View Java Class Source Code in JAR file
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- Click menu "File → Open File..." or just drag-and-drop the JAR file in the JD-GUI window lphy-1.4.3.jar file.
Once you open a JAR file, all the java classes in the JAR file will be displayed.
lphy.core
├─ lphy.core.Arguments.class - [JAR]
├─ lphy.core.CTMC.class - [JAR]
├─ lphy.core.GraphicalLPhyParser.class - [JAR]
├─ lphy.core.GraphicalModelChangeListener.class - [JAR]
├─ lphy.core.GraphicalModelListener.class - [JAR]
├─ lphy.core.LPhyMetaParser.class - [JAR]
├─ lphy.core.ParameterNames.class - [JAR]
├─ lphy.core.Sampler.class - [JAR]
├─ lphy.core.Script.class - [JAR]
├─ lphy.core.StringDoubleArrayMap.class - [JAR]
lphy.evolution.sitemodel
├─ lphy.evolution.sitemodel.SiteModel.class - [JAR]
lphy.mcmc
├─ lphy.mcmc.MCMC.class - [JAR]
├─ lphy.mcmc.Operator.class - [JAR]
lphy.evolution
├─ lphy.evolution.Attributable.class - [JAR]
├─ lphy.evolution.EvolutionConstants.class - [JAR]
├─ lphy.evolution.ExtractStringMetaData.class - [JAR]
├─ lphy.evolution.HasTaxa.class - [JAR]
├─ lphy.evolution.NChar.class - [JAR]
├─ lphy.evolution.Taxa.class - [JAR]
├─ lphy.evolution.TaxaData.class - [JAR]
├─ lphy.evolution.Taxon.class - [JAR]
lphy.evolution.continuous
├─ lphy.evolution.continuous.PhyloBrownian.class - [JAR]
├─ lphy.evolution.continuous.PhyloMultivariateBrownian.class - [JAR]
├─ lphy.evolution.continuous.PhyloOU.class - [JAR]
lphy.core.lightweight
├─ lphy.core.lightweight.GenerativeDistributionAdapter.class - [JAR]
├─ lphy.core.lightweight.GeneratorAdapter.class - [JAR]
├─ lphy.core.lightweight.LGenerativeDistribution.class - [JAR]
├─ lphy.core.lightweight.LGenerator.class - [JAR]
├─ lphy.core.lightweight.VectorizedGenerativeDistribution.class - [JAR]
├─ lphy.core.lightweight.VectorizedGenerator.class - [JAR]
lphy.evolution.alignment
├─ lphy.evolution.alignment.AbstractAlignment.class - [JAR]
├─ lphy.evolution.alignment.Alignment.class - [JAR]
├─ lphy.evolution.alignment.AlignmentUtils.class - [JAR]
├─ lphy.evolution.alignment.ContinuousCharacterData.class - [JAR]
├─ lphy.evolution.alignment.CopySites.class - [JAR]
├─ lphy.evolution.alignment.ErrorAlignment.class - [JAR]
├─ lphy.evolution.alignment.ErrorModel.class - [JAR]
├─ lphy.evolution.alignment.InvariableSites.class - [JAR]
├─ lphy.evolution.alignment.MissingSites.class - [JAR]
├─ lphy.evolution.alignment.SelectSitesByMissingFraction.class - [JAR]
├─ lphy.evolution.alignment.Sequence.class - [JAR]
├─ lphy.evolution.alignment.SimpleAlignment.class - [JAR]
├─ lphy.evolution.alignment.TaxaCharacterMatrix.class - [JAR]
├─ lphy.evolution.alignment.VariableSites.class - [JAR]
lphy.evolution.birthdeath
├─ lphy.evolution.birthdeath.BirthDeathConstants.class - [JAR]
├─ lphy.evolution.birthdeath.BirthDeathSamplingTree.class - [JAR]
├─ lphy.evolution.birthdeath.BirthDeathSamplingTreeDT.class - [JAR]
├─ lphy.evolution.birthdeath.BirthDeathSerialSamplingTree.class - [JAR]
├─ lphy.evolution.birthdeath.BirthDeathTree.class - [JAR]
├─ lphy.evolution.birthdeath.BirthDeathTreeDT.class - [JAR]
├─ lphy.evolution.birthdeath.FossilBirthDeathTree.class - [JAR]
├─ lphy.evolution.birthdeath.FullBirthDeathTree.class - [JAR]
├─ lphy.evolution.birthdeath.GLMBirthDeathTree.class - [JAR]
├─ lphy.evolution.birthdeath.RhoSampleTree.class - [JAR]
├─ lphy.evolution.birthdeath.SimBDReverse.class - [JAR]
├─ lphy.evolution.birthdeath.SimFBDAge.class - [JAR]
├─ lphy.evolution.birthdeath.SimFossilsPoisson.class - [JAR]
├─ lphy.evolution.birthdeath.Yule.class - [JAR]
lphy.graphicalModel.code
├─ lphy.graphicalModel.code.CanonicalCodeBuilder.class - [JAR]
├─ lphy.graphicalModel.code.CodeBuilder.class - [JAR]
├─ lphy.graphicalModel.code.LaTexCodeBuilder.class - [JAR]
lphy.nexus
├─ lphy.nexus.CharactersBlock.class - [JAR]
├─ lphy.nexus.NexusBlock.class - [JAR]
├─ lphy.nexus.NexusBuilder.class - [JAR]
├─ lphy.nexus.NexusWriter.class - [JAR]
├─ lphy.nexus.TaxaBlock.class - [JAR]
├─ lphy.nexus.TreesBlock.class - [JAR]
lphy.core.narrative
├─ lphy.core.narrative.Narrative.class - [JAR]
├─ lphy.core.narrative.NarrativeName.class - [JAR]
├─ lphy.core.narrative.Section.class - [JAR]
lphy.core.functions
├─ lphy.core.functions.ARange.class - [JAR]
├─ lphy.core.functions.ArgI.class - [JAR]
├─ lphy.core.functions.ArrayFunction.class - [JAR]
├─ lphy.core.functions.BinaryRateMatrix.class - [JAR]
├─ lphy.core.functions.BooleanArray.class - [JAR]
├─ lphy.core.functions.CoalescentCorrection.class - [JAR]
├─ lphy.core.functions.Concat2Str.class - [JAR]
├─ lphy.core.functions.ConcatArray.class - [JAR]
├─ lphy.core.functions.ConcatStr.class - [JAR]
├─ lphy.core.functions.DoubleArray.class - [JAR]
├─ lphy.core.functions.ElementsAt.class - [JAR]
├─ lphy.core.functions.Exp.class - [JAR]
├─ lphy.core.functions.GeneralLinearFunction.class - [JAR]
├─ lphy.core.functions.Get.class - [JAR]
├─ lphy.core.functions.IfElse.class - [JAR]
├─ lphy.core.functions.IntegerArray.class - [JAR]
├─ lphy.core.functions.Intersect.class - [JAR]
├─ lphy.core.functions.Length.class - [JAR]
├─ lphy.core.functions.Log.class - [JAR]
├─ lphy.core.functions.Map.class - [JAR]
├─ lphy.core.functions.MigrationMatrix.class - [JAR]
├─ lphy.core.functions.NumberArray.class - [JAR]
├─ lphy.core.functions.ParseInt.class - [JAR]
├─ lphy.core.functions.Pow.class - [JAR]
├─ lphy.core.functions.Product.class - [JAR]
├─ lphy.core.functions.Range.class - [JAR]
├─ lphy.core.functions.Rep.class - [JAR]
├─ lphy.core.functions.RepArray.class - [JAR]
├─ lphy.core.functions.Round.class - [JAR]
├─ lphy.core.functions.Select.class - [JAR]
├─ lphy.core.functions.Slice.class - [JAR]
├─ lphy.core.functions.SliceDoubleArray.class - [JAR]
├─ lphy.core.functions.SliceTimeTreeArray.class - [JAR]
├─ lphy.core.functions.Sort.class - [JAR]
├─ lphy.core.functions.Split.class - [JAR]
├─ lphy.core.functions.StringArray.class - [JAR]
├─ lphy.core.functions.Sum.class - [JAR]
├─ lphy.core.functions.Sum2dArray.class - [JAR]
├─ lphy.core.functions.SumBoolean.class - [JAR]
├─ lphy.core.functions.SumCols.class - [JAR]
├─ lphy.core.functions.SumRows.class - [JAR]
├─ lphy.core.functions.SumUtils.class - [JAR]
├─ lphy.core.functions.Unique.class - [JAR]
├─ lphy.core.functions.VectorizedFunction.class - [JAR]
lphy.core.lightweight.distributions
├─ lphy.core.lightweight.distributions.Bernoulli.class - [JAR]
├─ lphy.core.lightweight.distributions.Beta.class - [JAR]
├─ lphy.core.lightweight.distributions.Binomial.class - [JAR]
├─ lphy.core.lightweight.distributions.Categorical.class - [JAR]
├─ lphy.core.lightweight.distributions.Cauchy.class - [JAR]
├─ lphy.core.lightweight.distributions.Dirichlet.class - [JAR]
├─ lphy.core.lightweight.distributions.DiscretizedGamma.class - [JAR]
├─ lphy.core.lightweight.distributions.Exp.class - [JAR]
├─ lphy.core.lightweight.distributions.Gamma.class - [JAR]
├─ lphy.core.lightweight.distributions.Geometric.class - [JAR]
├─ lphy.core.lightweight.distributions.LogNormal.class - [JAR]
├─ lphy.core.lightweight.distributions.MVN.class - [JAR]
├─ lphy.core.lightweight.distributions.Normal.class - [JAR]
├─ lphy.core.lightweight.distributions.Poisson.class - [JAR]
├─ lphy.core.lightweight.distributions.Uniform.class - [JAR]
├─ lphy.core.lightweight.distributions.package-info.class - [JAR]
lphy.parser.newickParser
├─ lphy.parser.newickParser.NewickASTVisitor.class - [JAR]
├─ lphy.parser.newickParser.NewickLexer.class - [JAR]
├─ lphy.parser.newickParser.NewickParser.class - [JAR]
├─ lphy.parser.newickParser.NewickParserBaseListener.class - [JAR]
├─ lphy.parser.newickParser.NewickParserBaseVisitor.class - [JAR]
├─ lphy.parser.newickParser.NewickParserListener.class - [JAR]
├─ lphy.parser.newickParser.NewickParserVisitor.class - [JAR]
├─ lphy.parser.newickParser.TreeParsingException.class - [JAR]
lphy.reflection
├─ lphy.reflection.Utils.class - [JAR]
lphy.evolution.datatype
├─ lphy.evolution.datatype.Binary.class - [JAR]
├─ lphy.evolution.datatype.BinaryState.class - [JAR]
├─ lphy.evolution.datatype.Continuous.class - [JAR]
├─ lphy.evolution.datatype.DataType.class - [JAR]
├─ lphy.evolution.datatype.SequenceTypeFactory.class - [JAR]
├─ lphy.evolution.datatype.Standard.class - [JAR]
├─ lphy.evolution.datatype.StandardState.class - [JAR]
lphy.mcmc.operators
├─ lphy.mcmc.operators.ScaleOperator.class - [JAR]
lphy.evolution.tree
├─ lphy.evolution.tree.LTTUtils.class - [JAR]
├─ lphy.evolution.tree.TaxaConditionedTreeGenerator.class - [JAR]
├─ lphy.evolution.tree.TimeTree.class - [JAR]
├─ lphy.evolution.tree.TimeTreeNode.class - [JAR]
├─ lphy.evolution.tree.TimeTreeNodeVisitor.class - [JAR]
├─ lphy.evolution.tree.TimeTreeUtils.class - [JAR]
lphy.evolution.coalescent
├─ lphy.evolution.coalescent.Coalescent.class - [JAR]
├─ lphy.evolution.coalescent.CoalescentConstants.class - [JAR]
├─ lphy.evolution.coalescent.MultispeciesCoalescent.class - [JAR]
├─ lphy.evolution.coalescent.SerialCoalescent.class - [JAR]
├─ lphy.evolution.coalescent.SkylineCoalescent.class - [JAR]
├─ lphy.evolution.coalescent.StructuredCoalescent.class - [JAR]
lphy.core.functions.tree
├─ lphy.core.functions.tree.ExtantTree.class - [JAR]
├─ lphy.core.functions.tree.MigrationCount.class - [JAR]
├─ lphy.core.functions.tree.Newick.class - [JAR]
├─ lphy.core.functions.tree.NodeCount.class - [JAR]
├─ lphy.core.functions.tree.PruneTree.class - [JAR]
├─ lphy.core.functions.tree.TreeLength.class - [JAR]
lphy.graphicalModel.types
├─ lphy.graphicalModel.types.Array2DUtils.class - [JAR]
├─ lphy.graphicalModel.types.BooleanArray2DValue.class - [JAR]
├─ lphy.graphicalModel.types.BooleanArrayValue.class - [JAR]
├─ lphy.graphicalModel.types.BooleanValue.class - [JAR]
├─ lphy.graphicalModel.types.CompoundVectorValue.class - [JAR]
├─ lphy.graphicalModel.types.DoubleArray2DValue.class - [JAR]
├─ lphy.graphicalModel.types.DoubleArrayValue.class - [JAR]
├─ lphy.graphicalModel.types.DoubleValue.class - [JAR]
├─ lphy.graphicalModel.types.IntegerArray2DValue.class - [JAR]
├─ lphy.graphicalModel.types.IntegerArrayValue.class - [JAR]
├─ lphy.graphicalModel.types.IntegerValue.class - [JAR]
├─ lphy.graphicalModel.types.MapValue.class - [JAR]
├─ lphy.graphicalModel.types.NumberArrayValue.class - [JAR]
├─ lphy.graphicalModel.types.NumberValue.class - [JAR]
├─ lphy.graphicalModel.types.StringArray2DValue.class - [JAR]
├─ lphy.graphicalModel.types.StringArrayValue.class - [JAR]
├─ lphy.graphicalModel.types.StringValue.class - [JAR]
├─ lphy.graphicalModel.types.VectorValue.class - [JAR]
lphy.util
├─ lphy.util.LoggerUtils.class - [JAR]
├─ lphy.util.RandomUtils.class - [JAR]
├─ lphy.util.Symbols.class - [JAR]
lphy.parser.functions
├─ lphy.parser.functions.ElementWise1Arg.class - [JAR]
├─ lphy.parser.functions.ElementWise2Args.class - [JAR]
├─ lphy.parser.functions.ExpressionNode.class - [JAR]
├─ lphy.parser.functions.ExpressionNode1Arg.class - [JAR]
├─ lphy.parser.functions.ExpressionNode2Args.class - [JAR]
├─ lphy.parser.functions.ExpressionNodeWrapper.class - [JAR]
├─ lphy.parser.functions.MapFunction.class - [JAR]
├─ lphy.parser.functions.MethodCall.class - [JAR]
├─ lphy.parser.functions.RangeList.class - [JAR]
lphy.evolution.io
├─ lphy.evolution.io.MetaDataAlignment.class - [JAR]
├─ lphy.evolution.io.MetaDataOptions.class - [JAR]
├─ lphy.evolution.io.NexusParser.class - [JAR]
lphy.math
├─ lphy.math.MathUtils.class - [JAR]
lphy.core.functions.taxa
├─ lphy.core.functions.taxa.CreateTaxa.class - [JAR]
├─ lphy.core.functions.taxa.ExtantTaxa.class - [JAR]
├─ lphy.core.functions.taxa.ExtractTrait.class - [JAR]
├─ lphy.core.functions.taxa.NTaxaFunction.class - [JAR]
├─ lphy.core.functions.taxa.Species.class - [JAR]
├─ lphy.core.functions.taxa.TaxaAgesFromFunction.class - [JAR]
├─ lphy.core.functions.taxa.TaxaFunction.class - [JAR]
lphy.spi
├─ lphy.spi.LPhyExtImpl.class - [JAR]
├─ lphy.spi.LPhyExtension.class - [JAR]
lphy.bmodeltest
├─ lphy.bmodeltest.BModelSet.class - [JAR]
├─ lphy.bmodeltest.BModelSetFunction.class - [JAR]
├─ lphy.bmodeltest.NucleotideModel.class - [JAR]
├─ lphy.bmodeltest.bSiteModelFunction.class - [JAR]
├─ lphy.bmodeltest.bSiteRates.class - [JAR]
lphy.core.functions.alignment
├─ lphy.core.functions.alignment.NCharFunction.class - [JAR]
├─ lphy.core.functions.alignment.ReadFasta.class - [JAR]
├─ lphy.core.functions.alignment.ReadNexus.class - [JAR]
├─ lphy.core.functions.alignment.Simulate.class - [JAR]
lphy.evolution.substitutionmodel
├─ lphy.evolution.substitutionmodel.F81.class - [JAR]
├─ lphy.evolution.substitutionmodel.GTR.class - [JAR]
├─ lphy.evolution.substitutionmodel.GeneralTimeReversible.class - [JAR]
├─ lphy.evolution.substitutionmodel.HKY.class - [JAR]
├─ lphy.evolution.substitutionmodel.JukesCantor.class - [JAR]
├─ lphy.evolution.substitutionmodel.K80.class - [JAR]
├─ lphy.evolution.substitutionmodel.LewisMK.class - [JAR]
├─ lphy.evolution.substitutionmodel.RateMatrix.class - [JAR]
├─ lphy.evolution.substitutionmodel.TN93.class - [JAR]
├─ lphy.evolution.substitutionmodel.WAG.class - [JAR]
lphy.graphicalModel.logger
├─ lphy.graphicalModel.logger.AlignmentFileLogger.class - [JAR]
├─ lphy.graphicalModel.logger.RandomNumberLogger.class - [JAR]
├─ lphy.graphicalModel.logger.TreeFileLogger.class - [JAR]
├─ lphy.graphicalModel.logger.VarFileLogger.class - [JAR]
lphy
├─ lphy.LPhyExtensionFactory.class - [JAR]
lphy.evolution.branchrates
├─ lphy.evolution.branchrates.LocalBranchRates.class - [JAR]
lphy.doc
├─ lphy.doc.GenerateDocs.class - [JAR]
├─ lphy.doc.GeneratorMarkdown.class - [JAR]
lphy.graphicalModel
├─ lphy.graphicalModel.Argument.class - [JAR]
├─ lphy.graphicalModel.ArgumentValue.class - [JAR]
├─ lphy.graphicalModel.Citation.class - [JAR]
├─ lphy.graphicalModel.Command.class - [JAR]
├─ lphy.graphicalModel.CompoundVector.class - [JAR]
├─ lphy.graphicalModel.DeterministicFunction.class - [JAR]
├─ lphy.graphicalModel.Func.class - [JAR]
├─ lphy.graphicalModel.GenerativeDistribution.class - [JAR]
├─ lphy.graphicalModel.GenerativeDistribution1D.class - [JAR]
├─ lphy.graphicalModel.Generator.class - [JAR]
├─ lphy.graphicalModel.GeneratorCategory.class - [JAR]
├─ lphy.graphicalModel.GeneratorInfo.class - [JAR]
├─ lphy.graphicalModel.GraphicalModel.class - [JAR]
├─ lphy.graphicalModel.GraphicalModelNode.class - [JAR]
├─ lphy.graphicalModel.GraphicalModelNodeVisitor.class - [JAR]
├─ lphy.graphicalModel.IndexedRandomVariable.class - [JAR]
├─ lphy.graphicalModel.Loggable.class - [JAR]
├─ lphy.graphicalModel.MethodInfo.class - [JAR]
├─ lphy.graphicalModel.MultiDimensional.class - [JAR]
├─ lphy.graphicalModel.NarrativeUtils.class - [JAR]
├─ lphy.graphicalModel.ParameterInfo.class - [JAR]
├─ lphy.graphicalModel.PlaceHolder.class - [JAR]
├─ lphy.graphicalModel.RandomValueLogger.class - [JAR]
├─ lphy.graphicalModel.RandomVariable.class - [JAR]
├─ lphy.graphicalModel.RangeElement.class - [JAR]
├─ lphy.graphicalModel.SliceValue.class - [JAR]
├─ lphy.graphicalModel.TypeInfo.class - [JAR]
├─ lphy.graphicalModel.Utils.class - [JAR]
├─ lphy.graphicalModel.Value.class - [JAR]
├─ lphy.graphicalModel.ValueListener.class - [JAR]
├─ lphy.graphicalModel.ValueUtils.class - [JAR]
├─ lphy.graphicalModel.VariableUtils.class - [JAR]
├─ lphy.graphicalModel.Vector.class - [JAR]
├─ lphy.graphicalModel.VectorUtils.class - [JAR]
├─ lphy.graphicalModel.VectorizedRandomVariable.class - [JAR]
lphy.core.functions.datatype
├─ lphy.core.functions.datatype.AminoAcidsFunction.class - [JAR]
├─ lphy.core.functions.datatype.BinaryDatatypeFunction.class - [JAR]
├─ lphy.core.functions.datatype.NucleotidesFunction.class - [JAR]
├─ lphy.core.functions.datatype.StandardDatatypeFunction.class - [JAR]
lphy.core.distributions
├─ lphy.core.distributions.Bernoulli.class - [JAR]
├─ lphy.core.distributions.BernoulliMulti.class - [JAR]
├─ lphy.core.distributions.Beta.class - [JAR]
├─ lphy.core.distributions.Binomial.class - [JAR]
├─ lphy.core.distributions.Categorical.class - [JAR]
├─ lphy.core.distributions.Cauchy.class - [JAR]
├─ lphy.core.distributions.CompoundDistribution.class - [JAR]
├─ lphy.core.distributions.Dirichlet.class - [JAR]
├─ lphy.core.distributions.DiscretizedGamma.class - [JAR]
├─ lphy.core.distributions.DistributionConstants.class - [JAR]
├─ lphy.core.distributions.Exp.class - [JAR]
├─ lphy.core.distributions.ExpMarkovChain.class - [JAR]
├─ lphy.core.distributions.ExpMulti.class - [JAR]
├─ lphy.core.distributions.Gamma.class - [JAR]
├─ lphy.core.distributions.GeneralLinearModel.class - [JAR]
├─ lphy.core.distributions.Geometric.class - [JAR]
├─ lphy.core.distributions.IID.class - [JAR]
├─ lphy.core.distributions.InverseGamma.class - [JAR]
├─ lphy.core.distributions.LogNormal.class - [JAR]
├─ lphy.core.distributions.LogNormalMulti.class - [JAR]
├─ lphy.core.distributions.MVN.class - [JAR]
├─ lphy.core.distributions.NegativeBinomial.class - [JAR]
├─ lphy.core.distributions.Normal.class - [JAR]
├─ lphy.core.distributions.NormalGamma.class - [JAR]
├─ lphy.core.distributions.OrnsteinUhlenbeck.class - [JAR]
├─ lphy.core.distributions.ParametricDistribution.class - [JAR]
├─ lphy.core.distributions.Poisson.class - [JAR]
├─ lphy.core.distributions.RandomBooleanArray.class - [JAR]
├─ lphy.core.distributions.RandomComposition.class - [JAR]
├─ lphy.core.distributions.Sample.class - [JAR]
├─ lphy.core.distributions.Uniform.class - [JAR]
├─ lphy.core.distributions.UniformDiscrete.class - [JAR]
├─ lphy.core.distributions.VectorizedDistribution.class - [JAR]
├─ lphy.core.distributions.Weibull.class - [JAR]
├─ lphy.core.distributions.WeightedDirichlet.class - [JAR]
lphy.parser
├─ lphy.parser.AbstractLightweightBaseListener.class - [JAR]
├─ lphy.parser.DataClampingUtils.class - [JAR]
├─ lphy.parser.LPhyBaseErrorListener.class - [JAR]
├─ lphy.parser.LPhyBaseListener.class - [JAR]
├─ lphy.parser.LPhyBaseVisitor.class - [JAR]
├─ lphy.parser.LPhyLexer.class - [JAR]
├─ lphy.parser.LPhyListener.class - [JAR]
├─ lphy.parser.LPhyListenerImpl.class - [JAR]
├─ lphy.parser.LPhyParser.class - [JAR]
├─ lphy.parser.LPhyParserAction.class - [JAR]
├─ lphy.parser.LPhyVisitor.class - [JAR]
├─ lphy.parser.ParserSingleton.class - [JAR]
├─ lphy.parser.ParserUtils.class - [JAR]
├─ lphy.parser.REPL.class - [JAR]
├─ lphy.parser.SimulatorParsingException.class - [JAR]
├─ lphy.parser.Var.class - [JAR]
lphy.layeredgraph
├─ lphy.layeredgraph.BrandesKopfHorizontalCoordinateAssignment.class - [JAR]
├─ lphy.layeredgraph.LatticePoint.class - [JAR]
├─ lphy.layeredgraph.LayeredGraph.class - [JAR]
├─ lphy.layeredgraph.LayeredNode.class - [JAR]
├─ lphy.layeredgraph.Layering.class - [JAR]
├─ lphy.layeredgraph.NodeWrapper.class - [JAR]
├─ lphy.layeredgraph.Ordering.class - [JAR]
├─ lphy.layeredgraph.ProperLayeredGraph.class - [JAR]
lphy.system
├─ lphy.system.PathVariables.class - [JAR]
├─ lphy.system.UserDir.class - [JAR]
lphy.evolution.traits
├─ lphy.evolution.traits.CharSetBlock.class - [JAR]
lphy.evolution.likelihood
├─ lphy.evolution.likelihood.AbstractPhyloCTMC.class - [JAR]
├─ lphy.evolution.likelihood.PhyloCTMC.class - [JAR]
├─ lphy.evolution.likelihood.PhyloCTMCSiteModel.class - [JAR]
