bpp Namespace Reference

Classes
class	AAExteriorSubstitutionRegister
	Indexes only substitutions between amino-acids. Groups are distinguished by their direction. More...
class	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. More...
class	AbstractAgglomerativeDistanceMethod
	Partial implementation of the AgglomerativeDistanceMethod interface. More...
class	AbstractBiblioMixedSubstitutionModel
	Abstract class for mixture models based on the bibliography. More...
class	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. More...
class	AbstractCodonDistanceSubstitutionModel
	Abstract class for modelling of non-synonymous abd synonymous substitution rates in codon models. More...
class	AbstractCodonFitnessSubstitutionModel
	Abstract class for modelling of ratios of substitution rates between codons, whatever they are synonymous or not. More...
class	AbstractCodonFrequenciesSubstitutionModel
	Abstract Class for substitution models on codons parametrized by frequencies. More...
class	AbstractCodonPhaseFrequenciesSubstitutionModel
	Abstract Class for substitution models on codons parametrized by a frequency. More...
class	AbstractCodonSubstitutionModel
	Abstract class for substitution models on codons. More...
class	AbstractDendrogramPlot
	Basic implementation of dendrogram plots. More...
class	AbstractDiscreteRatesAcrossSitesTreeLikelihood
	Partial implementation of the DiscreteRatesAcrossSitesTreeLikelihood interface. More...
class	AbstractFrequenciesSet
	Basic implementation of the FrequenciesSet interface. More...
class	AbstractHomogeneousTreeLikelihood
	Partial implementation for homogeneous model of the TreeLikelihood interface. More...
class	AbstractIDistanceMatrix
	Partial implementation of the IDistanceMatrix interface. More...
class	AbstractIMultiTree
	Partial implementation of the IMultiTree interface. More...
class	AbstractITree
	Partial implementation of the ITree interface. More...
class	AbstractMapping
	Partial implementation of the mapping interface. More...
class	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. More...
class	AbstractMutationProcess
	Partial implmentation of the MutationProcess interface. More...
class	AbstractNonHomogeneousTreeLikelihood
	Partial implementation for branch non-homogeneous models of the TreeLikelihood interface. More...
class	AbstractODistanceMatrix
	Partial implementation of the ODistanceMatrix interface. More...
class	AbstractOMultiTree
	Partial implementation of the OTree interface. More...
class	AbstractOTree
	Partial implementation of the OTree interface. More...
class	AbstractReversibleSubstitutionModel
	Partial implementation of the ReversibleSubstitutionModel interface. More...
class	AbstractReward
	Basic implementation of the the Reward interface. More...
class	AbstractRewardMapping
	Partial implementation of the reward mapping interface. More...
class	AbstractStateMap
	A convenience partial implementation of the StateMap interface. More...
class	AbstractSubstitutionCount
	Basic implementation of the the SubstitutionCount interface. More...
class	AbstractSubstitutionMapping
	Partial implementation of the substitution mapping interface. More...
class	AbstractSubstitutionModel
	Partial implementation of the SubstitutionModel interface. More...
class	AbstractSubstitutionRegister
class	AbstractTreeDrawing
	Partial implementation of the TreeDrawing interface. More...
class	AbstractTreeLikelihood
	Partial implementation of the TreeLikelihood interface. More...
class	AbstractTreeLikelihoodData
	Partial implementation of the TreeLikelihoodData interface. More...
class	AbstractTreeParsimonyData
	Partial implementation of the TreeParsimonyData interface. More...
class	AbstractTreeParsimonyScore
	Partial implementation of the TreeParsimonyScore interface. More...
class	AbstractWeightedSubstitutionCount
	Partial implementation of the WeightedSubstitutionCount interface. More...
class	AbstractWordFrequenciesSet
class	AbstractWordSubstitutionModel
	Abstract Basal class for words of substitution models. More...
class	AgglomerativeDistanceMethod
	Interface for agglomerative distance methods. More...
class	AncestralStateReconstruction
	Interface for ancestral states reconstruction methods. More...
class	BasicTreeDrawingDisplayControler
	Easy tune of tree drawings display, a basic implementation: More...
class	BinarySubstitutionModel
	The Model on two states. More...
class	BioNJ
	The BioNJ distance method. More...
class	BipartitionList
	This class deals with the bipartitions defined by trees. More...
class	BipartitionTools
	This class provides tools related to the BipartitionList class. More...
class	BootstrapValuesTreeDrawingListener
	A TreeDrawingListener implementation that write the bootstrap values of inner nodes. More...
class	BppOFrequenciesSetFormat
	Frequencies set I/O in BppO format. More...
class	BppORateDistributionFormat
	Rate Distribution I/O in BppO format. More...
class	BppOSubstitutionModelFormat
	Substitution model I/O in BppO format. More...
class	BranchLengthsTreeDrawingListener
	A TreeDrawingListener implementation that write the branch lengths of inner nodes. More...
class	BranchLikelihood
	Compute likelihood for a 4-tree. More...
class	CanonicalStateMap
	This class implements a state map where all resolved states are modeled. More...
class	CategorySubstitutionRegister
	Gather states into defined categories, and count the changes between categories. More...
class	CladogramDrawBranchEvent
class	CladogramPlot
	Cladogram representation of trees. More...
class	ClockTreeLikelihood
	Interface for likelihood computation with a global clock. More...
class	ClusterInfos
class	Coala
	The Coala branch-heterogeneous amino-acid substitution model. More...
class	CoalaCore
	This class is the core class inherited by the Coala class. COaLA is a branch-heterogeneous amino-acid substitution model. More...
class	CodonDistanceFitnessPhaseFrequenciesSubstitutionModel
	Class for asynonymous and synonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic basic models. More...
class	CodonDistanceFrequenciesSubstitutionModel
	Class for asynonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic models. More...
class	CodonDistancePhaseFrequenciesSubstitutionModel
	Class for asynonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic basic models. More...
class	CodonDistanceSubstitutionModel
	Class for substitution models of codons with non-synonymous/synonymous ratios of substitution rates defined through a distance between amino-acids. More...
class	CodonFrequenciesSet
	Parametrize a set of state frequencies for codons. More...
class	CodonFromIndependentFrequenciesSet
	the Frequencies in codons are the product of Independent Frequencies in letters with the frequencies of stop codons set to zero. More...
class	CodonFromUniqueFrequenciesSet
	the Frequencies in codons are the product of the frequencies for a unique FrequenciesSet in letters, with the frequencies of stop codons set to zero. More...
class	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. More...
class	CodonRateSubstitutionModel
	Class for substitution models on non stop codons, with different rates on the models, depending on their phase. More...
class	CodonSubstitutionModel
	Abstract class for codon models. More...
class	CompleteSubstitutionRegister
	Completion of a given substitution register to consider all substitutions. The new substitutions are considered in an additional type. More...
class	ComprehensiveSubstitutionRegister
	Distinguishes all types of substitutions. More...
class	ConstantRateDistribution
class	Cursor
	Data structure describing a plotting direction. More...
class	DecompositionReward
	Analytical reward using the eigen decomposition method. More...
class	DecompositionSubstitutionCount
	Analytical substitution count using the eigen decomposition method. More...
class	DetailedSiteSimulator
	This interface adds the dSimulate method to the SiteSimulator interface. More...
class	DiscreteRatesAcrossSitesClockTreeLikelihood
	Interface for likelihood computation with a global clock and rate across sites variation. More...
class	DiscreteRatesAcrossSitesTreeLikelihood
	Interface for rate across sites (RAS) implementation. More...
class	DistanceEstimation
	Estimate a distance matrix from sequence data, according to a given model. More...
class	DistanceMethod
	General interface for distance-based phylogenetic reconstruction methods. More...
class	DnDsSubstitutionRegister
	Distinguishes synonymous from non-synonymous substitutions. More...
class	DRASDRTreeLikelihoodData
	Likelihood data structure for rate across sites models, using a double-recursive algorithm. More...
class	DRASDRTreeLikelihoodLeafData
	Likelihood data structure for a leaf. More...
class	DRASDRTreeLikelihoodNodeData
	Likelihood data structure for a node. More...
class	DRASRTreeLikelihoodData
	discrete Rate Across Sites, (simple) Recursive likelihood data structure. More...
class	DRASRTreeLikelihoodNodeData
	Likelihood data structure for a node. More...
class	DrawBranchEvent
	Event class used by TreeDrawing classes. More...
class	DrawIBranchEvent
	Event class that uses INode object (more efficient than relying on nodes id, but less generic). More...
class	DrawINodeEvent
	Event class that uses INode object (more efficient than relying on nodes id, but less generic). More...
class	DrawNodeEvent
	Event class used by TreeDrawing classes. More...
class	DrawTreeEvent
	Event class used by TreeDrawing classes. More...
class	DRHomogeneousMixedTreeLikelihood
	A class to compute the average of several DRHomogeneousTreeLikelihood defined from a Mixed Substitution Model. More...
class	DRHomogeneousTreeLikelihood
	This class implements the likelihood computation for a tree using the double-recursive algorithm. More...
class	DRNonHomogeneousTreeLikelihood
	This class implements the likelihood computation for a tree using the double-recursive algorithm, allowing for non-homogeneous models of substitutions. More...
class	DRTreeLikelihood
	Interface for double-recursive (DR) implementation of the likelihood computation. More...
class	DRTreeLikelihoodTools
	Utilitary methods dealing with objects implementing the DRTreeLikelihood interface. More...
class	DRTreeParsimonyData
	Parsimony data structure for double-recursive (DR) algorithm. More...
class	DRTreeParsimonyLeafData
	Parsimony data structure for a leaf. More...
class	DRTreeParsimonyNodeData
	Parsimony data structure for a node. More...
class	DRTreeParsimonyScore
	Double recursive implementation of interface TreeParsimonyScore. More...
class	DSO78
	The Dayhoff, Schwartz and Orcutt substitution model for proteins. More...
class	ExponentialDiscreteRateDistribution
class	F84
	The Felsenstein (1984) substitution model for nucleotides. More...
class	FixedCodonFrequenciesSet
	FrequenciesSet useful for homogeneous and stationary models, codon implementation. More...
class	FixedFrequenciesSet
	FrequenciesSet useful for homogeneous and stationary models. More...
class	FixedNucleotideFrequenciesSet
	FrequenciesSet useful for homogeneous and stationary models, nucleotide implementation. More...
class	FixedProteinFrequenciesSet
	FrequenciesSet useful for homogeneous and stationary models, protein implementation. More...
class	FrequenciesSet
	Parametrize a set of state frequencies. More...
class	FullCodonFrequenciesSet
	A generic FrequenciesSet for Full Codon alphabets. More...
class	FullFrequenciesSet
	A generic FrequenciesSet allowing for the estimation of all frequencies. More...
class	FullNucleotideFrequenciesSet
	Nucleotide FrequenciesSet using three independent parameters (theta, theta1, theta2) to modelize the four frequencies: More...
class	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. More...
class	FullProteinFrequenciesSet
	Protein FrequenciesSet using 19 independent parameters to model the 20 frequencies. More...
class	G2001
	Galtier's 2001 covarion model. More...
class	GammaDiscreteRateDistribution
class	GaussianDiscreteRateDistribution
class	gBGC
	gBGC model. More...
class	GCFrequenciesSet
	Nucleotide FrequenciesSet using only one parameter, the GC content. More...
class	GCSubstitutionRegister
	Distinguishes AT<->GC from GC<->AT. More...
class	GCSynonymousSubstitutionRegister
	Distinguishes AT->GC vs GC->AT inside synonymous substitutions on third codon position. More...
class	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. More...
class	GlobalClockTreeLikelihoodFunctionWrapper
class	GTR
	The General Time-Reversible substitution model for nucleotides. More...
class	GY94
	The Goldman and Yang (1994) substitution model for codons. More...
class	HierarchicalClustering
	Hierarchical clustering. More...
class	HKY85
	The Hasegawa M, Kishino H and Yano T (1985) substitution model for nucleotides. More...
class	HomogeneousSequenceSimulator
	Site and sequences simulation under homogeneous models. More...
class	HomogeneousTreeLikelihood
	Specialization of the TreeLikelihood interface for the Homogeneous case. More...
class	IDistanceMatrix
	General interface for distance matrix readers. More...
class	IFrequenciesSet
	General interface for distance matrix readers. More...
class	IMultiTree
	General interface for multiple trees readers. More...
class	IODistanceMatrix
	General interface for distance matrix I/O. More...
class	IODistanceMatrixFactory
	Utilitary class for creating distance matrix readers and writers. More...
class	IoFrequenciesSet
	General interface for model I/O. More...
class	IOFrequenciesSetFactory
	Utilitary class for creating frequencies set readers and writers. More...
class	IOPairedSiteLikelihoods
	Base class for I/O on paired-site likelihoods. More...
class	IOPhymlPairedSiteLikelihoods
	This class provides input for the Phyml paired-site likelihoods format. More...
class	IoSubstitutionModel
	General interface for model I/O. More...
class	IOSubstitutionModelFactory
	Utilitary class for creating substitution model readers and writers. More...
class	IOTree
	General interface for tree I/O. More...
class	IOTreeFactory
	Utilitary class for creating tree readers and writers. More...
class	IOTreepuzzlePairedSiteLikelihoods
	This class provides I/O for the Tree-Puzzle/RAxML (phylip-like) paired-site likelihoods format. More...
class	ISubstitutionModel
	General interface for distance matrix readers. More...
class	ITree
	General interface for tree readers. More...
class	JCnuc
	The Jukes-Cantor substitution model for nucleotides. More...
class	JCprot
	The Jukes-Cantor substitution model for proteins. More...
class	JTT92
	The Jones, Taylor and Thornton substitution model for proteins. More...
class	K80
	The Kimura 2-rates substitution model for nucleotides. More...
class	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. More...
class	LabelCollapsedNodesTreeDrawingListener
	A TreeDrawingListener implementation that label the collapsed nodes. More...
class	LabelInnerNodesTreeDrawingListener
	A TreeDrawingListener implementation that write the names of inner nodes. More...
class	LabelSubstitutionCount
	Labelling substitution count. More...
class	LaplaceSubstitutionCount
	Laplace estimate of the substitution count. More...
class	LeafNamesTreeDrawingListener
	A TreeDrawingListener implementation that write leaf names. More...
class	LG08
	The Le and Gascuel substitution model for proteins. More...
class	LG10_EX_EHO
	The Le and Gascuel (2010) EX_EHO substitution model for proteins. More...
class	LGL08_CAT
	The Le et al (2008) CAT substitution model for proteins. More...
class	LLG08_EHO
	The Le et al (2008) EH0 substitution model for proteins. More...
class	LLG08_EX2
	The Le et al (2008) EX2 substitution model for proteins. More...
class	LLG08_EX3
	The Le et al (2008) EX3 substitution model for proteins. More...
class	LLG08_UL2
	The Le et al (2008) UL2 substitution model for proteins. More...
class	LLG08_UL3
	The Le et al (2008) UL3 substitution model for proteins. More...
class	Mapping
	General interface for storing mapping data. More...
class	MarginalAncestralStateReconstruction
	Likelihood ancestral states reconstruction: marginal method. More...
class	MarkovModulatedFrequenciesSet
	FrequenciesSet to be used with a Markov-modulated substitution model. More...
class	MarkovModulatedStateMap
	This class implements a state map for Markov modulated models. More...
class	MarkovModulatedSubstitutionModel
	Partial implementation of the Markov-modulated class of substitution models. More...
class	MG94
	The Muse and Gaut (1994) substitution model for codons. More...
class	MixedSubstitutionModel
	Interface for Substitution models, defined as a mixture of "simple" substitution models. More...
class	MixedSubstitutionModelSet
	Substitution models manager for Mixed Substitution Models. This class inherits from SubstitutionModelSet. More...
class	MixtureOfASubstitutionModel
	Substitution models defined as a mixture of nested substitution models. More...
class	MixtureOfSubstitutionModels
	Substitution models defined as a mixture of several substitution models. More...
class	MutationPath
	This class is used by MutationProcess to store detailed results of simulations. More...
class	MutationProcess
	Interface for simulations. More...
class	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. More...
class	NaiveSubstitutionCount
	Naive substitution count. More...
class	NaNListener
	A listener which capture NaN function values and throw an exception in case this happens. More...
class	NeighborJoining
	The neighbor joining distance method. More...
class	Newick
	The so-called 'newick' parenthetic format. More...
class	NexusIOTree
	a simple parser for reading trees from a Nexus file. More...
class	Nhx
	The so-called 'Nhx - New Hampshire eXtended' parenthetic format. More...
class	NNIHomogeneousTreeLikelihood
	This class adds support for NNI topology estimation to the DRHomogeneousTreeLikelihood class. More...
class	NNISearchable
	Interface for Nearest Neighbor Interchanges algorithms. More...
class	NNITopologyListener
	Listener used internally by the optimizeTreeNNI method. More...
class	NNITopologyListener2
	Listener used internally by the optimizeTreeNNI2 method. More...
class	NNITopologySearch
	NNI topology search method. More...
class	Node
	The phylogenetic node class. More...
class	NodeException
	General exception thrown when something is wrong with a particular node. More...
class	NodeNotFoundException
	Exception thrown when something is wrong with a particular node. More...
class	NodePException
	General exception thrown when something is wrong with a particular node. More...
class	NodesIdTreeDrawingListener
	A TreeDrawingListener implementation that writes nodes id. More...
class	NodeTemplate
	The NodeTemplate class. More...
class	NonHomogeneousSequenceSimulator
	Site and sequences simulation under non-homogeneous models. More...
class	NonHomogeneousTreeLikelihood
	Specialization of the TreeLikelihood interface for the branch non-homogeneous and non-stationary models. More...
class	NucleotideFrequenciesSet
	Parametrize a set of state frequencies for nucleotides. More...
class	NucleotideSubstitutionModel
	Specialisation interface for nucleotide substitution model. More...
class	ODistanceMatrix
	General interface for distance matrix writers. More...
class	OFrequenciesSet
	General interface for distance matrix writers. More...
class	OMultiTree
	General interface for tree writers. More...
class	OneJumpSubstitutionCount
	Computes the probability that at least one jump occured on a branch, given the initial and final state. More...
class	OptimizationTools
	Optimization methods for phylogenetic inference. More...
class	OSubstitutionModel
	General interface for distance matrix writers. More...
class	OTree
	General interface for tree writers. More...
class	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). More...
class	PatternTools
	Utilitary methods to compute site patterns. More...
class	PGMA
	Compute WPGMA and UPGMA trees from a distance matrix. More...
struct	PGMAInfos
	Inner data structure for WPGMA and UPGMA distance methods. More...
class	PhylipDistanceMatrixFormat
	Distance matrix I/O in Phylip format. More...
class	PhylogeneticsApplicationTools
	This class provides some common tools for applications. More...
class	PhylogramDrawBranchEvent
class	PhylogramPlot
	Phylogram representation of trees. More...
class	PhyloStatistics
	Compute several quantities on a tree simulateously, optimizing the recursions on the tree. More...
class	ProbabilisticRewardMapping
	Data storage class for probabilistic rewards mappings. More...
class	ProbabilisticSubstitutionMapping
	Data storage class for probabilistic substitution mappings. More...
class	PropertyNotFoundException
	General exception thrown if a property could not be found. More...
class	ProteinFrequenciesSet
	Parametrize a set of state frequencies for proteins. More...
class	ProteinSubstitutionModel
	Specialized interface for protein substitution model. More...
class	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. More...
class	RASiteSimulationResult
	Data structure to store the result of a DetailedSiteSimulator. More...
class	RASTools
	Tools to deal with Rates Across Sites (RAS) models. More...
class	RateDistributionFactory
	Utilitary class for creating rate distributions. More...
class	RE08
	The Rivas-Eddy substitution model with gap characters. More...
class	ReversibleSubstitutionModel
	Interface for reversible substitution models. More...
class	Reward
	The Reward interface. More...
class	RewardMapping
	General interface for storing reward mapping data. More...
class	RewardMappingTools
	Provide methods to compute reward mappings. More...
class	RHomogeneousClockTreeLikelihood
	Likelihood computation with a global clock. More...
class	RHomogeneousMixedTreeLikelihood
class	RHomogeneousTreeLikelihood
	This class implement the 'traditional' way of computing likelihood for a tree. More...
class	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. More...
class	RN95s
	Intersection of models RN95 and L95. More...
class	RNonHomogeneousMixedTreeLikelihood
class	RNonHomogeneousTreeLikelihood
	This class implement the 'traditional' way of computing likelihood for a tree, allowing for non-homogeneous models of substitutions. More...
class	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. More...
class	SelfMutationProcess
	This class is mainly for testing purpose. It allow "self" mutation of the kind i->i;. More...
class	SequenceSimulationTools
	Tools for sites and sequences simulation. More...
class	SequenceSimulator
	The SequenceSimulator interface. SequenceSimulator classes can simulate whole datasets. More...
class	SimData
class	SimpleMutationProcess
	Generally used mutation process model. More...
class	SitePartitionHomogeneousTreeLikelihood
	Specialization of the TreeLikelihood interface for partition models, homogeneous case. More...
class	SitePatterns
	Data structure for site patterns. More...
class	SiteSimulationResult
	Data structure to store the result of a DetailedSiteSimulator. More...
class	SiteSimulator
	The SiteSimulator interface. SiteSimulator classes can simulate single sites. More...
class	SSR
	The Strand Symmetric Reversible substitution model for nucleotides. More...
class	StateMap
	Map the states of a given alphabet which have a model state. More...
class	SubstitutionCount
	The SubstitutionsCount interface. More...
class	SubstitutionMapping
	General interface for storing mapping data. More...
class	SubstitutionMappingTools
	Provide methods to compute substitution mappings. More...
class	SubstitutionModel
	Interface for all substitution models. More...
class	SubstitutionModelException
	Exception that may be thrown by susbstitution models. More...
class	SubstitutionModelFactory
	Utilitary class for creating substitution models. More...
class	SubstitutionModelSet
	Substitution models manager for non-homogeneous / non-reversible models of evolution. More...
class	SubstitutionModelSetTools
	Tools for automatically creating SubstitutionModelSet objects. More...
class	SubstitutionRegister
	The SubstitutionRegister interface. More...
class	T92
	The Tamura (1992) substitution model for nucleotides. More...
class	TN93
	The Tamura and Nei (1993) substitution model for nucleotides. More...
class	TopologyChangeEvent
	Class for notifying new toplogy change events. More...
class	TopologyListener
	Implement this interface to be notified when the topology of a tree has changed during topology search. More...
class	TopologySearch
	Interface for topology search methods. More...
class	TotalSubstitutionRegister
	Count all substitutions. More...
class	Tree
	Interface for phylogenetic tree objects. More...
class	TreeDrawing
	Basal interface for tree drawing classes. More...
class	TreeDrawingDisplayControler
	Easy tune of tree drawings display. More...
class	TreeDrawingListener
	Interface allowing to capture drawing events. More...
class	TreeDrawingListenerAdapter
	An empty implementation of the TreeDrawingListener interface. More...
class	TreeDrawingNodeInfo
class	TreeDrawingSettings
	A set of options to tune the display of a TreeDrawing object. More...
class	TreeException
	General exception thrown when something wrong happened in a tree. More...
class	TreeLikelihood
	The TreeLikelihood interface. More...
class	TreeLikelihoodData
	TreeLikelihood data structure. More...
class	TreeLikelihoodNodeData
	TreeLikelihood partial data structure. More...
class	TreeLikelihoodTools
	Utilitary methods that work with TreeLikelihood objects. More...
class	TreeParsimonyData
	TreeParsimonyScore data structure. More...
class	TreeParsimonyNodeData
	TreeParsimonyScore node data structure. More...
class	TreeParsimonyScore
	Compute a parsimony score. More...
class	TreeTemplate
	The phylogenetic tree class. More...
class	TreeTemplateTools
	Utilitary methods working with TreeTemplate and Node objects. More...
class	TreeTools
	Generic utilitary methods dealing with trees. More...
class	TripletSubstitutionModel
	Class for neutral substitution models on triplets, which correspond to codons that do not have any significance (whether they are STOP or functional). More...
class	TS98
	Tuffley and Steel's 1998 covarion model. More...
class	TsTvSubstitutionRegister
	Distinguishes transitions from transversions. More...
class	TwoTreeLikelihood
	This class is a simplified version of DRHomogeneousTreeLikelihood for 2-Trees. More...
class	UniformizationSubstitutionCount
	Analytical (weighted) substitution count using the uniformization method. More...
class	UnrootedTreeException
	Exception thrown when a tree is expected to be rooted. More...
class	UserProteinSubstitutionModel
	Build an empirical protein substitution model from a file. More...
class	WAG01
	The Whelan and Goldman substitution model for proteins. More...
class	WeightedSubstitutionCount
	Interface allowing for weighting of substitution counts according to state properties. More...
class	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. More...
class	WordFromIndependentFrequenciesSet
	the Frequencies in words are the product of Independent Frequencies in letters More...
class	WordFromUniqueFrequenciesSet
class	WordSubstitutionModel
	Basal class for words of reversible substitution models. More...
class	YN98
	The Yang and Nielsen (1998) substitution model for codons. More...
class	YNGKP_M1
	The Yang et al (2000) M1 substitution model for codons, with the more realistic modification in Wong & al (2004). More...
class	YNGKP_M2
	The Yang et al (2000) M2 substitution model for codons, with the more realistic modification in Wong & al (2004). More...
class	YNGKP_M3
	The Yang et al (2000) M3 substitution model for codons. More...
class	YNGKP_M7
	The Yang et al (2000) M7 substitution model for codons. More...
class	YNGKP_M8
	The Yang et al (2000) M8 substitution model for codons. More...
class	YpR
	YpR model. More...
class	YpR_Gen
	General YpR model. More...
class	YpR_Sym
	symetrical YpR model. More...

Typedefs
typedef NodeTemplate< TreeDrawingNodeInfo >	INode
typedef std::bitset< 21 >	Bitset
typedef NodeTemplate< SimData >	SNode

Typedef Documentation

Bitset

typedef std::bitset<21> bpp::Bitset

Definition at line 55 of file DRTreeParsimonyData.h.

INode

typedef NodeTemplate<TreeDrawingNodeInfo> bpp::INode

Definition at line 78 of file AbstractTreeDrawing.h.

SNode

typedef NodeTemplate<SimData> bpp::SNode

Definition at line 88 of file NonHomogeneousSequenceSimulator.h.