BEAST v2.5.0 Documentation index

beast.app.beauti
...BeautiAlignmentProvider
...BeautiConfig
...BeautiConnector
...BeautiDoc
...BeautiPanelConfig
...BeautiSubTemplate
...Fragment
beast.app.draw
...BEASTObjectSet
beast.app.seqgen
...MergeDataWith
...SequenceSimulator
...SimulatedAlignment
beast.core
..DirectSimulator
..Logger
..MCMC
..OperatorSchedule
..State
beast.core.parameter
...BooleanParameter
...BooleanParameterList
...CompoundValuable
...IntegerParameter
...IntegerParameterList
...RealParameter
...RealParameterList
beast.core.util
...CompoundDistribution
...ESS
...Sum
beast.evolution.alignment
...Alignment
...AscertainedAlignment
...FilteredAlignment
...Sequence
...Taxon
...TaxonSet
beast.evolution.alignment.distance
....Distance$Base
....F84Distance
....HammingDistance
....JukesCantorDistance
....SMMDistance
beast.evolution.branchratemodel
...RandomLocalClockModel
...RateStatistic
...StrictClockModel
...UCRelaxedClockModel
beast.evolution.datatype
...Aminoacid
...Binary
...IntegerData
...Nucleotide
...StandardData
...TwoStateCovarion
...UserDataType
beast.evolution.likelihood
...BeagleTreeLikelihood
...GenericTreeLikelihood
...ThreadedTreeLikelihood
...TreeLikelihood
beast.evolution.operators
...BitFlipOperator
...DeltaExchangeOperator
...Exchange
...IntRandomWalkOperator
...IntUniformOperator
...JointOperator
...NodeReheight
...RealRandomWalkOperator
...ScaleOperator
...SliceOperator
...SubtreeSlide
...SwapOperator
...TipDatesRandomWalker
...TipDatesScaler
...Uniform
...UniformOperator
...UpDownOperator
...WilsonBalding
beast.evolution.sitemodel
...SiteModel
beast.evolution.speciation
...BirthDeathGernhard08Model
...CalibratedBirthDeathModel
...CalibratedYuleInitialTree
...CalibratedYuleModel
...CalibrationPoint
...GeneTreeForSpeciesTreeDistribution
...RandomGeneTree
...SpeciesTreeLogger
...SpeciesTreePrior
...StarBeastStartState
...TreeTopFinder
...YuleModel
beast.evolution.substitutionmodel
...BinaryCovarion
...Blosum62
...CPREV
...Dayhoff
...Frequencies
...GTR
...GeneralSubstitutionModel
...HKY
...JTT
...JukesCantor
...MTREV
...MutationDeathModel
...SYM
...TIM
...TN93
...TVM
...WAG
beast.evolution.tree
...Node
...RandomTree
...TraitSet
...Tree
...TreeDistribution
...TreeHeightLogger
...TreeStatLogger
...TreeWithMetaDataLogger
beast.evolution.tree.coalescent
....BayesianSkyline
....Coalescent
....CompoundPopulationFunction
....ConstantPopulation
....ExponentialGrowth
....SampleOffValues
....ScaledPopulationFunction
....TreeIntervals
beast.math.distributions
...Beta
...ChiSquare
...Dirichlet
...Exponential
...Gamma
...InverseGamma
...LaplaceDistribution
...LogNormalDistributionModel
...MRCAPrior
...MarkovChainDistribution
...Normal
...OneOnX
...Poisson
...Prior
...Uniform
beast.math.statistic
...RPNcalculator
beast.util
..ClusterTree
..TreeParser