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119 lines (114 loc) · 7.89 KB
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<package name='BEASTLabs' version='2.1.0'>
<depends on='BEAST.base' atleast='2.8.0'/>
<packageapp description="View parametric distributions"
class="beastlabs.app.beauti.DistributionViewer"
args=""
/>
<service type="beastfx.app.inputeditor.InputEditor">
<provider classname="beastlabs.app.beauti.MultiMonophyleticConstraintInputEditor"/>
</service>
<service type="beastfx.app.beauti.PriorProvider">
<provider classname="beastlabs.app.beauti.MultiMonophyleticConstraintInputEditor"/>
</service>
<service type="beast.base.core.BEASTInterface">
<provider classname="beastlabs.core.DataNode"/>
<provider classname="beastlabs.core.FilteredValuable"/>
<provider classname="beastlabs.core.GridSearch"/>
<provider classname="beastlabs.core.Likelihood"/>
<provider classname="beastlabs.core.MCMC2"/>
<provider classname="beastlabs.core.Posterior"/>
<provider classname="beastlabs.core.parameter.CompoundRealParameter"/>
<provider classname="beastlabs.core.parameter.NormalisedRealParameter"/>
<provider classname="beastlabs.core.util.LoggableSum"/>
<provider classname="beastlabs.core.util.ParameterConstrainer"/>
<provider classname="beastlabs.core.util.Slice"/>
<provider classname="beastlabs.evolution.alignment.PrunedAlignment"/>
<provider classname="beastlabs.evolution.branchratemodel.PrunedRelaxedClockModel"/>
<provider classname="beastlabs.evolution.likelihood.AncestralStateLogger"/>
<provider classname="beastlabs.evolution.likelihood.ExperimentalTreeLikelihood"/>
<provider classname="beastlabs.evolution.likelihood.SupertreeLikelihood"/>
<provider classname="beastlabs.evolution.likelihood.TraitedTreeLikelihood"/>
<provider classname="beastlabs.evolution.likelihood.MultiPartitionTreeLikelihood"/>
<provider classname="beastlabs.evolution.likelihood.SelfTuningMCMC"/>
<provider classname="beastlabs.evolution.likelihood.SelfTuningCompoundDistribution"/>
<provider classname="beastlabs.evolution.operators.AttachAndUniformOperator"/>
<provider classname="beastlabs.evolution.operators.AttachOperator"/>
<provider classname="beastlabs.evolution.operators.CladeInternalAttachOperator"/>
<provider classname="beastlabs.evolution.operators.CombinedOperator"/>
<provider classname="beastlabs.evolution.operators.CompoundOperator"/>
<provider classname="beastlabs.evolution.operators.MultiCladeAttachOperator"/>
<provider classname="beastlabs.evolution.operators.NNI"/>
<provider classname="beastlabs.evolution.operators.RestrictedSubtreeSlide"/>
<provider classname="beastlabs.evolution.operators.RootHeightScaleOperator"/>
<provider classname="beastlabs.evolution.operators.SPR"/>
<provider classname="beastlabs.evolution.operators.TreeWithMetaDataRandomWalker"/>
<provider classname="beastlabs.evolution.operators.UniformOperatorSelective"/>
<provider classname="beastlabs.evolution.operators.UniformSelective"/>
<provider classname="beastlabs.evolution.sitemodel.SiteModelGI"/>
<provider classname="beastlabs.evolution.speciation.RandomLocalYuleModel"/>
<provider classname="beastlabs.evolution.substitutionmodel.CladeSubstitutionModel"/>
<provider classname="beastlabs.evolution.substitutionmodel.EpochSubstitutionModel"/>
<provider classname="beastlabs.evolution.substitutionmodel.GeneralLazySubstitutionModel"/>
<provider classname="beastlabs.evolution.substitutionmodel.LazyHKY"/>
<provider classname="beastlabs.evolution.substitutionmodel.EmpiricalAAModelFromFile"/>
<provider classname="beastlabs.evolution.taxonomy.Taxon"/>
<provider classname="beastlabs.evolution.tree.ConstrainedClusterTree"/>
<provider classname="beastlabs.evolution.tree.ConstrainedRandomTree"/>
<provider classname="beastlabs.evolution.tree.InitParamFromTree"/>
<provider classname="beastlabs.evolution.tree.MonophyleticConstraint"/>
<provider classname="beastlabs.evolution.tree.PrunedTree"/>
<provider classname="beastlabs.evolution.tree.RNNIMetric"/>
<provider classname="beastlabs.evolution.tree.RobinsonsFouldMetric"/>
<provider classname="beastlabs.evolution.tree.SimpleConstrainedRandomTree"/>
<provider classname="beastlabs.evolution.tree.SimplePrunedTree"/>
<provider classname="beastlabs.evolution.tree.SimpleRandomTree"/>
<provider classname="beastlabs.evolution.tree.TreeDistanceLogger"/>
<provider classname="beastlabs.evolution.tree.coalescent.CauchyPlusConstant"/>
<provider classname="beastlabs.evolution.tree.coalescent.ExponentialGrowthPlusConstant"/>
<provider classname="beastlabs.evolution.tree.coalescent.StructuredCoalescentTree"/>
<provider classname="beastlabs.inference.ConvergableMCMC"/>
<provider classname="beastlabs.inference.HeatedMCMC"/>
<provider classname="beastlabs.inference.IndependentMCMC"/>
<provider classname="beastlabs.inference.MCMCMC"/>
<provider classname="beastlabs.inference.MCMCParticle"/>
<provider classname="beastlabs.inference.MCMCParticleAsync"/>
<provider classname="beastlabs.inference.ML"/>
<provider classname="beastlabs.inference.MultiMCMC"/>
<provider classname="beastlabs.inference.ParticleFilter"/>
<provider classname="beastlabs.inference.SimulatedAnnealing"/>
<provider classname="beastlabs.inference.TreeStoreLogger"/>
<provider classname="beastlabs.math.distributions.BernoulliDistribution"/>
<provider classname="beastlabs.math.distributions.BetaRange"/>
<provider classname="beastlabs.math.distributions.ExcludablePrior"/>
<provider classname="beastlabs.math.distributions.ExcludablePriorIndex"/>
<provider classname="beastlabs.math.distributions.GammaOneP"/>
<provider classname="beastlabs.math.distributions.MRCAPriorWithRogues"/>
<provider classname="beastlabs.math.distributions.MixtureDistribution"/>
<provider classname="beastlabs.math.distributions.MonoPoints"/>
<provider classname="beastlabs.math.distributions.MultiMRCAPriors"/>
<provider classname="beastlabs.math.distributions.MultiMonophyleticConstraint"/>
<provider classname="beastlabs.math.distributions.RandomCompositionPositive"/>
<provider classname="beastlabs.math.distributions.SingleParamGamma"/>
<provider classname="beastlabs.math.distributions.WeibullDistribution"/>
<provider classname="beastlabs.math.distributions.WeightedDirichlet"/>
<provider classname="beastlabs.parsimony.FitchParsimony"/>
<provider classname="beastlabs.parsimony.FitchParsimony32"/>
<provider classname="beastlabs.parsimony.FitchParsimony64"/>
<provider classname="beastlabs.prevalence.AddOperator"/>
<provider classname="beastlabs.prevalence.DelOperator"/>
<provider classname="beastlabs.prevalence.MoveOperator"/>
<provider classname="beastlabs.prevalence.PrevalenceLikelihood"/>
<provider classname="beastlabs.prevalence.PrevalenceList"/>
<provider classname="beastlabs.prevalence.SubtreeSlide"/>
<provider classname="beastlabs.prevalence.TreeForPrevalenceLikelihood"/>
<provider classname="beastlabs.prevalence.TreeScaleOperator"/>
<provider classname="beastlabs.prevalence.Uniform"/>
<provider classname="beastlabs.prevalence.WilsonBalding"/>
<provider classname="beastlabs.util.BEASTVector"/>
<provider classname="beastlabs.util.Script"/>
<provider classname="beastlabs.util.TimeLogger"/>
<provider classname="beastlabs.tools.PostHocAnalyser"/>
<provider classname="beastlabs.tools.TraceStateNodeSource"/>
<provider classname="beastlabs.tools.TreeStateNodeSource"/>
</service>
</package>