp::TreeLikelihoodTools | Utilitary methods that work with TreeLikelihood objects |
| bpp::TreeParsimonyData | TreeParsimonyScore data structure |
| bpp::TreeParsimonyNodeData | TreeParsimonyScore node data structure |
| bpp::TreeParsimonyScore | Compute a parsimony score |
| bpp::TreeTemplate< N > | The phylogenetic tree class |
| bpp::TreeTemplateTools | Utilitary methods working with TreeTemplate and Node objects |
| bpp::TreeTools | Generic utilitary methods dealing with trees |
| 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::TS98 | Tuffley and Steel's 1998 covarion model |
| bpp::TsTvSubstitutionRegister | Distinguishes transitions from transversions |
| bpp::TwoTreeLikelihood | This class is a simplified version of DRHomogeneousTreeLikelihood for 2-Trees |
| bpp::UniformizationSubstitutionCount | Analytical (weighted) substitution count using the uniformization method |
| bpp::UnrootedTreeException | Exception thrown when a tree is expected to be rooted |
| bpp::UserProteinSubstitutionModel | Build an empirical protein substitution model from a file |
| bpp::WAG01 | The Whelan and Goldman substitution model for proteins |
| bpp::WeightedSubstitutionCount | Interface allowing for weighting of substitution counts according to state properties |
| 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::WordFromIndependentFrequenciesSet | Frequencies in words are the product of Independent Frequencies in letters |
| bpp::WordFromUniqueFrequenciesSet | |
| bpp::WordSubstitutionModel | Basal class for words of reversible substitution models |
| 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::YpR | YpR model |
| bpp::YpR_Gen | General YpR model |
| bpp::YpR_Sym | Symetrical YpR model |
1.7.6.1 
