BEAST v2.7.8 Documentation index

beast.base.core
...Function$Constant
beast.base.evolution
...RateStatistic
...Sum
...TreeWithMetaDataLogger
beast.base.evolution.alignment
....Alignment
....AscertainedAlignment
....FilteredAlignment
....Sequence
....Taxon
....TaxonSet
beast.base.evolution.branchratemodel
....RandomLocalClockModel
....StrictClockModel
....UCRelaxedClockModel
beast.base.evolution.datatype
....Aminoacid
....Binary
....IntegerData
....Nucleotide
....StandardData
....TwoStateCovarion
....UserDataType
beast.base.evolution.distance
....F84Distance
....HammingDistance
....JukesCantorDistance
....SMMDistance
beast.base.evolution.likelihood
....BeagleTreeLikelihood
....GenericTreeLikelihood
....ThreadedTreeLikelihood
....TreeLikelihood
beast.base.evolution.operator
....AdaptableOperatorSampler
....EpochFlexOperator
....Exchange
....NodeReheight
....ScaleOperator
....SubtreeSlide
....TipDatesRandomWalker
....TipDatesScaler
....TreeStretchOperator
....Uniform
....WilsonBalding
beast.base.evolution.operator.kernel
.....AdaptableVarianceMultivariateNormalOperator
.....BactrianNodeOperator
.....BactrianOperatorSchedule
.....BactrianScaleOperator
.....BactrianSubtreeSlide
.....BactrianTipDatesRandomWalker
beast.base.evolution.sitemodel
....SiteModel
beast.base.evolution.speciation
....BirthDeathGernhard08Model
....CalibratedBirthDeathModel
....CalibratedYuleInitialTree
....CalibratedYuleModel
....CalibrationPoint
....GeneTreeForSpeciesTreeDistribution
....RandomGeneTree
....SpeciesTreeLogger
....SpeciesTreePopFunction
....SpeciesTreePrior
....StarBeastStartState
....TreeTopFinder
....YuleModel
beast.base.evolution.substitutionmodel
....BinaryCovarion
....Blosum62
....CPREV
....ComplexSubstitutionModel
....Dayhoff
....Frequencies
....GTR
....GeneralSubstitutionModel
....HKY
....JTT
....JukesCantor
....MTREV
....MutationDeathModel
....SYM
....TIM
....TN93
....TVM
....WAG
beast.base.evolution.tree
....ClusterTree
....MRCAPrior
....Node
....TraitSet
....Tree
....TreeDistribution
....TreeHeightLogger
....TreeIntervals
....TreeParser
....TreeStatLogger
beast.base.evolution.tree.coalescent
.....BayesianSkyline
.....Coalescent
.....CompoundPopulationFunction
.....ConstantPopulation
.....ExponentialGrowth
.....RandomTree
.....SampleOffValues
.....ScaledPopulationFunction
beast.base.inference
...CompoundDistribution
...DirectSimulator
...Logger
...MCMC
...OperatorSchedule
...State
beast.base.inference.distribution
....Beta
....ChiSquare
....Dirichlet
....Exponential
....Gamma
....InverseGamma
....LaplaceDistribution
....LogNormalDistributionModel
....MarkovChainDistribution
....Normal
....OneOnX
....Poisson
....Prior
....Uniform
beast.base.inference.operator
....BitFlipOperator
....DeltaExchangeOperator
....IntRandomWalkOperator
....IntUniformOperator
....JointOperator
....RealRandomWalkOperator
....SliceOperator
....SwapOperator
....UniformOperator
....UpDownOperator
beast.base.inference.operator.kernel
.....BactrianDeltaExchangeOperator
.....BactrianIntervalOperator
.....BactrianRandomWalkOperator
.....BactrianUpDownOperator
.....KernelDistribution$Bactrian
.....Transform$FisherZTransform
.....Transform$LogConstrainedSumTransform
.....Transform$LogTransform
.....Transform$LogitTransform
.....Transform$NegateTransform
.....Transform$NoTransform
.....Transform$NoTransformMultivariable
.....Transform$PowerTransform
beast.base.inference.parameter
....BooleanParameter
....BooleanParameterList
....CompoundRealParameter
....CompoundValuable
....IntegerParameter
....IntegerParameterList
....RealParameter
....RealParameterList
beast.base.inference.util
....ESS
....RPNcalculator

beastclassic.app.beauti
...BeautiDiscreteTraitProvider
...BeautiLocationTraitProvider
beastclassic.continuous
..MultivariateDiffusionModel
..SampledMultivariateTraitLikelihood
beastclassic.evolution.alignment
...AlignmentFromTrait
...AlignmentFromTraitMap
beastclassic.evolution.datatype
...ContinuousDataType
...LocationDataType
beastclassic.evolution.likelihood
...AncestralSequenceLogger
...AncestralStateTreeLikelihood
...LeafTrait
beastclassic.evolution.operators
...BitFlipBSSVSOperator
...GMRFMultilocusSkyrideBlockUpdateOperator
...GMRFSkyrideBlockUpdateOperator
...GeneralIntegerOperator
...PickIndicatorOperator
...PrecisionMatrixGibbsOperator
...RegressionGibbsEffectOperator
...RegressionGibbsPrecisionOperator
...RootTraitRandowWalkOperator
...SphereRandomWalker
...TraitGibbsOperator
beastclassic.evolution.speciation
...BirthDeathSerialSampling
beastclassic.evolution.substitutionmodel
...FLU
...GLM
...GLMBasedSubstModel
...LG
...LogLinear
...SVSGeneralSubstitutionModel
...SVSGeneralSubstitutionModelLogger
beastclassic.evolution.tree
...RootTrait
...TreeTraitMap
...TreeWithTraitLogger
beastclassic.evolution.tree.coalescent
....Expansion
....GMRFMultilocusSkyrideLikelihood
....GMRFSkyrideLikelihood
....LogisticGrowth
....TreeList
beastclassic.geo
..GeoSpatialDistribution
beastclassic.inference.distribution
...GeneralizedLinearModel
...LinearRegression
...LogisticRegression
beastclassic.math.distributions
...CTMCScalePrior
...MultivariateNormalDistribution
...WishartDistribution
beastclassic.phylogeography
..RateIndicatorInitializer

beastfx.app.beauti
...Fragment
beastfx.app.draw
...BEASTObjectSet
beastfx.app.inputeditor
...BeautiAlignmentProvider
...BeautiConfig
...BeautiConnector
...BeautiDoc
...BeautiPanelConfig
...BeautiSubTemplate
beastfx.app.seqgen
...MergeDataWith
...SequenceSimulator
...SimulatedAlignment
beastfx.app.tools
...ClassEnumerator
...JarHealthChecker
...PackageHealthChecker

beastlabs.core
..DataNode
..FilteredValuable
..GridSearch
..Likelihood
..MCMC2
..Posterior
beastlabs.core.parameter
...CompoundRealParameter
...NormalisedRealParameter
beastlabs.core.util
...LoggableSum
...ParameterConstrainer
...Slice
beastlabs.evolution.alignment
...PrunedAlignment
beastlabs.evolution.branchratemodel
...PrunedRelaxedClockModel
beastlabs.evolution.likelihood
...AncestralStateLogger
...ExperimentalTreeLikelihood
...MultiPartitionTreeLikelihood
...SelfTuningCompoundDistribution
...SelfTuningMCMC
...SupertreeLikelihood
...TraitedTreeLikelihood
beastlabs.evolution.operators
...AttachAndUniformOperator
...AttachOperator
...CladeInternalAttachOperator
...CombinedOperator
...CompoundOperator
...MultiCladeAttachOperator
...NNI
...RestrictedSubtreeSlide
...RootHeightScaleOperator
...SPR
...TreeWithMetaDataRandomWalker
...UniformOperatorSelective
...UniformSelective
beastlabs.evolution.sitemodel
...SiteModelGI
beastlabs.evolution.speciation
...RandomLocalYuleModel
beastlabs.evolution.substitutionmodel
...CladeSubstitutionModel
...EmpiricalAAModelFromFile
...EpochSubstitutionModel
...GeneralLazySubstitutionModel
...LazyHKY
beastlabs.evolution.tree
...ConstrainedClusterTree
...ConstrainedRandomTree
...InitParamFromTree
...MonophyleticConstraint
...PrunedTree
...RNNIMetric
...RobinsonsFouldMetric
...SimpleConstrainedRandomTree
...SimplePrunedTree
...SimpleRandomTree
...TreeDistanceLogger
beastlabs.evolution.tree.coalescent
....CauchyPlusConstant
....ExponentialGrowthPlusConstant
....StructuredCoalescentTree
beastlabs.inference
..ConvergableMCMC
..HeatedMCMC
..IndependentMCMC
..MCMCMC
..MCMCParticle
..MCMCParticleAsync
..ML
..MultiMCMC
..ParticleFilter
..SimulatedAnnealing
..TreeStoreLogger
beastlabs.math.distributions
...BernoulliDistribution
...BetaRange
...ExcludablePrior
...ExcludablePriorIndex
...GammaOneP
...MRCAPriorWithRogues
...MixtureDistribution
...MonoPoints
...MultiMRCAPriors
...MultiMonophyleticConstraint
...SingleParamGamma
...WeibullDistribution
...WeightedDirichlet
beastlabs.prevalence
..AddOperator
..DelOperator
..MoveOperator
..PrevalenceLikelihood
..PrevalenceList
..SubtreeSlide
..TreeForPrevalenceLikelihood
..TreeScaleOperator
..Uniform
..WilsonBalding
beastlabs.tools
..PostHocAnalyser
..TraceStateNodeSource
..TreeStateNodeSource
beastlabs.util
..Script
..TimeLogger

bmodeltest.app.tools
...BModelAnalyser
bmodeltest.evolution.operators
...BMTBirthDeathOperator
...BMTExchangeOperator
...BMTMergeSplitOperator
...BMTScaleOperator
bmodeltest.evolution.sitemodel
...BEASTModelTest
...BEASTModelTestSiteModel
bmodeltest.evolution.substitutionmodel
...ActiveLogger
...CorrelatedEvolution
...ModelFrequencies
...NucleotideRevJumpSubstModel
bmodeltest.math.distributions
...BMTPrior
...ModelSetPrior
...NucleotideRevJumpSubstModelRatePrior

feast.expressions
..ExpCalculator
..ExpCalculatorDistribution
..ExpCalculatorParametricDistribution
feast.fileio
..AlignmentFromFasta
..AlignmentFromFile
..AlignmentFromNexus
..RealParameterFromLabelledXSV
..RealParameterFromXSV
..TaxonSetFromTree
..TipDatesFromTree
..TraitSetFromTaxonSet
..TraitSetFromXSV
..TreeFromNewickFile
..TreeFromNexusFile
feast.fileio.logfileiterator
...DummyPosterior
...LogFileIterator
...LogFileRealParameter
...TraceLogFileState
...TreeLogFileState
feast.function
..Concatenate
..Interleave
..Reverse
..SampleAges
..Scale
..Sequence
..Slice
..TraitSetAsFunction
..UniqueElementCount
feast.mapping
..DensityMapper
feast.modelselect
..DirichletProcessOperator
..DirichletProcessPrior
..ModelSelectionParameter
feast.operators
..BlockIntRandomWalkOperator
..BlockIntUniformOperator
..BlockScaleOperator
..DiscreteUniformJumpOperator
..SmartRealRandomWalkOperator
..SmartScaleOperator
feast.parameter
..RandomRealParameter
..RealParameterFromFunction
..TimeParameter
feast.popmodels
..CompoundPopulationModel
..ExpressionPopulationModel
..ShiftedPopulationModel
feast.simulation
..GPSimulator
..ShuffledAlignment
..SimulatedAlignment

orc.consoperators
..InConstantDistanceOperator
..PiecewiseLinearDistribution
..SimpleDistance
..SmallPulley
..UcldScalerOperator
orc.inference
..TipRateLogger
orc.ner
..NEROperator_dAB
..NEROperator_dAB_dAC
..NEROperator_dAB_dAC_dAE
..NEROperator_dAB_dAC_dAE_dBC
..NEROperator_dAB_dAC_dAE_dBC_dCE
..NEROperator_dAB_dAC_dAE_dCE
..NEROperator_dAB_dAC_dBC
..NEROperator_dAB_dAC_dBC_dBE
..NEROperator_dAB_dAC_dBC_dCE
..NEROperator_dAB_dAC_dBE
..NEROperator_dAB_dAC_dCE
..NEROperator_dAB_dAE
..NEROperator_dAB_dAE_dBC
..NEROperator_dAB_dAE_dBC_dCE
..NEROperator_dAB_dAE_dCE
..NEROperator_dAB_dBC
..NEROperator_dAB_dBC_dBE
..NEROperator_dAB_dBC_dCE
..NEROperator_dAB_dBE
..NEROperator_dAB_dBE_dCE
..NEROperator_dAB_dCE
..NEROperator_dAC
..NEROperator_dAC_dAE
..NEROperator_dAC_dAE_dBC
..NEROperator_dAC_dAE_dBC_dCE
..NEROperator_dAC_dAE_dBE
..NEROperator_dAC_dAE_dBE_dCE
..NEROperator_dAC_dAE_dCE
..NEROperator_dAC_dBC
..NEROperator_dAC_dBC_dBE
..NEROperator_dAC_dBC_dCE
..NEROperator_dAC_dBE
..NEROperator_dAC_dBE_dCE
..NEROperator_dAC_dCE
..NEROperator_dAE
..NEROperator_dAE_dBC
..NEROperator_dAE_dBC_dBE
..NEROperator_dAE_dBC_dCE
..NEROperator_dAE_dBE
..NEROperator_dAE_dBE_dCE
..NEROperator_dAE_dCE
..NEROperator_dBC
..NEROperator_dBC_dBE
..NEROperator_dBC_dCE
..NEROperator_dBE
..NEROperator_dBE_dCE
..NEROperator_dCE
orc.operators
..MetaNEROperator
..SampleFromPriorOperator

sa.app.tools
...FullToExtantTreeConverter
...SampledAncestorTreeAnalyser
sa.evolution.operators
...Binary
...IntRandomWalkWithExclusion
...IntSwapWithExclusion
...IntUniformWithExclusion
...JumpToPoint
...LeafToSampledAncestorJump
...SAExchange
...SAScaleOperator
...SAUniform
...SAWilsonBalding
...SampledNodeDateRandomWalker
...TreeDimensionJump
...WilsonBaldingWithRateCategories
sa.evolution.speciation
...DiversificationTurnoverParameterization
...DiversificationTurnoverPsiExpectedNParameterization
...ParameterizedSABirthDeathModel
...ProbabilitySA
...RateParameterization
...SABirthDeathModel
sa.evolution.tree
...AncestryConstraint
...CladeConstraint
...OffsetLogger
...SampledAncestorLogger
...SamplingDate
...TreeWOffset
sa.math.distributions
...DegenerateBeta
...DegenerateUniform
...SAMRCAPrior
...SpecialMRCAPrior
sa.util
..ClusterZBSATree
..ZeroBranchSATreeParser

starbeast3.app.beauti
...StarBeast3MorphModelAlignmentProvider
...StarBeastAlignmentProvider3
starbeast3.core
..MCMCsb3
..OperatorScheduleRecalculator
..ParallelMCMC
..SampleTimeLog
..SpeciesTreeLogger
..StarBeastStartState
starbeast3.evolution.branchratemodel
...RandomLocalClockModelSB3
...SharedSpeciesClockModel
...StarBeast3Clock
...StrictClockModelSB3
...UCRelaxedClockModelSB3
starbeast3.evolution.speciation
...BirthProcess
...ConstantPopulations
...GeneTreeForSpeciesTreeDistribution
...SpeciesTreePrior
starbeast3.evolution.substitutionmodel
...LewisMK
starbeast3.genekernel
..GTKGeneTree
..GTKPointerTree
..GTKPrior
..GeneTreeKernel
starbeast3.inference
..ShortChainsMCMC
..ShortMCMC
..ShortMCMCLogger
starbeast3.math.distributions
...InverseGamma
...MRCAPriorSB3
starbeast3.operators
..AVMNCubeOperator
..BactrianSubtreeSlide
..BactrianTreeScaleOperator
..BactrianUpDownOperator
..ConstantDistanceOperatorSpeciesTree
..CoordinatedExchangeRates
..CoordinatedExponential
..CoordinatedUniform
..DiscreteRateCycle
..DiscreteRateUniform
..EpochOperator
..FixedHeightSubtreePruneRegraftOperator
..GTKExpander
..MultiStepOperatorSchedule
..NEROperator_dAE_dBE_dCE
..NodeReheight2
..ParallelDistSet
..ParallelMCMCRealParameterOperator
..ParallelMCMCTreeOperator
..ParallelMCMCTreeOperatorTreeDistribution
..PopSizeGibbsSampler
..RealCycle
..SampledNodeDateRandomWalkerSB3
starbeast3.simulation
..DirectSimulator
..SampleGeneTreeTopologyCount
starbeast3.tree
..BinaryTree
..BranchLengthLogger
..SpeciesTree
..StarBeast3TaxonSet

substmodels.nucleotide
..F81
..GTR
..HKY
..JC
..K80
..SYM
..TIM1
..TIM1uf
..TIM2
..TIM2uf
..TIM3
..TIM3uf
..TPM1
..TPM1uf
..TPM2
..TPM2uf
..TPM3
..TPM3uf
..TVM
..TVMef
..TrN
..TrNef

treestat2
.TreeStat
.TreeStat2Logger
treestat2.statistics
..B1Statistic
..BetaTreeDiversityStatistic
..BranchLengths
..BranchRates
..CCD0ExpectedRFDistance
..CCD0Information
..CCD0RFDistance
..CCD1ExpectedRFDistance
..CCD1Information
..CCD1RFDistance
..CherryStatistic
..CladeMRCAAttributeStatistic
..CladeMeanAttributeStatistic
..CollessIndex
..DeltaStatistic
..ExternalBranchLengths
..ExternalBranchRates
..ExternalInternalRatio
..FuLiD
..GammaStatistic
..GetTypeChanges
..InternalBranchLengths
..InternalBranchRates
..InternalNodeAttribute
..IntervalKStatistic
..LineageCountStatistic
..LongestBranchLength
..LttSlopeRatio
..MRCAOlderThanStatistic
..MonophylyStatistic
..Nbar
..NodeHeights
..NumberOfTips
..RankBranchLength
..RelativeTrunkLength
..RootBranchTrait
..RootToTipLengths
..SAStatistic
..SamplingTimesInterval
..SecondInternalNodeHeight
..SingleChildCountStatistic
..SingleChildTransitionCounts
..SortedNodeAges
..TMRCASummaryStatistic
..TimeMaximumLineages
..TopologyStringStatistic
..TreeHeight
..TreeLength
..TreenessStatistic
..UniqueBranchTraitValues