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    Download tassel JAR 5.2.78 with all dependencies


    Files of the artifact tassel version 5.2.78 from the group net.maizegenetics.

    Artifact tassel
    Group net.maizegenetics
    Version 5.2.78


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    Source code of tassel version 5.2.78

    META-INF
    META-INF.META-INF.MANIFEST.MF
    net.maizegenetics.analysis
    net.maizegenetics.analysis.net.maizegenetics.analysis.ListPluginParameters.kt
    net.maizegenetics.analysis.net.maizegenetics.analysis.ListPlugins
    net.maizegenetics.analysis.association
    net.maizegenetics.analysis.association.net.maizegenetics.analysis.association.AbstractFixedEffectLM
    net.maizegenetics.analysis.association.net.maizegenetics.analysis.association.AlleleProbabilityFELM
    net.maizegenetics.analysis.association.net.maizegenetics.analysis.association.AssociationConstants
    net.maizegenetics.analysis.association.net.maizegenetics.analysis.association.AssociationUtils
    net.maizegenetics.analysis.association.net.maizegenetics.analysis.association.CompressedDoubleMatrix
    net.maizegenetics.analysis.association.net.maizegenetics.analysis.association.CompressedMLMusingDoubleMatrix
    net.maizegenetics.analysis.association.net.maizegenetics.analysis.association.DiscreteSitesFELM
    net.maizegenetics.analysis.association.net.maizegenetics.analysis.association.EqtlAssociationPlugin
    net.maizegenetics.analysis.association.net.maizegenetics.analysis.association.FastMultithreadedAssociationPlugin
    net.maizegenetics.analysis.association.net.maizegenetics.analysis.association.FixedEffectLM
    net.maizegenetics.analysis.association.net.maizegenetics.analysis.association.FixedEffectLMPlugin
    net.maizegenetics.analysis.association.net.maizegenetics.analysis.association.GenomicSelectionPlugin
    net.maizegenetics.analysis.association.net.maizegenetics.analysis.association.MLMPlugin
    net.maizegenetics.analysis.association.net.maizegenetics.analysis.association.PhenotypeLM
    net.maizegenetics.analysis.association.net.maizegenetics.analysis.association.ReferenceProbabilityFELM
    net.maizegenetics.analysis.association.net.maizegenetics.analysis.association.RegRidgeEmmaDoubleMatrix
    net.maizegenetics.analysis.association.net.maizegenetics.analysis.association.RidgeRegressionEmmaPlugin
    net.maizegenetics.analysis.association.net.maizegenetics.analysis.association.WeightedMLMPlugin
    net.maizegenetics.analysis.association.net.maizegenetics.analysis.association.package-info
    net.maizegenetics.analysis.avro
    net.maizegenetics.analysis.avro.net.maizegenetics.analysis.avro.AvroConstants
    net.maizegenetics.analysis.avro.net.maizegenetics.analysis.avro.ExportAvro
    net.maizegenetics.analysis.avro.net.maizegenetics.analysis.avro.GenericArrayPositions
    net.maizegenetics.analysis.avro.net.maizegenetics.analysis.avro.GenericArrayTaxa
    net.maizegenetics.analysis.avro.net.maizegenetics.analysis.avro.GenericMapAnnotations
    net.maizegenetics.analysis.avro.net.maizegenetics.analysis.avro.GenericRecordChromosome
    net.maizegenetics.analysis.avro.net.maizegenetics.analysis.avro.GenericRecordGenotype
    net.maizegenetics.analysis.avro.net.maizegenetics.analysis.avro.GenericRecordGenotypeTable
    net.maizegenetics.analysis.avro.net.maizegenetics.analysis.avro.GenericRecordPosition
    net.maizegenetics.analysis.avro.net.maizegenetics.analysis.avro.GenericRecordTaxon
    net.maizegenetics.analysis.avro.net.maizegenetics.analysis.avro.ImportAvro
    net.maizegenetics.analysis.b4r
    net.maizegenetics.analysis.b4r.net.maizegenetics.analysis.b4r.B4RPhenotypeUtils
    net.maizegenetics.analysis.b4r.net.maizegenetics.analysis.b4r.GetPhenotypeFromB4RPlugin
    net.maizegenetics.analysis.chart
    net.maizegenetics.analysis.chart.net.maizegenetics.analysis.chart.AbstractDisplayPlugin
    net.maizegenetics.analysis.chart.net.maizegenetics.analysis.chart.BarChart.gif
    net.maizegenetics.analysis.chart.net.maizegenetics.analysis.chart.BarChartPanel
    net.maizegenetics.analysis.chart.net.maizegenetics.analysis.chart.BasicChartPanel
    net.maizegenetics.analysis.chart.net.maizegenetics.analysis.chart.BasicGraphFrame
    net.maizegenetics.analysis.chart.net.maizegenetics.analysis.chart.ChartDisplayPlugin
    net.maizegenetics.analysis.chart.net.maizegenetics.analysis.chart.HistogramPanel
    net.maizegenetics.analysis.chart.net.maizegenetics.analysis.chart.ManhattanDisplayPlugin
    net.maizegenetics.analysis.chart.net.maizegenetics.analysis.chart.ManhattanNumberFormat
    net.maizegenetics.analysis.chart.net.maizegenetics.analysis.chart.PieChartPanel
    net.maizegenetics.analysis.chart.net.maizegenetics.analysis.chart.QQDisplayPlugin
    net.maizegenetics.analysis.chart.net.maizegenetics.analysis.chart.TableDisplayPlugin
    net.maizegenetics.analysis.chart.net.maizegenetics.analysis.chart.TableReportBoxWhiskerCatDataset
    net.maizegenetics.analysis.chart.net.maizegenetics.analysis.chart.TableReportManhattanDataset
    net.maizegenetics.analysis.chart.net.maizegenetics.analysis.chart.TableReportPieDataset
    net.maizegenetics.analysis.chart.net.maizegenetics.analysis.chart.TableReportQQDataset
    net.maizegenetics.analysis.chart.net.maizegenetics.analysis.chart.TableReportStatCategoryDataset
    net.maizegenetics.analysis.chart.net.maizegenetics.analysis.chart.TableReportXYDataset
    net.maizegenetics.analysis.chart.net.maizegenetics.analysis.chart.XYAndLineToolTipGenerator
    net.maizegenetics.analysis.chart.net.maizegenetics.analysis.chart.XYMultipleYToolTipGenerator
    net.maizegenetics.analysis.chart.net.maizegenetics.analysis.chart.XYScatterAndLinePanel
    net.maizegenetics.analysis.chart.net.maizegenetics.analysis.chart.XYScatterMultipleYPanel
    net.maizegenetics.analysis.chart.net.maizegenetics.analysis.chart.XYScatterPanel
    net.maizegenetics.analysis.chart.net.maizegenetics.analysis.chart.package-info
    net.maizegenetics.analysis.clustering
    net.maizegenetics.analysis.clustering.net.maizegenetics.analysis.clustering.Haplotype
    net.maizegenetics.analysis.clustering.net.maizegenetics.analysis.clustering.HaplotypeCluster
    net.maizegenetics.analysis.clustering.net.maizegenetics.analysis.clustering.HaplotypeClusterer
    net.maizegenetics.analysis.clustering.net.maizegenetics.analysis.clustering.package-info
    net.maizegenetics.analysis.data
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.AddReferenceAlleleToHDF5Plugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.AddReferenceToGenotypePlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.AdjustPhasingPlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.BuildUnfinishedHDF5GenotypesPlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.CombineDataSetsPlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.ConvertAlignmentCoordinatesPlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.CountAssociationsPlugin.kt
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.CreateHybridGenotypesPlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.ExportMultiplePlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.ExportPlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.ExtractHapmapSubsetPlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.FeatureListToPositionsPlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.FileLoadPlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.FindInversionsPlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.GenomeAnnosDBQueryToPositionListPlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.GenosToABHPlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.GenotypeSummaryPlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.GenotypeToAdditiveValuesPlugin.kt
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.GetPositionListPlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.GetTaxaListPlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.HDF5SummaryPlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.HetsToUnknownPlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.IdentityRecognitionPlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.IndelsToUnknownPlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.IntersectionAlignmentPlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.KmerCountingPlugin.kt
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.LIXPlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.LowLevelCopyOfHDF5
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.MaskGenotypePlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.MeanR2FromLDPlugin.kt
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.MemoryUsagePlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.MergeAlignmentsSameSitesPlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.MergeGenotypeTablesPlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.MergeGenotypeTablesPluginV2
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.MergeHDF5GenotypesSameSitesPlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.MergeRenameDeleteTaxaPlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.MigrateHDF5FromT4T5
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.PassThroughPlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.PlinkLoadPlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.PrincipalComponentsPlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.ProjectPcsAndRunModelSelectionPlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.ProjectionLoadPlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.SeparatePlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.SetLowDepthGenosToMissingPlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.SortGenotypeFilePlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.SortTaxaAlphabeticallyPlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.SplitHDF5ByChromosomePlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.SubtractGenotypesPlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.SynonymizerPlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.ThinSitesByPositionPlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.UnionAlignmentPlugin
    net.maizegenetics.analysis.data.net.maizegenetics.analysis.data.package-info
    net.maizegenetics.analysis.distance
    net.maizegenetics.analysis.distance.net.maizegenetics.analysis.distance.AMatrixPlugin
    net.maizegenetics.analysis.distance.net.maizegenetics.analysis.distance.AddDistanceMatrixPlugin
    net.maizegenetics.analysis.distance.net.maizegenetics.analysis.distance.DistanceMatrixPlugin
    net.maizegenetics.analysis.distance.net.maizegenetics.analysis.distance.DistanceMatrixRangesPlugin
    net.maizegenetics.analysis.distance.net.maizegenetics.analysis.distance.DominanceNormalizedIBSMatrix
    net.maizegenetics.analysis.distance.net.maizegenetics.analysis.distance.DominanceRelationshipMatrix
    net.maizegenetics.analysis.distance.net.maizegenetics.analysis.distance.EndelmanDistanceMatrix
    net.maizegenetics.analysis.distance.net.maizegenetics.analysis.distance.GCTADistanceMatrix
    net.maizegenetics.analysis.distance.net.maizegenetics.analysis.distance.HMatrixPlugin
    net.maizegenetics.analysis.distance.net.maizegenetics.analysis.distance.IBSDistanceMatrix
    net.maizegenetics.analysis.distance.net.maizegenetics.analysis.distance.IBSDistanceMatrix2Alleles
    net.maizegenetics.analysis.distance.net.maizegenetics.analysis.distance.IBSDistanceMatrix3Alleles
    net.maizegenetics.analysis.distance.net.maizegenetics.analysis.distance.IBSDistanceMatrixOneByAll
    net.maizegenetics.analysis.distance.net.maizegenetics.analysis.distance.Kinship
    net.maizegenetics.analysis.distance.net.maizegenetics.analysis.distance.KinshipPlugin
    net.maizegenetics.analysis.distance.net.maizegenetics.analysis.distance.MultiDimensionalScalingPlugin
    net.maizegenetics.analysis.distance.net.maizegenetics.analysis.distance.RemoveNaNFromDistanceMatrixPlugin
    net.maizegenetics.analysis.distance.net.maizegenetics.analysis.distance.SubtractDistanceMatrixPlugin
    net.maizegenetics.analysis.distance.net.maizegenetics.analysis.distance.VCAPScanPlugin
    net.maizegenetics.analysis.distance.net.maizegenetics.analysis.distance.package-info
    net.maizegenetics.analysis.filter
    net.maizegenetics.analysis.filter.net.maizegenetics.analysis.filter.FilterAlignmentPlugin
    net.maizegenetics.analysis.filter.net.maizegenetics.analysis.filter.FilterBySites
    net.maizegenetics.analysis.filter.net.maizegenetics.analysis.filter.FilterByTaxa
    net.maizegenetics.analysis.filter.net.maizegenetics.analysis.filter.FilterDataSetPlugin
    net.maizegenetics.analysis.filter.net.maizegenetics.analysis.filter.FilterSiteBuilderPlugin
    net.maizegenetics.analysis.filter.net.maizegenetics.analysis.filter.FilterSiteNamePlugin
    net.maizegenetics.analysis.filter.net.maizegenetics.analysis.filter.FilterSubsetPlugin
    net.maizegenetics.analysis.filter.net.maizegenetics.analysis.filter.FilterTaxaBuilderPlugin
    net.maizegenetics.analysis.filter.net.maizegenetics.analysis.filter.FilterTaxaPropertiesPlugin
    net.maizegenetics.analysis.filter.net.maizegenetics.analysis.filter.FilterTraitsDialog
    net.maizegenetics.analysis.filter.net.maizegenetics.analysis.filter.FilterTraitsPlugin
    net.maizegenetics.analysis.filter.net.maizegenetics.analysis.filter.package-info
    net.maizegenetics.analysis.gbs
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.AnnotateTOPM
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.AnnotateTOPMwSAMPlugin
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.Barcode
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.BinaryToTextPlugin
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.Clusters
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.CompareGenosBetweenHapMapFilesPlugin
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.ContigPETagCountPlugin
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.FastqToPETagCountPlugin
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.FastqToTBTPlugin
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.FastqToTagCountPlugin
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.KeepSpecifiedReadsinFastqPlugin
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.KeepSpecifiedSitesInTOPMPlugin
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.KmerToTBTPlugin
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.KmerToTagCountPlugin
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.MergeDuplicateSNPsPlugin
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.MergeMultipleTOPMPlugin
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.MergeMultipleTagCountPlugin
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.MergePETagCountPlugin
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.MergeTagsByTaxaFilesByRowPlugin
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.MergeTagsByTaxaFilesPlugin
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.ModifyTBTHDF5Plugin
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.PEParseBarcodeRead
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.PEReadBarcodeResult
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.ParseBarcodeRead
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.PolymorphismFinder
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.ProductionPipeline
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.ProductionPipelineMain
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.ProductionSNPCallerPlugin
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.QseqToPETagCountPlugin
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.QseqToTBTPlugin
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.QseqToTagCountPlugin
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.ReadBarcodeResult
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.SAMConverterPlugin
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.SAMWGMapConverterPlugin
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.SNPLogging
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.SeqToTBTHDF5Plugin
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.ShortReadBarcodeResult
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.SimpleGenotypeSBit
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.SmithWaterman
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.TOPMSummaryPlugin
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.TagAgainstAnchor
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.TagAgainstAnchorHypothesis
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.TagAgainstAnchorPlugin
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.TagBlockPosition
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.TagCountToFastqPlugin
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.TagMatchFinder
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.TerryPipelines
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.TextToBinaryPlugin
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.UNetworkFilter
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.UTagCountToTagPairPlugin
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.UTagPairFinder
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.UTagPairToTOPMPlugin
    net.maizegenetics.analysis.gbs.neobio
    net.maizegenetics.analysis.gbs.neobio.net.maizegenetics.analysis.gbs.neobio.AlignmentBlock
    net.maizegenetics.analysis.gbs.neobio.net.maizegenetics.analysis.gbs.neobio.BasicScoringScheme
    net.maizegenetics.analysis.gbs.neobio.net.maizegenetics.analysis.gbs.neobio.CharSequence
    net.maizegenetics.analysis.gbs.neobio.net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelson
    net.maizegenetics.analysis.gbs.neobio.net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelsonGlobalAlignment
    net.maizegenetics.analysis.gbs.neobio.net.maizegenetics.analysis.gbs.neobio.CrochemoreLandauZivUkelsonLocalAlignment
    net.maizegenetics.analysis.gbs.neobio.net.maizegenetics.analysis.gbs.neobio.Factor
    net.maizegenetics.analysis.gbs.neobio.net.maizegenetics.analysis.gbs.neobio.FactorSequence
    net.maizegenetics.analysis.gbs.neobio.net.maizegenetics.analysis.gbs.neobio.IncompatibleScoringSchemeException
    net.maizegenetics.analysis.gbs.neobio.net.maizegenetics.analysis.gbs.neobio.InvalidScoringMatrixException
    net.maizegenetics.analysis.gbs.neobio.net.maizegenetics.analysis.gbs.neobio.InvalidSequenceException
    net.maizegenetics.analysis.gbs.neobio.net.maizegenetics.analysis.gbs.neobio.LocalAlignmentBlock
    net.maizegenetics.analysis.gbs.neobio.net.maizegenetics.analysis.gbs.neobio.Matrix
    net.maizegenetics.analysis.gbs.neobio.net.maizegenetics.analysis.gbs.neobio.NeedlemanWunsch
    net.maizegenetics.analysis.gbs.neobio.net.maizegenetics.analysis.gbs.neobio.OutMatrix
    net.maizegenetics.analysis.gbs.neobio.net.maizegenetics.analysis.gbs.neobio.PairwiseAlignment
    net.maizegenetics.analysis.gbs.neobio.net.maizegenetics.analysis.gbs.neobio.PairwiseAlignmentAlgorithm
    net.maizegenetics.analysis.gbs.neobio.net.maizegenetics.analysis.gbs.neobio.ScoringMatrix
    net.maizegenetics.analysis.gbs.neobio.net.maizegenetics.analysis.gbs.neobio.ScoringScheme
    net.maizegenetics.analysis.gbs.neobio.net.maizegenetics.analysis.gbs.neobio.Smawk
    net.maizegenetics.analysis.gbs.neobio.net.maizegenetics.analysis.gbs.neobio.SmithWaterman
    net.maizegenetics.analysis.gbs.neobio.net.maizegenetics.analysis.gbs.neobio.Trie
    net.maizegenetics.analysis.gbs
    net.maizegenetics.analysis.gbs.net.maizegenetics.analysis.gbs.package-info
    net.maizegenetics.analysis.gbs.pana
    net.maizegenetics.analysis.gbs.pana.net.maizegenetics.analysis.gbs.pana.PanAAddPosToTagMapPlugin
    net.maizegenetics.analysis.gbs.pana.net.maizegenetics.analysis.gbs.pana.PanABuildPivotTBTPlugin
    net.maizegenetics.analysis.gbs.pana.net.maizegenetics.analysis.gbs.pana.PanABuildTagBlockPosPlugin
    net.maizegenetics.analysis.gbs.pana.net.maizegenetics.analysis.gbs.pana.PanABuildTagGWASMapPlugin
    net.maizegenetics.analysis.gbs.pana.net.maizegenetics.analysis.gbs.pana.PanABuildTrainingSetPlugin
    net.maizegenetics.analysis.gbs.pana.net.maizegenetics.analysis.gbs.pana.PanAFilteringTagMapPlugin
    net.maizegenetics.analysis.gbs.pana.net.maizegenetics.analysis.gbs.pana.PanAH5ToAnchorPlugin
    net.maizegenetics.analysis.gbs.pana.net.maizegenetics.analysis.gbs.pana.PanAMergeMappingResultPlugin
    net.maizegenetics.analysis.gbs.pana.net.maizegenetics.analysis.gbs.pana.PanAModelTrainingPlugin
    net.maizegenetics.analysis.gbs.pana.net.maizegenetics.analysis.gbs.pana.PanAPredictionPlugin
    net.maizegenetics.analysis.gbs.pana.net.maizegenetics.analysis.gbs.pana.PanAReadDigestPlugin
    net.maizegenetics.analysis.gbs.pana.net.maizegenetics.analysis.gbs.pana.PanAReadToKmerPlugin
    net.maizegenetics.analysis.gbs.pana.net.maizegenetics.analysis.gbs.pana.PanASamToMultiPositionTOPMPlugin
    net.maizegenetics.analysis.gbs.pana.net.maizegenetics.analysis.gbs.pana.PanASplitTBTPlugin
    net.maizegenetics.analysis.gbs.pana.net.maizegenetics.analysis.gbs.pana.PanASplitTagBlockPosPlugin
    net.maizegenetics.analysis.gbs.pana.net.maizegenetics.analysis.gbs.pana.PanATagGWASMappingPlugin
    net.maizegenetics.analysis.gbs.pana.net.maizegenetics.analysis.gbs.pana.PanATagMapToFastaPlugin
    net.maizegenetics.analysis.gbs.pana.net.maizegenetics.analysis.gbs.pana.PanAUsageExample
    net.maizegenetics.analysis.gbs.pana.net.maizegenetics.analysis.gbs.pana.package-info
    net.maizegenetics.analysis.gbs.repgen
    net.maizegenetics.analysis.gbs.repgen.net.maizegenetics.analysis.gbs.repgen.AlignmentInfo
    net.maizegenetics.analysis.gbs.repgen.net.maizegenetics.analysis.gbs.repgen.RGBSProductionSNPCallerPlugin
    net.maizegenetics.analysis.gbs.repgen.net.maizegenetics.analysis.gbs.repgen.RampSeqAlignFromBlastTags
    net.maizegenetics.analysis.gbs.repgen.net.maizegenetics.analysis.gbs.repgen.RefTagData
    net.maizegenetics.analysis.gbs.repgen.net.maizegenetics.analysis.gbs.repgen.RepGenAlignerPlugin
    net.maizegenetics.analysis.gbs.repgen.net.maizegenetics.analysis.gbs.repgen.RepGenLDAnalysisPlugin
    net.maizegenetics.analysis.gbs.repgen.net.maizegenetics.analysis.gbs.repgen.RepGenLoadSeqToDBPlugin
    net.maizegenetics.analysis.gbs.repgen.net.maizegenetics.analysis.gbs.repgen.RepGenPhase2AlignerPlugin
    net.maizegenetics.analysis.gbs.repgen.net.maizegenetics.analysis.gbs.repgen.TagCorrelationInfo
    net.maizegenetics.analysis.gbs.v2
    net.maizegenetics.analysis.gbs.v2.net.maizegenetics.analysis.gbs.v2.BarcodeTrie
    net.maizegenetics.analysis.gbs.v2.net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2
    net.maizegenetics.analysis.gbs.v2.net.maizegenetics.analysis.gbs.v2.EnzymeList
    net.maizegenetics.analysis.gbs.v2.net.maizegenetics.analysis.gbs.v2.GBSEnzyme
    net.maizegenetics.analysis.gbs.v2.net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin
    net.maizegenetics.analysis.gbs.v2.net.maizegenetics.analysis.gbs.v2.GBSUtils
    net.maizegenetics.analysis.gbs.v2.net.maizegenetics.analysis.gbs.v2.GetTagSequenceFromDBPlugin
    net.maizegenetics.analysis.gbs.v2.net.maizegenetics.analysis.gbs.v2.GetTagTaxaDistFromDBPlugin
    net.maizegenetics.analysis.gbs.v2.net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2
    net.maizegenetics.analysis.gbs.v2.net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin
    net.maizegenetics.analysis.gbs.v2.net.maizegenetics.analysis.gbs.v2.SNPCutPosTagVerificationPlugin
    net.maizegenetics.analysis.gbs.v2.net.maizegenetics.analysis.gbs.v2.SNPQualityProfilerPlugin
    net.maizegenetics.analysis.gbs.v2.net.maizegenetics.analysis.gbs.v2.TagExportToFastqPlugin
    net.maizegenetics.analysis.gbs.v2.net.maizegenetics.analysis.gbs.v2.UpdateSNPPositionQualityPlugin
    net.maizegenetics.analysis.gobii
    net.maizegenetics.analysis.gobii.net.maizegenetics.analysis.gobii.BMSConnection
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    net.maizegenetics.analysis.gobii.net.maizegenetics.analysis.gobii.GOBIIPlugin
    net.maizegenetics.analysis.gobii.net.maizegenetics.analysis.gobii.GOBIIPostgresConnection
    net.maizegenetics.analysis.gobii.net.maizegenetics.analysis.gobii.GOBII_IFLUtils
    net.maizegenetics.analysis.gobii.net.maizegenetics.analysis.gobii.GWAS_IFLPlugin
    net.maizegenetics.analysis.gobii.net.maizegenetics.analysis.gobii.HapBreakpoints_IFLFilePlugin
    net.maizegenetics.analysis.gobii.net.maizegenetics.analysis.gobii.MarkerDNARun_IFLFilePlugin
    net.maizegenetics.analysis.gobii.net.maizegenetics.analysis.gobii.MonetDB_IFLFilePlugin
    net.maizegenetics.analysis.gobii.net.maizegenetics.analysis.gobii.PreProcessGOBIIMappingFilePlugin
    net.maizegenetics.analysis.gobii.net.maizegenetics.analysis.gobii.SplitFile_IFLFilePlugin
    net.maizegenetics.analysis.gobii.net.maizegenetics.analysis.gobii.UpdateMarkerAndDNA_idxes
    net.maizegenetics.analysis.images
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    net.maizegenetics.analysis.imputation
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    net.maizegenetics.analysis.imputation.net.maizegenetics.analysis.imputation.CrossProgenyEmissionMatrix
    net.maizegenetics.analysis.imputation.net.maizegenetics.analysis.imputation.EmissionProbability
    net.maizegenetics.analysis.imputation.net.maizegenetics.analysis.imputation.FILLINDonorGenotypeUtils
    net.maizegenetics.analysis.imputation.net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin
    net.maizegenetics.analysis.imputation.net.maizegenetics.analysis.imputation.FILLINImputationAccuracy
    net.maizegenetics.analysis.imputation.net.maizegenetics.analysis.imputation.FILLINImputationPlugin
    net.maizegenetics.analysis.imputation.net.maizegenetics.analysis.imputation.FILLINImputationUtils
    net.maizegenetics.analysis.imputation.net.maizegenetics.analysis.imputation.FSFHapImputationPlugin
    net.maizegenetics.analysis.imputation.net.maizegenetics.analysis.imputation.FindMergeHaplotypesPlugin
    net.maizegenetics.analysis.imputation.net.maizegenetics.analysis.imputation.ImputationAccuracyPlugin
    net.maizegenetics.analysis.imputation.net.maizegenetics.analysis.imputation.ImputationUtils
    net.maizegenetics.analysis.imputation.net.maizegenetics.analysis.imputation.ImputeCrossProgeny
    net.maizegenetics.analysis.imputation.net.maizegenetics.analysis.imputation.ImputeProgenyStatesPlugin
    net.maizegenetics.analysis.imputation.net.maizegenetics.analysis.imputation.ImputedTaxon
    net.maizegenetics.analysis.imputation.net.maizegenetics.analysis.imputation.LDKNNiImputationHetV2Plugin
    net.maizegenetics.analysis.imputation.net.maizegenetics.analysis.imputation.LDKNNiImputationHetV3Plugin
    net.maizegenetics.analysis.imputation.net.maizegenetics.analysis.imputation.LDKNNiImputationPlugin
    net.maizegenetics.analysis.imputation.net.maizegenetics.analysis.imputation.MergeBreakpointFilesPlugin
    net.maizegenetics.analysis.imputation.net.maizegenetics.analysis.imputation.NucleotideImputationUtils
    net.maizegenetics.analysis.imputation.net.maizegenetics.analysis.imputation.ParentPhasingPlugin
    net.maizegenetics.analysis.imputation.net.maizegenetics.analysis.imputation.PhaseHighCoverage
    net.maizegenetics.analysis.imputation.net.maizegenetics.analysis.imputation.PopulationData
    net.maizegenetics.analysis.imputation.net.maizegenetics.analysis.imputation.RandomGenotypeImputationPlugin
    net.maizegenetics.analysis.imputation.net.maizegenetics.analysis.imputation.ReImputeUpdatedTaxaByFILLINPlugin
    net.maizegenetics.analysis.imputation.net.maizegenetics.analysis.imputation.RemoveIndelsForBeaglePlugin
    net.maizegenetics.analysis.imputation.net.maizegenetics.analysis.imputation.RephaseParents
    net.maizegenetics.analysis.imputation.net.maizegenetics.analysis.imputation.SelfedHaplotypeFinder
    net.maizegenetics.analysis.imputation.net.maizegenetics.analysis.imputation.SubpopulationFinder
    net.maizegenetics.analysis.imputation.net.maizegenetics.analysis.imputation.TransitionProbability
    net.maizegenetics.analysis.imputation.net.maizegenetics.analysis.imputation.TransitionProbabilityWithVariableRecombination
    net.maizegenetics.analysis.imputation.net.maizegenetics.analysis.imputation.UseParentHaplotypes
    net.maizegenetics.analysis.imputation.net.maizegenetics.analysis.imputation.ViterbiAlgorithm
    net.maizegenetics.analysis.imputation.net.maizegenetics.analysis.imputation.ViterbiAlgorithmPlugin
    net.maizegenetics.analysis.imputation.net.maizegenetics.analysis.imputation.ViterbiAlgorithmVariableStateNumber
    net.maizegenetics.analysis.imputation.net.maizegenetics.analysis.imputation.WritePopulationAlignmentPlugin
    net.maizegenetics.analysis.imputation.net.maizegenetics.analysis.imputation.package-info
    net.maizegenetics.analysis.modelfitter
    net.maizegenetics.analysis.modelfitter.net.maizegenetics.analysis.modelfitter.AbstractAdditiveSite
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    net.maizegenetics.analysis.modelfitter.net.maizegenetics.analysis.modelfitter.AddDomPermutationTestSpliterator
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    net.maizegenetics.analysis.modelfitter.net.maizegenetics.analysis.modelfitter.AdditiveResidualForwardRegression
    net.maizegenetics.analysis.modelfitter.net.maizegenetics.analysis.modelfitter.AdditiveSite
    net.maizegenetics.analysis.modelfitter.net.maizegenetics.analysis.modelfitter.AdditiveSiteStorePlugin
    net.maizegenetics.analysis.modelfitter.net.maizegenetics.analysis.modelfitter.CovariatePermutationTestSpliterator
    net.maizegenetics.analysis.modelfitter.net.maizegenetics.analysis.modelfitter.ForwardRegression
    net.maizegenetics.analysis.modelfitter.net.maizegenetics.analysis.modelfitter.ForwardStepAddDomSpliterator
    net.maizegenetics.analysis.modelfitter.net.maizegenetics.analysis.modelfitter.ForwardStepAdditiveSpliterator
    net.maizegenetics.analysis.modelfitter.net.maizegenetics.analysis.modelfitter.ForwardStepNestedAdditiveSpliterator
    net.maizegenetics.analysis.modelfitter.net.maizegenetics.analysis.modelfitter.ForwardStepSubsettingAdditiveSpliterator
    net.maizegenetics.analysis.modelfitter.net.maizegenetics.analysis.modelfitter.ForwardStepSubsettingNestedAdditiveSpliterator
    net.maizegenetics.analysis.modelfitter.net.maizegenetics.analysis.modelfitter.GenotypeAdditiveSite
    net.maizegenetics.analysis.modelfitter.net.maizegenetics.analysis.modelfitter.NestedCovariatePermutationTestSpliterator
    net.maizegenetics.analysis.modelfitter.net.maizegenetics.analysis.modelfitter.RefProbAdditiveSite
    net.maizegenetics.analysis.modelfitter.net.maizegenetics.analysis.modelfitter.ResamplingGWASPlugin
    net.maizegenetics.analysis.modelfitter.net.maizegenetics.analysis.modelfitter.SNP
    net.maizegenetics.analysis.modelfitter.net.maizegenetics.analysis.modelfitter.StepwiseAddDomModelFitter
    net.maizegenetics.analysis.modelfitter.net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitter
    net.maizegenetics.analysis.modelfitter.net.maizegenetics.analysis.modelfitter.StepwiseAdditiveModelFitterPlugin
    net.maizegenetics.analysis.modelfitter.net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitter
    net.maizegenetics.analysis.modelfitter.net.maizegenetics.analysis.modelfitter.StepwiseOLSModelFitterPlugin
    net.maizegenetics.analysis.modelfitter.net.maizegenetics.analysis.modelfitter.package-info
    net.maizegenetics.analysis.modelfitter.net.maizegenetics.analysis.modelfitter.stepwise.gif
    net.maizegenetics.analysis.monetdb
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    net.maizegenetics.analysis.monetdb.net.maizegenetics.analysis.monetdb.ColumnsToBinarySNPOnlyTablePlugin
    net.maizegenetics.analysis.monetdb.net.maizegenetics.analysis.monetdb.ColumnsToBinaryUtils
    net.maizegenetics.analysis.monetdb.net.maizegenetics.analysis.monetdb.LittleEndianDataOutputStream
    net.maizegenetics.analysis.numericaltransform
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    net.maizegenetics.analysis.numericaltransform.net.maizegenetics.analysis.numericaltransform.AvgPhenotypeByTaxaPlugin
    net.maizegenetics.analysis.numericaltransform.net.maizegenetics.analysis.numericaltransform.BoxCoxTransformation
    net.maizegenetics.analysis.numericaltransform.net.maizegenetics.analysis.numericaltransform.BoxCoxTransformationPlugin
    net.maizegenetics.analysis.numericaltransform.net.maizegenetics.analysis.numericaltransform.ImputationByMean
    net.maizegenetics.analysis.numericaltransform.net.maizegenetics.analysis.numericaltransform.ImputationPlugin
    net.maizegenetics.analysis.numericaltransform.net.maizegenetics.analysis.numericaltransform.NumericalGenotypePlugin
    net.maizegenetics.analysis.numericaltransform.net.maizegenetics.analysis.numericaltransform.SubtractPhenotype
    net.maizegenetics.analysis.numericaltransform.net.maizegenetics.analysis.numericaltransform.SubtractPhenotypeByTaxaPlugin
    net.maizegenetics.analysis.numericaltransform.net.maizegenetics.analysis.numericaltransform.TransformDataDialog
    net.maizegenetics.analysis.numericaltransform.net.maizegenetics.analysis.numericaltransform.TransformDataPlugin
    net.maizegenetics.analysis.numericaltransform.net.maizegenetics.analysis.numericaltransform.kNearestNeighbors
    net.maizegenetics.analysis.numericaltransform.net.maizegenetics.analysis.numericaltransform.package-info
    net.maizegenetics.analysis
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    net.maizegenetics.analysis.phg
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    net.maizegenetics.analysis.popgen
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    net.maizegenetics.analysis.popgen.net.maizegenetics.analysis.popgen.LDResult
    net.maizegenetics.analysis.popgen.net.maizegenetics.analysis.popgen.LinkageDiseqDisplayPlugin
    net.maizegenetics.analysis.popgen.net.maizegenetics.analysis.popgen.LinkageDisequilibrium
    net.maizegenetics.analysis.popgen.net.maizegenetics.analysis.popgen.LinkageDisequilibriumComponent
    net.maizegenetics.analysis.popgen.net.maizegenetics.analysis.popgen.LinkageDisequilibriumMinimapComponent
    net.maizegenetics.analysis.popgen.net.maizegenetics.analysis.popgen.LinkageDisequilibriumPlugin
    net.maizegenetics.analysis.popgen.net.maizegenetics.analysis.popgen.PolymorphismDistribution
    net.maizegenetics.analysis.popgen.net.maizegenetics.analysis.popgen.SequenceDiversityPlugin
    net.maizegenetics.analysis.popgen.net.maizegenetics.analysis.popgen.package-info
    net.maizegenetics.analysis.rna
    net.maizegenetics.analysis.rna.net.maizegenetics.analysis.rna.FindMatchByWordHash
    net.maizegenetics.analysis.rna.net.maizegenetics.analysis.rna.LoadRNAContigsToGBSDBPlugin
    net.maizegenetics.analysis.rna.net.maizegenetics.analysis.rna.RNADeMultiPlexSeqToDBPlugin
    net.maizegenetics.analysis.rna.net.maizegenetics.analysis.rna.RNADeMultiplexProductionPlugin
    net.maizegenetics.analysis.tree
    net.maizegenetics.analysis.tree.net.maizegenetics.analysis.tree.ArchaeopteryxPlugin
    net.maizegenetics.analysis.tree.net.maizegenetics.analysis.tree.ConvertTreeNamesPlugin.kt
    net.maizegenetics.analysis.tree.net.maizegenetics.analysis.tree.CreateTreePlugin
    net.maizegenetics.analysis.tree.net.maizegenetics.analysis.tree.MergeTreesPlugin.kt
    net.maizegenetics.analysis.tree.net.maizegenetics.analysis.tree.RemoveBranchLengthsPlugin.kt
    net.maizegenetics.analysis.tree.net.maizegenetics.analysis.tree.SubsetTreePlugin.kt
    net.maizegenetics.analysis.tree.net.maizegenetics.analysis.tree.package-info
    net.maizegenetics.analysis.workflow
    net.maizegenetics.analysis.workflow.net.maizegenetics.analysis.workflow.GLM_(PCA).xml
    net.maizegenetics.analysis.workflow.net.maizegenetics.analysis.workflow.GLM_(Q).xml
    net.maizegenetics.analysis.workflow.net.maizegenetics.analysis.workflow.MLM_(PCA+K).xml
    net.maizegenetics.analysis.workflow.net.maizegenetics.analysis.workflow.MLM_(Q+K).xml
    net.maizegenetics.analysis.workflow.net.maizegenetics.analysis.workflow.Taxa_Quality_Control.xml
    net.maizegenetics.analysis.workflow.net.maizegenetics.analysis.workflow.WorkflowPlugin
    net.maizegenetics.dna
    net.maizegenetics.dna.net.maizegenetics.dna.BaseEncoder
    net.maizegenetics.dna.net.maizegenetics.dna.WHICH_ALLELE
    net.maizegenetics.dna.map
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.AbstractPETagsOnPhysicalMap
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.AbstractTagsOnPhysicalMap
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.Chromosome
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.DonorHaplotypes
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.GVCFGenomeSequence
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.GVCFGenomeSequenceBuilder
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.GeneralPosition
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.GenomeFeature
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.GenomeFeatureBuilder
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.GenomeFeatureMap
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.GenomeFeatureMapBuilder
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.GenomeSequence
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.GenomeSequenceBuilder
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.PETagsOnPhysicalMap
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.PETagsOnPhysicalMapV3
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.Position
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.PositionArrayList
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.PositionHDF5List
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.PositionList
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.PositionListBuilder
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.PositionListIOUtils
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.PositionListTableReport
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.TOPMInterface
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.TOPMTableReport
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.TOPMUtils
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.TagGWASMap
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.TagGWASMapInfo
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.TagGeneticMappingInfo
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.TagLocus
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.TagMappingInfo
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.TagMappingInfoV3
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.TagsOnGeneticMap
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.TagsOnPhysMapHDF5
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.TagsOnPhysicalMap
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.TagsOnPhysicalMapV3
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.UpdateTOPMWithGeneticMapping
    net.maizegenetics.dna.map.net.maizegenetics.dna.map.package-info
    net.maizegenetics.dna
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