View Java Class Source Code in JAR file
- Download JD-GUI to open JAR file and explore Java source code file (.class .java)
- Click menu "File → Open File..." or just drag-and-drop the JAR file in the JD-GUI window lphy-base-1.5.0.jar file.
Once you open a JAR file, all the java classes in the JAR file will be displayed.
lphy.base.evolution.datatype
├─ lphy.base.evolution.datatype.Binary.class - [JAR]
├─ lphy.base.evolution.datatype.BinaryState.class - [JAR]
├─ lphy.base.evolution.datatype.Continuous.class - [JAR]
├─ lphy.base.evolution.datatype.DataType.class - [JAR]
├─ lphy.base.evolution.datatype.Standard.class - [JAR]
├─ lphy.base.evolution.datatype.StandardState.class - [JAR]
lphy.base.array
├─ lphy.base.array.StringDoubleArrayMap.class - [JAR]
lphy.base.function.taxa
├─ lphy.base.function.taxa.CreateTaxa.class - [JAR]
├─ lphy.base.function.taxa.ExtantTaxa.class - [JAR]
├─ lphy.base.function.taxa.ExtractTrait.class - [JAR]
├─ lphy.base.function.taxa.NTaxaFunction.class - [JAR]
├─ lphy.base.function.taxa.SpeciesTaxa.class - [JAR]
├─ lphy.base.function.taxa.TaxaAgesFromFunction.class - [JAR]
├─ lphy.base.function.taxa.TaxaFunction.class - [JAR]
lphy.base.evolution.branchrate
├─ lphy.base.evolution.branchrate.LocalBranchRates.class - [JAR]
lphy.base.bmodeltest
├─ lphy.base.bmodeltest.BModelSet.class - [JAR]
├─ lphy.base.bmodeltest.BModelSetFunction.class - [JAR]
├─ lphy.base.bmodeltest.NucleotideModel.class - [JAR]
├─ lphy.base.bmodeltest.bSiteModelFunction.class - [JAR]
├─ lphy.base.bmodeltest.bSiteRates.class - [JAR]
lphy.base.function
├─ lphy.base.function.ARange.class - [JAR]
├─ lphy.base.function.ArgI.class - [JAR]
├─ lphy.base.function.BinaryRateMatrix.class - [JAR]
├─ lphy.base.function.CoalescentCorrection.class - [JAR]
├─ lphy.base.function.Concat2Str.class - [JAR]
├─ lphy.base.function.ConcatArray.class - [JAR]
├─ lphy.base.function.ConcatStr.class - [JAR]
├─ lphy.base.function.Copy.class - [JAR]
├─ lphy.base.function.GeneralLinearFunction.class - [JAR]
├─ lphy.base.function.Get.class - [JAR]
├─ lphy.base.function.IfElse.class - [JAR]
├─ lphy.base.function.Intersect.class - [JAR]
├─ lphy.base.function.Length.class - [JAR]
├─ lphy.base.function.Map.class - [JAR]
├─ lphy.base.function.MigrationMatrix.class - [JAR]
├─ lphy.base.function.ParseInt.class - [JAR]
├─ lphy.base.function.Pow.class - [JAR]
├─ lphy.base.function.Product.class - [JAR]
├─ lphy.base.function.Rep.class - [JAR]
├─ lphy.base.function.RepArray.class - [JAR]
├─ lphy.base.function.Select.class - [JAR]
├─ lphy.base.function.SliceTimeTreeArray.class - [JAR]
├─ lphy.base.function.Sort.class - [JAR]
├─ lphy.base.function.Split.class - [JAR]
├─ lphy.base.function.Sum.class - [JAR]
├─ lphy.base.function.Sum2dArray.class - [JAR]
├─ lphy.base.function.SumBoolean.class - [JAR]
├─ lphy.base.function.SumCols.class - [JAR]
├─ lphy.base.function.SumRows.class - [JAR]
├─ lphy.base.function.SumUtils.class - [JAR]
├─ lphy.base.function.ToDouble.class - [JAR]
├─ lphy.base.function.Unique.class - [JAR]
lphy.base.evolution.coalescent
├─ lphy.base.evolution.coalescent.Coalescent.class - [JAR]
├─ lphy.base.evolution.coalescent.CoalescentConstants.class - [JAR]
├─ lphy.base.evolution.coalescent.MultispeciesCoalescent.class - [JAR]
├─ lphy.base.evolution.coalescent.SerialCoalescent.class - [JAR]
├─ lphy.base.evolution.coalescent.SkylineCoalescent.class - [JAR]
├─ lphy.base.evolution.coalescent.StructuredCoalescent.class - [JAR]
lphy.base.parser.newick
├─ lphy.base.parser.newick.NewickASTVisitor.class - [JAR]
├─ lphy.base.parser.newick.NewickLexer.class - [JAR]
├─ lphy.base.parser.newick.NewickParser.class - [JAR]
├─ lphy.base.parser.newick.NewickParserBaseListener.class - [JAR]
├─ lphy.base.parser.newick.NewickParserBaseVisitor.class - [JAR]
├─ lphy.base.parser.newick.NewickParserListener.class - [JAR]
├─ lphy.base.parser.newick.NewickParserVisitor.class - [JAR]
├─ lphy.base.parser.newick.TreeParsingException.class - [JAR]
lphy.base
├─ lphy.base.ParameterNames.class - [JAR]
lphy.base.logger
├─ lphy.base.logger.NexusAlignmentFormatter.class - [JAR]
├─ lphy.base.logger.NexusTreeFormatter.class - [JAR]
lphy.base.function.tree
├─ lphy.base.function.tree.ExtantTree.class - [JAR]
├─ lphy.base.function.tree.MigrationCount.class - [JAR]
├─ lphy.base.function.tree.Newick.class - [JAR]
├─ lphy.base.function.tree.NodeCount.class - [JAR]
├─ lphy.base.function.tree.PruneTree.class - [JAR]
├─ lphy.base.function.tree.TreeLength.class - [JAR]
lphy.base.evolution.tree
├─ lphy.base.evolution.tree.LTTUtils.class - [JAR]
├─ lphy.base.evolution.tree.TaxaConditionedTreeGenerator.class - [JAR]
├─ lphy.base.evolution.tree.TimeTree.class - [JAR]
├─ lphy.base.evolution.tree.TimeTreeNode.class - [JAR]
├─ lphy.base.evolution.tree.TimeTreeNodeVisitor.class - [JAR]
├─ lphy.base.evolution.tree.TimeTreeUtils.class - [JAR]
lphy.base.function.io
├─ lphy.base.function.io.ReadDelim.class - [JAR]
├─ lphy.base.function.io.ReadFasta.class - [JAR]
├─ lphy.base.function.io.ReadNexus.class - [JAR]
├─ lphy.base.function.io.ReaderConst.class - [JAR]
├─ lphy.base.function.io.WriteFasta.class - [JAR]
lphy.base.evolution.alignment
├─ lphy.base.evolution.alignment.AbstractAlignment.class - [JAR]
├─ lphy.base.evolution.alignment.Alignment.class - [JAR]
├─ lphy.base.evolution.alignment.AlignmentUtils.class - [JAR]
├─ lphy.base.evolution.alignment.CharSetBlock.class - [JAR]
├─ lphy.base.evolution.alignment.ContinuousCharacterData.class - [JAR]
├─ lphy.base.evolution.alignment.ErrorAlignment.class - [JAR]
├─ lphy.base.evolution.alignment.ErrorModel.class - [JAR]
├─ lphy.base.evolution.alignment.FastaAlignment.class - [JAR]
├─ lphy.base.evolution.alignment.MetaDataAlignment.class - [JAR]
├─ lphy.base.evolution.alignment.Sequence.class - [JAR]
├─ lphy.base.evolution.alignment.SimpleAlignment.class - [JAR]
├─ lphy.base.evolution.alignment.TaxaCharacterMatrix.class - [JAR]
lphy.base.evolution.continuous
├─ lphy.base.evolution.continuous.PhyloBrownian.class - [JAR]
├─ lphy.base.evolution.continuous.PhyloMultivariateBrownian.class - [JAR]
├─ lphy.base.evolution.continuous.PhyloOU.class - [JAR]
lphy.base.evolution.likelihood
├─ lphy.base.evolution.likelihood.AbstractPhyloCTMC.class - [JAR]
├─ lphy.base.evolution.likelihood.CTMC.class - [JAR]
├─ lphy.base.evolution.likelihood.PhyloCTMC.class - [JAR]
├─ lphy.base.evolution.likelihood.PhyloCTMCSiteModel.class - [JAR]
lphy.base.distribution
├─ lphy.base.distribution.Bernoulli.class - [JAR]
├─ lphy.base.distribution.BernoulliMulti.class - [JAR]
├─ lphy.base.distribution.Beta.class - [JAR]
├─ lphy.base.distribution.Binomial.class - [JAR]
├─ lphy.base.distribution.Categorical.class - [JAR]
├─ lphy.base.distribution.Cauchy.class - [JAR]
├─ lphy.base.distribution.Dirichlet.class - [JAR]
├─ lphy.base.distribution.DiscretizedGamma.class - [JAR]
├─ lphy.base.distribution.DistributionConstants.class - [JAR]
├─ lphy.base.distribution.Exp.class - [JAR]
├─ lphy.base.distribution.ExpMarkovChain.class - [JAR]
├─ lphy.base.distribution.ExpMulti.class - [JAR]
├─ lphy.base.distribution.Gamma.class - [JAR]
├─ lphy.base.distribution.GeneralLinearModel.class - [JAR]
├─ lphy.base.distribution.Geometric.class - [JAR]
├─ lphy.base.distribution.InverseGamma.class - [JAR]
├─ lphy.base.distribution.LogNormal.class - [JAR]
├─ lphy.base.distribution.LogNormalMulti.class - [JAR]
├─ lphy.base.distribution.MVN.class - [JAR]
├─ lphy.base.distribution.NegativeBinomial.class - [JAR]
├─ lphy.base.distribution.Normal.class - [JAR]
├─ lphy.base.distribution.NormalGamma.class - [JAR]
├─ lphy.base.distribution.OrnsteinUhlenbeck.class - [JAR]
├─ lphy.base.distribution.ParametricDistribution.class - [JAR]
├─ lphy.base.distribution.Poisson.class - [JAR]
├─ lphy.base.distribution.RandomBooleanArray.class - [JAR]
├─ lphy.base.distribution.RandomComposition.class - [JAR]
├─ lphy.base.distribution.Sample.class - [JAR]
├─ lphy.base.distribution.Uniform.class - [JAR]
├─ lphy.base.distribution.UniformDiscrete.class - [JAR]
├─ lphy.base.distribution.Weibull.class - [JAR]
├─ lphy.base.distribution.WeightedDirichlet.class - [JAR]
lphy.base.evolution.substitutionmodel
├─ lphy.base.evolution.substitutionmodel.F81.class - [JAR]
├─ lphy.base.evolution.substitutionmodel.GTR.class - [JAR]
├─ lphy.base.evolution.substitutionmodel.GeneralTimeReversible.class - [JAR]
├─ lphy.base.evolution.substitutionmodel.HKY.class - [JAR]
├─ lphy.base.evolution.substitutionmodel.JukesCantor.class - [JAR]
├─ lphy.base.evolution.substitutionmodel.K80.class - [JAR]
├─ lphy.base.evolution.substitutionmodel.LewisMK.class - [JAR]
├─ lphy.base.evolution.substitutionmodel.RateMatrix.class - [JAR]
├─ lphy.base.evolution.substitutionmodel.TN93.class - [JAR]
├─ lphy.base.evolution.substitutionmodel.WAG.class - [JAR]
lphy.base.evolution.sitemodel
├─ lphy.base.evolution.sitemodel.SiteModel.class - [JAR]
lphy.base.math
├─ lphy.base.math.MathUtils.class - [JAR]
lphy.base.spi
├─ lphy.base.spi.LPhyBaseImpl.class - [JAR]
├─ lphy.base.spi.SequenceTypeBaseImpl.class - [JAR]
├─ lphy.base.spi.SequenceTypeExtension.class - [JAR]
├─ lphy.base.spi.ValueFormatterBaseImpl.class - [JAR]
lphy.base.evolution.birthdeath
├─ lphy.base.evolution.birthdeath.BirthDeathConstants.class - [JAR]
├─ lphy.base.evolution.birthdeath.BirthDeathSamplingTree.class - [JAR]
├─ lphy.base.evolution.birthdeath.BirthDeathSamplingTreeDT.class - [JAR]
├─ lphy.base.evolution.birthdeath.BirthDeathSerialSamplingTree.class - [JAR]
├─ lphy.base.evolution.birthdeath.BirthDeathTree.class - [JAR]
├─ lphy.base.evolution.birthdeath.BirthDeathTreeDT.class - [JAR]
├─ lphy.base.evolution.birthdeath.FossilBirthDeathTree.class - [JAR]
├─ lphy.base.evolution.birthdeath.FullBirthDeathTree.class - [JAR]
├─ lphy.base.evolution.birthdeath.GLMBirthDeathTree.class - [JAR]
├─ lphy.base.evolution.birthdeath.RhoSampleTree.class - [JAR]
├─ lphy.base.evolution.birthdeath.SimBDReverse.class - [JAR]
├─ lphy.base.evolution.birthdeath.SimFBDAge.class - [JAR]
├─ lphy.base.evolution.birthdeath.SimFossilsPoisson.class - [JAR]
├─ lphy.base.evolution.birthdeath.Yule.class - [JAR]
lphy.base.function.alignment
├─ lphy.base.function.alignment.CopySites.class - [JAR]
├─ lphy.base.function.alignment.InvariableSites.class - [JAR]
├─ lphy.base.function.alignment.MetaDataOptions.class - [JAR]
├─ lphy.base.function.alignment.MissingSites.class - [JAR]
├─ lphy.base.function.alignment.NCharFunction.class - [JAR]
├─ lphy.base.function.alignment.RemoveTaxa.class - [JAR]
├─ lphy.base.function.alignment.SelectSitesByMissingFraction.class - [JAR]
├─ lphy.base.function.alignment.VariableSites.class - [JAR]
lphy.base.parser
├─ lphy.base.parser.NexusParser.class - [JAR]
lphy.base.function.datatype
├─ lphy.base.function.datatype.AminoAcidsFunction.class - [JAR]
├─ lphy.base.function.datatype.BinaryDatatypeFunction.class - [JAR]
├─ lphy.base.function.datatype.NucleotidesFunction.class - [JAR]
├─ lphy.base.function.datatype.StandardDatatypeFunction.class - [JAR]
lphy.base.evolution
├─ lphy.base.evolution.Attributable.class - [JAR]
├─ lphy.base.evolution.EvolutionConstants.class - [JAR]
├─ lphy.base.evolution.ExtractStringMetaData.class - [JAR]
├─ lphy.base.evolution.HasTaxa.class - [JAR]
├─ lphy.base.evolution.NChar.class - [JAR]
├─ lphy.base.evolution.Taxa.class - [JAR]
├─ lphy.base.evolution.TaxaData.class - [JAR]
├─ lphy.base.evolution.Taxon.class - [JAR]
lphy.base.parser.nexus
├─ lphy.base.parser.nexus.CharactersBlock.class - [JAR]
├─ lphy.base.parser.nexus.NexusBlock.class - [JAR]
├─ lphy.base.parser.nexus.NexusBuilder.class - [JAR]
├─ lphy.base.parser.nexus.NexusUtils.class - [JAR]
├─ lphy.base.parser.nexus.NexusWriter.class - [JAR]
├─ lphy.base.parser.nexus.TaxaBlock.class - [JAR]
├─ lphy.base.parser.nexus.TreesBlock.class - [JAR]
