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version.xml
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version.xml
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<package name="BEAST.base" version="2.7.7">
<!-- note version="2.7.x" must be double quotes for Mac release script release/Mac/createdmg.sh -->
<!-- data types -->
<service type="beast.base.evolution.datatype.DataType">
<provider classname="beast.base.evolution.datatype.Aminoacid"/>
<provider classname="beast.base.evolution.datatype.Nucleotide"/>
<provider classname="beast.base.evolution.datatype.TwoStateCovarion"/>
<provider classname="beast.base.evolution.datatype.Binary"/>
<provider classname="beast.base.evolution.datatype.IntegerData"/>
<provider classname="beast.base.evolution.datatype.StandardData"/>
<provider classname="beast.base.evolution.datatype.UserDataType"/>
</service>
<!-- Model logger service: for breaking dependency between beast.base.inference and beast.base.parser -->
<service type="beast.base.inference.ModelLogger">
<provider classname="beast.base.inference.ModelLogger"/>
<provider classname="beast.base.parser.XMLModelLogger"/>
</service>
<service type="beast.base.core.BEASTInterface">
<provider classname="beast.base.core.VirtualBEASTObject"/>
<provider classname="beast.base.core.Function$Constant"/>
<provider classname="beast.base.evolution.RateStatistic"/>
<provider classname="beast.base.evolution.Sum"/>
<provider classname="beast.base.evolution.TreeWithMetaDataLogger"/>
<provider classname="beast.base.evolution.alignment.Alignment"/>
<provider classname="beast.base.evolution.alignment.AscertainedAlignment"/>
<provider classname="beast.base.evolution.alignment.FilteredAlignment"/>
<provider classname="beast.base.evolution.alignment.Sequence"/>
<provider classname="beast.base.evolution.alignment.Taxon"/>
<provider classname="beast.base.evolution.alignment.TaxonSet"/>
<provider classname="beast.base.evolution.branchratemodel.RandomLocalClockModel"/>
<provider classname="beast.base.evolution.branchratemodel.StrictClockModel"/>
<provider classname="beast.base.evolution.branchratemodel.UCRelaxedClockModel"/>
<provider classname="beast.base.evolution.datatype.Aminoacid"/>
<provider classname="beast.base.evolution.datatype.Binary"/>
<provider classname="beast.base.evolution.datatype.IntegerData"/>
<provider classname="beast.base.evolution.datatype.Nucleotide"/>
<provider classname="beast.base.evolution.datatype.StandardData"/>
<provider classname="beast.base.evolution.datatype.TwoStateCovarion"/>
<provider classname="beast.base.evolution.datatype.UserDataType"/>
<provider classname="beast.base.evolution.distance.F84Distance"/>
<provider classname="beast.base.evolution.distance.HammingDistance"/>
<provider classname="beast.base.evolution.distance.JukesCantorDistance"/>
<provider classname="beast.base.evolution.distance.SMMDistance"/>
<provider classname="beast.base.evolution.likelihood.BeagleTreeLikelihood"/>
<provider classname="beast.base.evolution.likelihood.GenericTreeLikelihood"/>
<provider classname="beast.base.evolution.likelihood.ThreadedTreeLikelihood"/>
<provider classname="beast.base.evolution.likelihood.TreeLikelihood"/>
<provider classname="beast.base.evolution.operator.AdaptableOperatorSampler"/>
<provider classname="beast.base.evolution.operator.EpochFlexOperator"/>
<provider classname="beast.base.evolution.operator.Exchange"/>
<provider classname="beast.base.evolution.operator.NodeReheight"/>
<provider classname="beast.base.evolution.operator.ScaleOperator"/>
<provider classname="beast.base.evolution.operator.SubtreeSlide"/>
<provider classname="beast.base.evolution.operator.TipDatesRandomWalker"/>
<provider classname="beast.base.evolution.operator.TipDatesScaler"/>
<provider classname="beast.base.evolution.operator.TreeStretchOperator"/>
<provider classname="beast.base.evolution.operator.Uniform"/>
<provider classname="beast.base.evolution.operator.WilsonBalding"/>
<provider classname="beast.base.inference.operator.kernel.KernelDistribution$Bactrian"/>
<provider classname="beast.base.evolution.operator.kernel.AdaptableVarianceMultivariateNormalOperator"/>
<provider classname="beast.base.evolution.operator.kernel.BactrianNodeOperator"/>
<provider classname="beast.base.evolution.operator.kernel.BactrianOperatorSchedule"/>
<provider classname="beast.base.evolution.operator.kernel.BactrianScaleOperator"/>
<provider classname="beast.base.evolution.operator.kernel.BactrianSubtreeSlide"/>
<provider classname="beast.base.evolution.operator.kernel.BactrianTipDatesRandomWalker"/>
<provider classname="beast.base.inference.operator.kernel.Transform$Array"/>
<provider classname="beast.base.inference.operator.kernel.Transform$Collection"/>
<provider classname="beast.base.inference.operator.kernel.Transform$Compose"/>
<provider classname="beast.base.inference.operator.kernel.Transform$ComposeMultivariable"/>
<provider classname="beast.base.inference.operator.kernel.Transform$FisherZTransform"/>
<provider classname="beast.base.inference.operator.kernel.Transform$Inverse"/>
<provider classname="beast.base.inference.operator.kernel.Transform$InverseMultivariate"/>
<provider classname="beast.base.inference.operator.kernel.Transform$LogConstrainedSumTransform"/>
<provider classname="beast.base.inference.operator.kernel.Transform$LogTransform"/>
<provider classname="beast.base.inference.operator.kernel.Transform$LogitTransform"/>
<provider classname="beast.base.inference.operator.kernel.Transform$MultivariableTransformWithParameter"/>
<provider classname="beast.base.inference.operator.kernel.Transform$MultivariateTransform"/>
<provider classname="beast.base.inference.operator.kernel.Transform$NegateTransform"/>
<provider classname="beast.base.inference.operator.kernel.Transform$NoTransform"/>
<provider classname="beast.base.inference.operator.kernel.Transform$NoTransformMultivariable"/>
<provider classname="beast.base.inference.operator.kernel.Transform$PositiveOrdered"/>
<provider classname="beast.base.inference.operator.kernel.Transform$PowerTransform"/>
<provider classname="beast.base.evolution.sitemodel.SiteModel"/>
<provider classname="beast.base.evolution.speciation.BirthDeathGernhard08Model"/>
<provider classname="beast.base.evolution.speciation.CalibratedBirthDeathModel"/>
<provider classname="beast.base.evolution.speciation.CalibratedYuleInitialTree"/>
<provider classname="beast.base.evolution.speciation.CalibratedYuleModel"/>
<provider classname="beast.base.evolution.speciation.CalibrationPoint"/>
<provider classname="beast.base.evolution.speciation.GeneTreeForSpeciesTreeDistribution"/>
<provider classname="beast.base.evolution.speciation.RandomGeneTree"/>
<provider classname="beast.base.evolution.speciation.SpeciesTreeLogger"/>
<provider classname="beast.base.evolution.speciation.SpeciesTreePopFunction"/>
<provider classname="beast.base.evolution.speciation.SpeciesTreePrior"/>
<provider classname="beast.base.evolution.speciation.StarBeastStartState"/>
<provider classname="beast.base.evolution.speciation.TreeTopFinder"/>
<provider classname="beast.base.evolution.speciation.YuleModel"/>
<provider classname="beast.base.evolution.substitutionmodel.BinaryCovarion"/>
<provider classname="beast.base.evolution.substitutionmodel.Blosum62"/>
<provider classname="beast.base.evolution.substitutionmodel.CPREV"/>
<provider classname="beast.base.evolution.substitutionmodel.Dayhoff"/>
<provider classname="beast.base.evolution.substitutionmodel.Frequencies"/>
<provider classname="beast.base.evolution.substitutionmodel.GTR"/>
<provider classname="beast.base.evolution.substitutionmodel.GeneralSubstitutionModel"/>
<provider classname="beast.base.evolution.substitutionmodel.ComplexSubstitutionModel"/>
<provider classname="beast.base.evolution.substitutionmodel.HKY"/>
<provider classname="beast.base.evolution.substitutionmodel.JTT"/>
<provider classname="beast.base.evolution.substitutionmodel.JukesCantor"/>
<provider classname="beast.base.evolution.substitutionmodel.MTREV"/>
<provider classname="beast.base.evolution.substitutionmodel.MutationDeathModel"/>
<provider classname="beast.base.evolution.substitutionmodel.SYM"/>
<provider classname="beast.base.evolution.substitutionmodel.TIM"/>
<provider classname="beast.base.evolution.substitutionmodel.TN93"/>
<provider classname="beast.base.evolution.substitutionmodel.TVM"/>
<provider classname="beast.base.evolution.substitutionmodel.WAG"/>
<provider classname="beast.base.evolution.tree.ClusterTree"/>
<provider classname="beast.base.evolution.tree.MRCAPrior"/>
<provider classname="beast.base.evolution.tree.Node"/>
<provider classname="beast.base.evolution.tree.TraitSet"/>
<provider classname="beast.base.evolution.tree.Tree"/>
<provider classname="beast.base.evolution.tree.TreeDistribution"/>
<provider classname="beast.base.evolution.tree.TreeHeightLogger"/>
<provider classname="beast.base.evolution.tree.TreeIntervals"/>
<provider classname="beast.base.evolution.tree.TreeParser"/>
<provider classname="beast.base.evolution.tree.TreeStatLogger"/>
<provider classname="beast.base.evolution.tree.coalescent.BayesianSkyline"/>
<provider classname="beast.base.evolution.tree.coalescent.Coalescent"/>
<provider classname="beast.base.evolution.tree.coalescent.CompoundPopulationFunction"/>
<provider classname="beast.base.evolution.tree.coalescent.ConstantPopulation"/>
<provider classname="beast.base.evolution.tree.coalescent.ExponentialGrowth"/>
<provider classname="beast.base.evolution.tree.coalescent.RandomTree"/>
<provider classname="beast.base.evolution.tree.coalescent.SampleOffValues"/>
<provider classname="beast.base.evolution.tree.coalescent.ScaledPopulationFunction"/>
<provider classname="beast.base.inference.CompoundDistribution"/>
<provider classname="beast.base.inference.DirectSimulator"/>
<provider classname="beast.base.inference.Logger"/>
<provider classname="beast.base.inference.MCMC"/>
<provider classname="beast.base.inference.Operator"/>
<provider classname="beast.base.inference.OperatorSchedule"/>
<provider classname="beast.base.inference.State"/>
<provider classname="beast.base.inference.Distribution"/>
<provider classname="beast.base.inference.distribution.Beta"/>
<provider classname="beast.base.inference.distribution.ChiSquare"/>
<provider classname="beast.base.inference.distribution.Dirichlet"/>
<provider classname="beast.base.inference.distribution.Exponential"/>
<provider classname="beast.base.inference.distribution.Gamma"/>
<provider classname="beast.base.inference.distribution.InverseGamma"/>
<provider classname="beast.base.inference.distribution.LaplaceDistribution"/>
<provider classname="beast.base.inference.distribution.LogNormalDistributionModel"/>
<provider classname="beast.base.inference.distribution.MarkovChainDistribution"/>
<provider classname="beast.base.inference.distribution.Normal"/>
<provider classname="beast.base.inference.distribution.OneOnX"/>
<provider classname="beast.base.inference.distribution.Poisson"/>
<provider classname="beast.base.inference.distribution.Prior"/>
<provider classname="beast.base.inference.distribution.Uniform"/>
<provider classname="beast.base.inference.operator.BitFlipOperator"/>
<provider classname="beast.base.inference.operator.DeltaExchangeOperator"/>
<provider classname="beast.base.inference.operator.IntRandomWalkOperator"/>
<provider classname="beast.base.inference.operator.IntUniformOperator"/>
<provider classname="beast.base.inference.operator.JointOperator"/>
<provider classname="beast.base.inference.operator.RealRandomWalkOperator"/>
<provider classname="beast.base.inference.operator.SliceOperator"/>
<provider classname="beast.base.inference.operator.SwapOperator"/>
<provider classname="beast.base.inference.operator.UniformOperator"/>
<provider classname="beast.base.inference.operator.UpDownOperator"/>
<provider classname="beast.base.inference.operator.kernel.BactrianDeltaExchangeOperator"/>
<provider classname="beast.base.inference.operator.kernel.BactrianIntervalOperator"/>
<provider classname="beast.base.inference.operator.kernel.BactrianRandomWalkOperator"/>
<provider classname="beast.base.inference.operator.kernel.BactrianUpDownOperator"/>
<provider classname="beast.base.inference.parameter.BooleanParameter"/>
<provider classname="beast.base.inference.parameter.BooleanParameterList"/>
<provider classname="beast.base.inference.parameter.CompoundRealParameter"/>
<provider classname="beast.base.inference.parameter.CompoundValuable"/>
<provider classname="beast.base.inference.parameter.IntegerParameter"/>
<provider classname="beast.base.inference.parameter.IntegerParameterList"/>
<provider classname="beast.base.inference.parameter.RealParameter"/>
<provider classname="beast.base.inference.parameter.RealParameterList"/>
<provider classname="beast.base.inference.util.ESS"/>
<provider classname="beast.base.inference.util.RPNcalculator"/>
</service>
</package>