Add a META.json to the distribution. Your buildtool should be able to autogenerate it.

Move your *.pm files in a directory named 'lib'. The directory structure should look like 'lib/Your/Module.pm' for a module named 'Your::Module'. If you need to provide additional files, e.g. for testing, that should not be considered for Kwalitee, then you should look at the 'provides' map in META.yml to limit the files scanned; or use the 'no_index' map to exclude parts of the distribution.

Error: Bio/Align/AlignI.pm, Bio/Align/DNAStatistics.pm, Bio/Align/PairwiseStatistics.pm, Bio/Align/ProteinStatistics.pm, Bio/Align/StatisticsI.pm, Bio/Align/Utilities.pm, Bio/AlignIO.pm, Bio/AlignIO/bl2seq.pm, Bio/AlignIO/clustalw.pm, Bio/AlignIO/emboss.pm, Bio/AlignIO/fasta.pm, Bio/AlignIO/largemultifasta.pm, Bio/AlignIO/maf.pm, Bio/AlignIO/mase.pm, Bio/AlignIO/mega.pm, Bio/AlignIO/meme.pm, Bio/AlignIO/metafasta.pm, Bio/AlignIO/msf.pm, Bio/AlignIO/nexus.pm, Bio/AlignIO/pfam.pm, Bio/AlignIO/phylip.pm, Bio/AlignIO/po.pm, Bio/AlignIO/prodom.pm, Bio/AlignIO/psi.pm, Bio/AlignIO/selex.pm, Bio/AlignIO/stockholm.pm, Bio/AnalysisI.pm, Bio/AnalysisI.pm, Bio/AnalysisParserI.pm, Bio/AnalysisResultI.pm, Bio/AnnotatableI.pm, Bio/Annotation/AnnotationFactory.pm, Bio/Annotation/Collection.pm, Bio/Annotation/Comment.pm, Bio/Annotation/DBLink.pm, Bio/Annotation/OntologyTerm.pm, Bio/Annotation/Reference.pm, Bio/Annotation/SimpleValue.pm, Bio/Annotation/StructuredValue.pm, Bio/Annotation/Target.pm, Bio/Annotation/TypeManager.pm, Bio/AnnotationCollectionI.pm, Bio/AnnotationI.pm, Bio/Assembly/Contig.pm, Bio/Assembly/ContigAnalysis.pm, Bio/Assembly/IO.pm, Bio/Assembly/IO/ace.pm, Bio/Assembly/IO/phrap.pm, Bio/Assembly/Scaffold.pm, Bio/Assembly/ScaffoldI.pm, Bio/Assembly/Singlet.pm, Bio/Biblio.pm, Bio/Biblio/Article.pm, Bio/Biblio/BiblioBase.pm, Bio/Biblio/Book.pm, Bio/Biblio/BookArticle.pm, Bio/Biblio/IO.pm, Bio/Biblio/IO/medline2ref.pm, Bio/Biblio/IO/medlinexml.pm, Bio/Biblio/IO/pubmed2ref.pm, Bio/Biblio/IO/pubmedxml.pm, Bio/Biblio/Journal.pm, Bio/Biblio/JournalArticle.pm, Bio/Biblio/MedlineArticle.pm, Bio/Biblio/MedlineBook.pm, Bio/Biblio/MedlineBookArticle.pm, Bio/Biblio/MedlineJournal.pm, Bio/Biblio/MedlineJournalArticle.pm, Bio/Biblio/Organisation.pm, Bio/Biblio/Patent.pm, Bio/Biblio/Person.pm, Bio/Biblio/Proceeding.pm, Bio/Biblio/Provider.pm, Bio/Biblio/PubmedArticle.pm, Bio/Biblio/PubmedBookArticle.pm, Bio/Biblio/PubmedJournalArticle.pm, Bio/Biblio/Ref.pm, Bio/Biblio/Service.pm, Bio/Biblio/TechReport.pm, Bio/Biblio/Thesis.pm, Bio/Biblio/WebResource.pm, Bio/Cluster/ClusterFactory.pm, Bio/Cluster/FamilyI.pm, Bio/Cluster/SequenceFamily.pm, Bio/Cluster/UniGene.pm, Bio/Cluster/UniGeneI.pm, Bio/ClusterI.pm, Bio/ClusterIO.pm, Bio/ClusterIO/dbsnp.pm, Bio/ClusterIO/unigene.pm, Bio/CodonUsage/IO.pm, Bio/CodonUsage/Table.pm, Bio/Coordinate/Chain.pm, Bio/Coordinate/Collection.pm, Bio/Coordinate/ExtrapolatingPair.pm, Bio/Coordinate/GeneMapper.pm, Bio/Coordinate/Graph.pm, Bio/Coordinate/MapperI.pm, Bio/Coordinate/Pair.pm, Bio/Coordinate/Result.pm, Bio/Coordinate/Result/Gap.pm, Bio/Coordinate/Result/Match.pm, Bio/Coordinate/ResultI.pm, Bio/Coordinate/Utils.pm, Bio/DB/Ace.pm, Bio/DB/Biblio/biofetch.pm, Bio/DB/Biblio/eutils.pm, Bio/DB/Biblio/pdf.pm, Bio/DB/Biblio/soap.pm, Bio/DB/BiblioI.pm, Bio/DB/BioFetch.pm, Bio/DB/CUTG.pm, Bio/DB/DBFetch.pm, Bio/DB/EMBL.pm, Bio/DB/EUtilities.pm, Bio/DB/EUtilities/Cookie.pm, Bio/DB/EUtilities/ElinkData.pm, Bio/DB/EUtilities/efetch.pm, Bio/DB/EUtilities/egquery.pm, Bio/DB/EUtilities/einfo.pm, Bio/DB/EUtilities/elink.pm, Bio/DB/EUtilities/epost.pm, Bio/DB/EUtilities/esearch.pm, Bio/DB/EUtilities/esummary.pm, Bio/DB/EntrezGene.pm, Bio/DB/Expression.pm, Bio/DB/Expression/geo.pm, Bio/DB/Failover.pm, Bio/DB/Fasta.pm, Bio/DB/Fasta.pm, Bio/DB/FileCache.pm, Bio/DB/Flat.pm, Bio/DB/Flat/BDB.pm, Bio/DB/Flat/BDB/embl.pm, Bio/DB/Flat/BDB/fasta.pm, Bio/DB/Flat/BDB/genbank.pm, Bio/DB/Flat/BDB/swiss.pm, Bio/DB/Flat/BDB/swissprot.pm, Bio/DB/Flat/BinarySearch.pm, Bio/DB/GDB.pm, Bio/DB/GFF.pm, Bio/DB/GFF/Adaptor/ace.pm, Bio/DB/GFF/Adaptor/berkeleydb.pm, Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm, Bio/DB/GFF/Adaptor/biofetch.pm, Bio/DB/GFF/Adaptor/biofetch_oracle.pm, Bio/DB/GFF/Adaptor/dbi.pm, Bio/DB/GFF/Adaptor/dbi/caching_handle.pm, Bio/DB/GFF/Adaptor/dbi/caching_handle.pm, Bio/DB/GFF/Adaptor/dbi/iterator.pm, Bio/DB/GFF/Adaptor/dbi/mysql.pm, Bio/DB/GFF/Adaptor/dbi/mysqlace.pm, Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm, Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm, Bio/DB/GFF/Adaptor/dbi/oracle.pm, Bio/DB/GFF/Adaptor/dbi/oracleace.pm, Bio/DB/GFF/Adaptor/dbi/pg.pm, Bio/DB/GFF/Adaptor/dbi/pg_fts.pm, Bio/DB/GFF/Adaptor/memory.pm, Bio/DB/GFF/Adaptor/memory/feature_serializer.pm, Bio/DB/GFF/Adaptor/memory/iterator.pm, Bio/DB/GFF/Aggregator.pm, Bio/DB/GFF/Aggregator/alignment.pm, Bio/DB/GFF/Aggregator/clone.pm, Bio/DB/GFF/Aggregator/coding.pm, Bio/DB/GFF/Aggregator/match.pm, Bio/DB/GFF/Aggregator/none.pm, Bio/DB/GFF/Aggregator/processed_transcript.pm, Bio/DB/GFF/Aggregator/so_transcript.pm, Bio/DB/GFF/Aggregator/transcript.pm, Bio/DB/GFF/Aggregator/ucsc_acembly.pm, Bio/DB/GFF/Aggregator/ucsc_ensgene.pm, Bio/DB/GFF/Aggregator/ucsc_genscan.pm, Bio/DB/GFF/Aggregator/ucsc_refgene.pm, Bio/DB/GFF/Aggregator/ucsc_sanger22.pm, Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm, Bio/DB/GFF/Aggregator/ucsc_softberry.pm, Bio/DB/GFF/Aggregator/ucsc_twinscan.pm, Bio/DB/GFF/Aggregator/ucsc_unigene.pm, Bio/DB/GFF/Featname.pm, Bio/DB/GFF/Feature.pm, Bio/DB/GFF/Homol.pm, Bio/DB/GFF.pm, Bio/DB/GFF/RelSegment.pm, Bio/DB/GFF/Segment.pm, Bio/DB/GFF/Typename.pm, Bio/DB/GFF/Util/Binning.pm, Bio/DB/GFF/Util/Rearrange.pm, Bio/DB/GenBank.pm, Bio/DB/GenPept.pm, Bio/DB/GenericWebDBI.pm, Bio/DB/InMemoryCache.pm, Bio/DB/LocationI.pm, Bio/DB/MeSH.pm, Bio/DB/NCBIHelper.pm, Bio/DB/Query/GenBank.pm, Bio/DB/Query/WebQuery.pm, Bio/DB/QueryI.pm, Bio/DB/RandomAccessI.pm, Bio/DB/RefSeq.pm, Bio/DB/ReferenceI.pm, Bio/DB/Registry.pm, Bio/DB/SeqFeature.pm, Bio/DB/SeqFeature/NormalizedFeature.pm, Bio/DB/SeqFeature/NormalizedFeatureI.pm, Bio/DB/SeqFeature/NormalizedTableFeatureI.pm, Bio/DB/SeqFeature/Segment.pm, Bio/DB/SeqFeature/Store.pm, Bio/DB/SeqFeature/Store/DBI/Iterator.pm, Bio/DB/SeqFeature/Store/DBI/mysql.pm, Bio/DB/SeqFeature/Store/GFF3Loader.pm, Bio/DB/SeqFeature/Store/bdb.pm, Bio/DB/SeqFeature/Store/berkeleydb.pm, Bio/DB/SeqFeature/Store/berkeleydb.pm, Bio/DB/SeqFeature/Store/memory.pm, Bio/DB/SeqFeature/Store/memory.pm, Bio/DB/SeqHound.pm, Bio/DB/SeqI.pm, Bio/DB/SeqVersion.pm, Bio/DB/SeqVersion/gi.pm, Bio/DB/SwissProt.pm, Bio/DB/Taxonomy.pm, Bio/DB/Taxonomy/entrez.pm, Bio/DB/Taxonomy/flatfile.pm, Bio/DB/Taxonomy/list.pm, Bio/DB/Universal.pm, Bio/DB/UpdateableSeqI.pm, Bio/DB/WebDBSeqI.pm, Bio/DB/XEMBL.pm, Bio/DB/XEMBLService.pm, Bio/DBLinkContainerI.pm, Bio/Das/FeatureTypeI.pm, Bio/Das/SegmentI.pm, Bio/DasI.pm, Bio/DescribableI.pm, Bio/Event/EventGeneratorI.pm, Bio/Event/EventHandlerI.pm, Bio/Expression/Contact.pm, Bio/Expression/DataSet.pm, Bio/Expression/FeatureGroup.pm, Bio/Expression/FeatureGroup/FeatureGroupMas50.pm, Bio/Expression/FeatureI.pm, Bio/Expression/FeatureSet/FeatureSetMas50.pm, Bio/Expression/Platform.pm, Bio/Expression/ProbeI.pm, Bio/Expression/Sample.pm, Bio/Factory/AnalysisI.pm, Bio/Factory/ApplicationFactoryI.pm, Bio/Factory/DriverFactory.pm, Bio/Factory/FTLocationFactory.pm, Bio/Factory/HitFactoryI.pm, Bio/Factory/LocationFactoryI.pm, Bio/Factory/MapFactoryI.pm, Bio/Factory/ObjectBuilderI.pm, Bio/Factory/ObjectFactory.pm, Bio/Factory/ObjectFactoryI.pm, Bio/Factory/ResultFactoryI.pm, Bio/Factory/SeqAnalysisParserFactory.pm, Bio/Factory/SeqAnalysisParserFactoryI.pm, Bio/Factory/SequenceFactoryI.pm, Bio/Factory/SequenceProcessorI.pm, Bio/Factory/SequenceStreamI.pm, Bio/Factory/TreeFactoryI.pm, Bio/FeatureHolderI.pm, Bio/FeatureIO.pm, Bio/FeatureIO/bed.pm, Bio/FeatureIO/gff.pm, Bio/FeatureIO/gtf.pm, Bio/FeatureIO/interpro.pm, Bio/FeatureIO/ptt.pm, Bio/Graph/Edge.pm, Bio/Graph/IO.pm, Bio/Graph/IO/dip.pm, Bio/Graph/IO/psi_xml.pm, Bio/Graph/ProteinGraph.pm, Bio/Graph/SimpleGraph.pm, Bio/Graph/SimpleGraph/Traversal.pm, Bio/Graphics.pm, Bio/Graphics/ConfiguratorI.pm, Bio/Graphics/Feature.pm, Bio/Graphics/FeatureBase.pm, Bio/Graphics/FeatureFile.pm, Bio/Graphics/FeatureFile/Iterator.pm, Bio/Graphics/Glyph.pm, Bio/Graphics/Glyph/Factory.pm, Bio/Graphics/Glyph/alignment.pm, Bio/Graphics/Glyph/anchored_arrow.pm, Bio/Graphics/Glyph/arrow.pm, Bio/Graphics/Glyph/box.pm, Bio/Graphics/Glyph/broken_line.pm, Bio/Graphics/Glyph/cds.pm, Bio/Graphics/Glyph/christmas_arrow.pm, Bio/Graphics/Glyph/crossbox.pm, Bio/Graphics/Glyph/dashed_line.pm, Bio/Graphics/Glyph/diamond.pm, Bio/Graphics/Glyph/dna.pm, Bio/Graphics/Glyph/dot.pm, Bio/Graphics/Glyph/dumbbell.pm, Bio/Graphics/Glyph/ellipse.pm, Bio/Graphics/Glyph/ex.pm, Bio/Graphics/Glyph/extending_arrow.pm, Bio/Graphics/Glyph/flag.pm, Bio/Graphics/Glyph/gene.pm, Bio/Graphics/Glyph/generic.pm, Bio/Graphics/Glyph/graded_segments.pm, Bio/Graphics/Glyph/group.pm, Bio/Graphics/Glyph/heterogeneous_segments.pm, Bio/Graphics/Glyph/image.pm, Bio/Graphics/Glyph/lightning.pm, Bio/Graphics/Glyph/line.pm, Bio/Graphics/Glyph/merge_parts.pm, Bio/Graphics/Glyph/merged_alignment.pm, Bio/Graphics/Glyph/minmax.pm, Bio/Graphics/Glyph/oval.pm, Bio/Graphics/Glyph/pentagram.pm, Bio/Graphics/Glyph/pinsertion.pm, Bio/Graphics/Glyph/primers.pm, Bio/Graphics/Glyph/processed_transcript.pm, Bio/Graphics/Glyph/protein.pm, Bio/Graphics/Glyph/ragged_ends.pm, Bio/Graphics/Glyph/redgreen_box.pm, Bio/Graphics/Glyph/redgreen_segment.pm, Bio/Graphics/Glyph/repeating_shape.pm, Bio/Graphics/Glyph/rndrect.pm, Bio/Graphics/Glyph/ruler_arrow.pm, Bio/Graphics/Glyph/saw_teeth.pm, Bio/Graphics/Glyph/segmented_keyglyph.pm, Bio/Graphics/Glyph/segments.pm, Bio/Graphics/Glyph/so_transcript.pm, Bio/Graphics/Glyph/span.pm, Bio/Graphics/Glyph/splice_site.pm, Bio/Graphics/Glyph/text_in_box.pm, Bio/Graphics/Glyph/three_letters.pm, Bio/Graphics/Glyph/tic_tac_toe.pm, Bio/Graphics/Glyph/toomany.pm, Bio/Graphics/Glyph/track.pm, Bio/Graphics/Glyph/transcript.pm, Bio/Graphics/Glyph/transcript2.pm, Bio/Graphics/Glyph/translation.pm, Bio/Graphics/Glyph/triangle.pm, Bio/Graphics/Glyph/two_bolts.pm, Bio/Graphics/Glyph/wave.pm, Bio/Graphics/Glyph/weighted_arrow.pm, Bio/Graphics/Glyph/whiskerplot.pm, Bio/Graphics/Glyph/xyplot.pm, Bio/Graphics/Panel.pm, Bio/Graphics/Pictogram.pm, Bio/Graphics/RendererI.pm, Bio/Graphics/Util.pm, Bio/IdCollectionI.pm, Bio/IdentifiableI.pm, Bio/Index/Abstract.pm, Bio/Index/AbstractSeq.pm, Bio/Index/Blast.pm, Bio/Index/EMBL.pm, Bio/Index/Fasta.pm, Bio/Index/Fastq.pm, Bio/Index/GenBank.pm, Bio/Index/Hmmer.pm, Bio/Index/Qual.pm, Bio/Index/SwissPfam.pm, Bio/Index/Swissprot.pm, Bio/LiveSeq/AARange.pm, Bio/LiveSeq/Chain.pm, Bio/LiveSeq/ChainI.pm, Bio/LiveSeq/DNA.pm, Bio/LiveSeq/Exon.pm, Bio/LiveSeq/Gene.pm, Bio/LiveSeq/IO/BioPerl.pm, Bio/LiveSeq/IO/Loader.pm, Bio/LiveSeq/Intron.pm, Bio/LiveSeq/Mutation.pm, Bio/LiveSeq/Mutator.pm, Bio/LiveSeq/Prim_Transcript.pm, Bio/LiveSeq/Range.pm, Bio/LiveSeq/Repeat_Region.pm, Bio/LiveSeq/Repeat_Unit.pm, Bio/LiveSeq/SeqI.pm, Bio/LiveSeq/Transcript.pm, Bio/LiveSeq/Translation.pm, Bio/LocatableSeq.pm, Bio/Location/Atomic.pm, Bio/Location/AvWithinCoordPolicy.pm, Bio/Location/CoordinatePolicyI.pm, Bio/Location/Fuzzy.pm, Bio/Location/FuzzyLocationI.pm, Bio/Location/NarrowestCoordPolicy.pm, Bio/Location/Simple.pm, Bio/Location/Split.pm, Bio/Location/SplitLocationI.pm, Bio/Location/WidestCoordPolicy.pm, Bio/LocationI.pm, Bio/Map/Clone.pm, Bio/Map/Contig.pm, Bio/Map/CytoMap.pm, Bio/Map/CytoMarker.pm, Bio/Map/CytoPosition.pm, Bio/Map/EntityI.pm, Bio/Map/FPCMarker.pm, Bio/Map/LinkageMap.pm, Bio/Map/LinkagePosition.pm, Bio/Map/MapI.pm, Bio/Map/Mappable.pm, Bio/Map/MappableI.pm, Bio/Map/Marker.pm, Bio/Map/MarkerI.pm, Bio/Map/Microsatellite.pm, Bio/Map/OrderedPosition.pm, Bio/Map/OrderedPositionWithDistance.pm, Bio/Map/Physical.pm, Bio/Map/Position.pm, Bio/Map/PositionHandler.pm, Bio/Map/PositionHandlerI.pm, Bio/Map/PositionI.pm, Bio/Map/Relative.pm, Bio/Map/RelativeI.pm, Bio/Map/SimpleMap.pm, Bio/MapIO.pm, Bio/MapIO/fpc.pm, Bio/MapIO/mapmaker.pm, Bio/Matrix/Generic.pm, Bio/Matrix/IO.pm, Bio/Matrix/IO/phylip.pm, Bio/Matrix/IO/scoring.pm, Bio/Matrix/MatrixI.pm, Bio/Matrix/PSM/IO.pm, Bio/Matrix/PSM/IO/mast.pm, Bio/Matrix/PSM/IO/masta.pm, Bio/Matrix/PSM/IO/meme.pm, Bio/Matrix/PSM/IO/psiblast.pm, Bio/Matrix/PSM/IO/transfac.pm, Bio/Matrix/PSM/InstanceSite.pm, Bio/Matrix/PSM/InstanceSiteI.pm, Bio/Matrix/PSM/ProtMatrix.pm, Bio/Matrix/PSM/ProtPsm.pm, Bio/Matrix/PSM/Psm.pm, Bio/Matrix/PSM/PsmHeader.pm, Bio/Matrix/PSM/PsmHeaderI.pm, Bio/Matrix/PSM/PsmI.pm, Bio/Matrix/PSM/SiteMatrix.pm, Bio/Matrix/PSM/SiteMatrixI.pm, Bio/Matrix/PhylipDist.pm, Bio/Matrix/Scoring.pm, Bio/Ontology/DocumentRegistry.pm, Bio/Ontology/GOterm.pm, Bio/Ontology/InterProTerm.pm, Bio/Ontology/OBOEngine.pm, Bio/Ontology/OBOterm.pm, Bio/Ontology/Ontology.pm, Bio/Ontology/OntologyEngineI.pm, Bio/Ontology/OntologyI.pm, Bio/Ontology/OntologyStore.pm, Bio/Ontology/Path.pm, Bio/Ontology/PathI.pm, Bio/Ontology/Relationship.pm, Bio/Ontology/RelationshipFactory.pm, Bio/Ontology/RelationshipI.pm, Bio/Ontology/RelationshipType.pm, Bio/Ontology/SimpleGOEngine.pm, Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm, Bio/Ontology/SimpleGOEngine/GraphAdaptor02.pm, Bio/Ontology/SimpleOntologyEngine.pm, Bio/Ontology/Term.pm, Bio/Ontology/TermFactory.pm, Bio/Ontology/TermI.pm, Bio/OntologyIO.pm, Bio/OntologyIO/Handlers/BaseSAXHandler.pm, Bio/OntologyIO/Handlers/InterProHandler.pm, Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm, Bio/OntologyIO/InterProParser.pm, Bio/OntologyIO/dagflat.pm, Bio/OntologyIO/goflat.pm, Bio/OntologyIO/obo.pm, Bio/OntologyIO/simplehierarchy.pm, Bio/OntologyIO/soflat.pm, Bio/Perl.pm, Bio/Phenotype/Correlate.pm, Bio/Phenotype/MeSH/Term.pm, Bio/Phenotype/MeSH/Twig.pm, Bio/Phenotype/Measure.pm, Bio/Phenotype/OMIM/MiniMIMentry.pm, Bio/Phenotype/OMIM/OMIMentry.pm, Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm, Bio/Phenotype/OMIM/OMIMparser.pm, Bio/Phenotype/Phenotype.pm, Bio/Phenotype/PhenotypeI.pm, Bio/PopGen/Genotype.pm, Bio/PopGen/GenotypeI.pm, Bio/PopGen/HtSNP.pm, Bio/PopGen/IO.pm, Bio/PopGen/IO/csv.pm, Bio/PopGen/IO/hapmap.pm, Bio/PopGen/IO/phase.pm, Bio/PopGen/IO/prettybase.pm, Bio/PopGen/Individual.pm, Bio/PopGen/IndividualI.pm, Bio/PopGen/Marker.pm, Bio/PopGen/MarkerI.pm, Bio/PopGen/PopStats.pm, Bio/PopGen/Population.pm, Bio/PopGen/PopulationI.pm, Bio/PopGen/Simulation/Coalescent.pm, Bio/PopGen/Simulation/GeneticDrift.pm, Bio/PopGen/Statistics.pm, Bio/PopGen/TagHaplotype.pm, Bio/PopGen/Utilities.pm, Bio/PrimarySeq.pm, Bio/DB/Fasta.pm, Bio/PrimarySeqI.pm, Bio/PullParserI.pm, Bio/Range.pm, Bio/RangeI.pm, Bio/Restriction/Analysis.pm, Bio/Restriction/Enzyme.pm, Bio/Restriction/Enzyme/MultiCut.pm, Bio/Restriction/Enzyme/MultiSite.pm, Bio/Restriction/EnzymeCollection.pm, Bio/Restriction/EnzymeI.pm, Bio/Restriction/IO.pm, Bio/Restriction/IO/bairoch.pm, Bio/Restriction/IO/base.pm, Bio/Restriction/IO/itype2.pm, Bio/Restriction/IO/withrefm.pm, Bio/Root/Exception.pm, Bio/Root/HTTPget.pm, Bio/Root/IO.pm, Bio/Root/Root.pm, Bio/Root/RootI.pm, Bio/Root/Storable.pm, Bio/Root/Version.pm, Bio/Search/BlastStatistics.pm, Bio/Search/BlastUtils.pm, Bio/Search/DatabaseI.pm, Bio/Search/GenericDatabase.pm, Bio/Search/GenericStatistics.pm, Bio/Search/HSP/BlastHSP.pm, Bio/Search/HSP/FastaHSP.pm, Bio/Search/HSP/GenericHSP.pm, Bio/Search/HSP/HMMERHSP.pm, Bio/Search/HSP/HSPFactory.pm, Bio/Search/HSP/HSPI.pm, Bio/Search/HSP/HmmpfamHSP.pm, Bio/Search/HSP/PSLHSP.pm, Bio/Search/HSP/PsiBlastHSP.pm, Bio/Search/HSP/PullHSPI.pm, Bio/Search/HSP/WABAHSP.pm, Bio/Search/Hit/BlastHit.pm, Bio/Search/Hit/Fasta.pm, Bio/Search/Hit/GenericHit.pm, Bio/Search/Hit/HMMERHit.pm, Bio/Search/Hit/HitFactory.pm, Bio/Search/Hit/HitI.pm, Bio/Search/Hit/HmmpfamHit.pm, Bio/Search/Hit/PsiBlastHit.pm, Bio/Search/Hit/PullHitI.pm, Bio/Search/Iteration/GenericIteration.pm, Bio/Search/Iteration/IterationI.pm, Bio/Search/Processor.pm, Bio/Search/Result/BlastResult.pm, Bio/Search/Result/GenericResult.pm, Bio/Search/Result/HMMERResult.pm, Bio/Search/Result/HmmpfamResult.pm, Bio/Search/Result/PullResultI.pm, Bio/Search/Result/ResultFactory.pm, Bio/Search/Result/ResultI.pm, Bio/Search/Result/WABAResult.pm, Bio/Search/SearchUtils.pm, Bio/Search/StatisticsI.pm, Bio/SearchDist.pm, Bio/SearchIO.pm, Bio/SearchIO/EventHandlerI.pm, Bio/SearchIO/FastHitEventBuilder.pm, Bio/SearchIO/IteratedSearchResultEventBuilder.pm, Bio/SearchIO/SearchResultEventBuilder.pm, Bio/SearchIO/SearchWriterI.pm, Bio/SearchIO/Writer/BSMLResultWriter.pm, Bio/SearchIO/Writer/GbrowseGFF.pm, Bio/SearchIO/Writer/HSPTableWriter.pm, Bio/SearchIO/Writer/HTMLResultWriter.pm, Bio/SearchIO/Writer/HitTableWriter.pm, Bio/SearchIO/Writer/ResultTableWriter.pm, Bio/SearchIO/Writer/TextResultWriter.pm, Bio/SearchIO/axt.pm, Bio/SearchIO/blast.pm, Bio/SearchIO/blasttable.pm, Bio/SearchIO/blastxml.pm, Bio/SearchIO/exonerate.pm, Bio/SearchIO/fasta.pm, Bio/SearchIO/hmmer.pm, Bio/SearchIO/hmmer_pull.pm, Bio/SearchIO/megablast.pm, Bio/SearchIO/psl.pm, Bio/SearchIO/sim4.pm, Bio/SearchIO/waba.pm, Bio/SearchIO/wise.pm, Bio/Seq.pm, Bio/Seq/BaseSeqProcessor.pm, Bio/Seq/EncodedSeq.pm, Bio/Seq/LargeLocatableSeq.pm, Bio/Seq/LargePrimarySeq.pm, Bio/Seq/LargeSeq.pm, Bio/Seq/LargeSeqI.pm, Bio/Seq/Meta.pm, Bio/Seq/Meta/Array.pm, Bio/Seq/MetaI.pm, Bio/Seq/PrimaryQual.pm, Bio/Seq/PrimedSeq.pm, Bio/Seq/QualI.pm, Bio/Seq/Quality.pm, Bio/Seq/RichSeq.pm, Bio/Seq/RichSeqI.pm, Bio/Seq/SeqBuilder.pm, Bio/Seq/SeqFactory.pm, Bio/Seq/SeqFastaSpeedFactory.pm, Bio/Seq/SeqWithQuality.pm, Bio/Seq/SequenceTrace.pm, Bio/Seq/TraceI.pm, Bio/SeqAnalysisParserI.pm, Bio/SeqFeature/Annotated.pm, Bio/SeqFeature/AnnotationAdaptor.pm, Bio/SeqFeature/Collection.pm, Bio/SeqFeature/CollectionI.pm, Bio/SeqFeature/Computation.pm, Bio/SeqFeature/FeaturePair.pm, Bio/SeqFeature/Gene/Exon.pm, Bio/SeqFeature/Gene/ExonI.pm, Bio/SeqFeature/Gene/GeneStructure.pm, Bio/SeqFeature/Gene/GeneStructureI.pm, Bio/SeqFeature/Gene/Intron.pm, Bio/SeqFeature/Gene/NC_Feature.pm, Bio/SeqFeature/Gene/Poly_A_site.pm, Bio/SeqFeature/Gene/Promoter.pm, Bio/SeqFeature/Gene/Transcript.pm, Bio/SeqFeature/Gene/TranscriptI.pm, Bio/SeqFeature/Gene/UTR.pm, Bio/SeqFeature/Generic.pm, Bio/SeqFeature/PositionProxy.pm, Bio/SeqFeature/Primer.pm, Bio/SeqFeature/SiRNA/Oligo.pm, Bio/SeqFeature/SiRNA/Pair.pm, Bio/SeqFeature/Similarity.pm, Bio/SeqFeature/SimilarityPair.pm, Bio/SeqFeature/Tools/FeatureNamer.pm, Bio/SeqFeature/Tools/IDHandler.pm, Bio/SeqFeature/Tools/TypeMapper.pm, Bio/SeqFeature/Tools/Unflattener.pm, Bio/SeqFeature/TypedSeqFeatureI.pm, Bio/SeqFeatureI.pm, Bio/SeqI.pm, Bio/SeqIO.pm, Bio/SeqIO/FTHelper.pm, Bio/SeqIO/MultiFile.pm, Bio/SeqIO/abi.pm, Bio/SeqIO/ace.pm, Bio/SeqIO/agave.pm, Bio/SeqIO/alf.pm, Bio/SeqIO/asciitree.pm, Bio/SeqIO/bsml.pm, Bio/SeqIO/bsml_sax.pm, Bio/SeqIO/chadoxml.pm, Bio/SeqIO/chaos.pm, Bio/SeqIO/chaosxml.pm, Bio/SeqIO/ctf.pm, Bio/SeqIO/embl.pm, Bio/SeqIO/entrezgene.pm, Bio/SeqIO/excel.pm, Bio/SeqIO/exp.pm, Bio/SeqIO/fasta.pm, Bio/SeqIO/fastq.pm, Bio/SeqIO/game.pm, Bio/SeqIO/game/featHandler.pm, Bio/SeqIO/game/gameHandler.pm, Bio/SeqIO/game/gameSubs.pm, Bio/SeqIO/game/gameWriter.pm, Bio/SeqIO/game/seqHandler.pm, Bio/SeqIO/gcg.pm, Bio/SeqIO/genbank.pm, Bio/SeqIO/interpro.pm, Bio/SeqIO/kegg.pm, Bio/SeqIO/largefasta.pm, Bio/SeqIO/lasergene.pm, Bio/SeqIO/locuslink.pm, Bio/SeqIO/metafasta.pm, Bio/SeqIO/phd.pm, Bio/SeqIO/pir.pm, Bio/SeqIO/pln.pm, Bio/SeqIO/qual.pm, Bio/SeqIO/raw.pm, Bio/SeqIO/scf.pm, Bio/SeqIO/strider.pm, Bio/SeqIO/swiss.pm, Bio/SeqIO/tab.pm, Bio/SeqIO/table.pm, Bio/SeqIO/tigr.pm, Bio/SeqIO/tigrxml.pm, Bio/SeqIO/tinyseq.pm, Bio/SeqIO/tinyseq/tinyseqHandler.pm, Bio/SeqIO/ztr.pm, Bio/SeqUtils.pm, Bio/SimpleAlign.pm, Bio/SimpleAnalysisI.pm, Bio/Species.pm, Bio/Structure/Atom.pm, Bio/Structure/Chain.pm, Bio/Structure/Entry.pm, Bio/Structure/IO.pm, Bio/Structure/IO/pdb.pm, Bio/Structure/Model.pm, Bio/Structure/Residue.pm, Bio/Structure/SecStr/DSSP/Res.pm, Bio/Structure/SecStr/STRIDE/Res.pm, Bio/Structure/StructureI.pm, Bio/Symbol/Alphabet.pm, Bio/Symbol/AlphabetI.pm, Bio/Symbol/DNAAlphabet.pm, Bio/Symbol/ProteinAlphabet.pm, Bio/Symbol/Symbol.pm, Bio/Symbol/SymbolI.pm, Bio/Taxon.pm, Bio/Taxonomy.pm, Bio/Taxonomy/FactoryI.pm, Bio/Taxonomy/Node.pm, Bio/Taxonomy/Taxon.pm, Bio/Taxonomy/Tree.pm, Bio/Tools/AlignFactory.pm, Bio/Tools/Alignment/Consed.pm, Bio/Tools/Alignment/Trim.pm, Bio/Tools/Analysis/DNA/ESEfinder.pm, Bio/Tools/Analysis/Protein/Domcut.pm, Bio/Tools/Analysis/Protein/ELM.pm, Bio/Tools/Analysis/Protein/GOR4.pm, Bio/Tools/Analysis/Protein/HNN.pm, Bio/Tools/Analysis/Protein/Mitoprot.pm, Bio/Tools/Analysis/Protein/NetPhos.pm, Bio/Tools/Analysis/Protein/Scansite.pm, Bio/Tools/Analysis/Protein/Sopma.pm, Bio/Tools/Analysis/SimpleAnalysisBase.pm, Bio/Tools/AnalysisResult.pm, Bio/Tools/BPbl2seq.pm, Bio/Tools/BPlite.pm, Bio/Tools/BPlite/HSP.pm, Bio/Tools/BPlite/Iteration.pm, Bio/Tools/BPlite/Sbjct.pm, Bio/Tools/BPpsilite.pm, Bio/Tools/Blat.pm, Bio/Tools/CodonTable.pm, Bio/Tools/Coil.pm, Bio/Tools/ECnumber.pm, Bio/Tools/EMBOSS/Palindrome.pm, Bio/Tools/EPCR.pm, Bio/Tools/ERPIN.pm, Bio/Tools/ESTScan.pm, Bio/Tools/Eponine.pm, Bio/Tools/Est2Genome.pm, Bio/Tools/Fgenesh.pm, Bio/Tools/FootPrinter.pm, Bio/Tools/GFF.pm, Bio/Tools/Gel.pm, Bio/Tools/Geneid.pm, Bio/Tools/Genemark.pm, Bio/Tools/Genewise.pm, Bio/Tools/Genomewise.pm, Bio/Tools/Genscan.pm, Bio/Tools/Glimmer.pm, Bio/Tools/Grail.pm, Bio/Tools/GuessSeqFormat.pm, Bio/Tools/HMM.pm, Bio/Tools/HMMER/Domain.pm, Bio/Tools/HMMER/Results.pm, Bio/Tools/HMMER/Set.pm, Bio/Tools/Hmmpfam.pm, Bio/Tools/IUPAC.pm, Bio/Tools/Lucy.pm, Bio/Tools/MZEF.pm, Bio/Tools/OddCodes.pm, Bio/Tools/Phylo/Molphy.pm, Bio/Tools/Phylo/Molphy/Result.pm, Bio/Tools/Phylo/PAML.pm, Bio/Tools/Phylo/PAML/ModelResult.pm, Bio/Tools/Phylo/PAML/Result.pm, Bio/Tools/Phylo/Phylip/ProtDist.pm, Bio/Tools/Prediction/Exon.pm, Bio/Tools/Prediction/Gene.pm, Bio/Tools/Primer3.pm, Bio/Tools/Primer/Assessor/Base.pm, Bio/Tools/Primer/AssessorI.pm, Bio/Tools/Primer/Feature.pm, Bio/Tools/Primer/Pair.pm, Bio/Tools/Prints.pm, Bio/Tools/Profile.pm, Bio/Tools/Promoterwise.pm, Bio/Tools/PrositeScan.pm, Bio/Tools/Pseudowise.pm, Bio/Tools/QRNA.pm, Bio/Tools/RNAMotif.pm, Bio/Tools/RandomDistFunctions.pm, Bio/Tools/RepeatMasker.pm, Bio/Tools/RestrictionEnzyme.pm, Bio/Tools/Run/GenericParameters.pm, Bio/Tools/Run/ParametersI.pm, Bio/Tools/Run/RemoteBlast.pm, Bio/Tools/Run/StandAloneBlast.pm, Bio/Tools/Run/WrapperBase.pm, Bio/Tools/Seg.pm, Bio/Tools/SeqPattern.pm, Bio/Tools/SeqStats.pm, Bio/Tools/SeqWords.pm, Bio/Tools/SiRNA.pm, Bio/Tools/SiRNA/Ruleset/saigo.pm, Bio/Tools/SiRNA/Ruleset/tuschl.pm, Bio/Tools/Sigcleave.pm, Bio/Tools/Signalp.pm, Bio/Tools/Sim4/Exon.pm, Bio/Tools/Sim4/Results.pm, Bio/Tools/Spidey/Exon.pm, Bio/Tools/Spidey/Results.pm, Bio/Tools/Tmhmm.pm, Bio/Tools/dpAlign.pm, Bio/Tools/ipcress.pm, Bio/Tools/isPcr.pm, Bio/Tools/pICalculator.pm, Bio/Tools/pSW.pm, Bio/Tools/tRNAscanSE.pm, Bio/Tree/AlleleNode.pm, Bio/Tree/Compatible.pm, Bio/Tree/DistanceFactory.pm, Bio/Tree/Draw/Cladogram.pm, Bio/Tree/Node.pm, Bio/Tree/NodeI.pm, Bio/Tree/NodeNHX.pm, Bio/Tree/RandomFactory.pm, Bio/Tree/Statistics.pm, Bio/Tree/Tree.pm, Bio/Tree/TreeFunctionsI.pm, Bio/Tree/TreeI.pm, Bio/TreeIO.pm, Bio/TreeIO/TreeEventBuilder.pm, Bio/TreeIO/cluster.pm, Bio/TreeIO/lintree.pm, Bio/TreeIO/newick.pm, Bio/TreeIO/nexus.pm, Bio/TreeIO/nhx.pm, Bio/TreeIO/pag.pm, Bio/TreeIO/svggraph.pm, Bio/TreeIO/tabtree.pm, Bio/UpdateableSeqI.pm, Bio/Variation/AAChange.pm, Bio/Variation/AAReverseMutate.pm, Bio/Variation/Allele.pm, Bio/Variation/DNAMutation.pm, Bio/Variation/IO.pm, Bio/Variation/IO/flat.pm, Bio/Variation/IO/xml.pm, Bio/Variation/RNAChange.pm, Bio/Variation/SNP.pm, Bio/Variation/SeqDiff.pm, Bio/Variation/VariantI.pm, Bio/WebAgent.pm, Bio/DB/GFF/Adaptor/berkeleydb.pm

Add 'use warnings' (or its equivalents) to all modules, or convince us that your favorite module is well-known enough and people can easily see the modules warn when something bad happens.

Error: Bio::Align::AlignI, Bio::Align::DNAStatistics, Bio::Align::PairwiseStatistics, Bio::Align::ProteinStatistics, Bio::Align::StatisticsI, Bio::Align::Utilities, Bio::AlignIO, Bio::AlignIO::bl2seq, Bio::AlignIO::clustalw, Bio::AlignIO::emboss, Bio::AlignIO::fasta, Bio::AlignIO::largemultifasta, Bio::AlignIO::maf, Bio::AlignIO::mase, Bio::AlignIO::mega, Bio::AlignIO::meme, Bio::AlignIO::metafasta, Bio::AlignIO::msf, Bio::AlignIO::nexus, Bio::AlignIO::pfam, Bio::AlignIO::phylip, Bio::AlignIO::po, Bio::AlignIO::prodom, Bio::AlignIO::psi, Bio::AlignIO::selex, Bio::AlignIO::stockholm, Bio::AnalysisI, Bio::AnalysisParserI, Bio::AnalysisResultI, Bio::AnnotatableI, Bio::Annotation::AnnotationFactory, Bio::Annotation::Collection, Bio::Annotation::Comment, Bio::Annotation::DBLink, Bio::Annotation::OntologyTerm, Bio::Annotation::Reference, Bio::Annotation::SimpleValue, Bio::Annotation::StructuredValue, Bio::Annotation::Target, Bio::Annotation::TypeManager, Bio::AnnotationCollectionI, Bio::AnnotationI, Bio::Assembly::Contig, Bio::Assembly::ContigAnalysis, Bio::Assembly::IO, Bio::Assembly::IO::ace, Bio::Assembly::IO::phrap, Bio::Assembly::Scaffold, Bio::Assembly::ScaffoldI, Bio::Assembly::Singlet, Bio::Biblio, Bio::Biblio::Article, Bio::Biblio::BiblioBase, Bio::Biblio::Book, Bio::Biblio::BookArticle, Bio::Biblio::IO, Bio::Biblio::IO::medline2ref, Bio::Biblio::IO::medlinexml, Bio::Biblio::IO::pubmed2ref, Bio::Biblio::IO::pubmedxml, Bio::Biblio::Journal, Bio::Biblio::JournalArticle, Bio::Biblio::MedlineArticle, Bio::Biblio::MedlineBook, Bio::Biblio::MedlineBookArticle, Bio::Biblio::MedlineJournal, Bio::Biblio::MedlineJournalArticle, Bio::Biblio::Organisation, Bio::Biblio::Patent, Bio::Biblio::Person, Bio::Biblio::Proceeding, Bio::Biblio::Provider, Bio::Biblio::PubmedArticle, Bio::Biblio::PubmedBookArticle, Bio::Biblio::PubmedJournalArticle, Bio::Biblio::Ref, Bio::Biblio::Service, Bio::Biblio::TechReport, Bio::Biblio::Thesis, Bio::Biblio::WebResource, Bio::Cluster::ClusterFactory, Bio::Cluster::FamilyI, Bio::Cluster::SequenceFamily, Bio::Cluster::UniGene, Bio::Cluster::UniGeneI, Bio::ClusterI, Bio::ClusterIO, Bio::ClusterIO::dbsnp, Bio::ClusterIO::unigene, Bio::CodonUsage::IO, Bio::CodonUsage::Table, Bio::Coordinate::Chain, Bio::Coordinate::Collection, Bio::Coordinate::ExtrapolatingPair, Bio::Coordinate::GeneMapper, Bio::Coordinate::Graph, Bio::Coordinate::MapperI, Bio::Coordinate::Pair, Bio::Coordinate::Result, Bio::Coordinate::Result::Gap, Bio::Coordinate::Result::Match, Bio::Coordinate::ResultI, Bio::Coordinate::Utils, Bio::DB::Ace, Bio::DB::Biblio::biofetch, Bio::DB::Biblio::eutils, Bio::DB::Biblio::pdf, Bio::DB::Biblio::soap, Bio::DB::BiblioI, Bio::DB::BioFetch, Bio::DB::CUTG, Bio::DB::DBFetch, Bio::DB::EMBL, Bio::DB::EUtilities, Bio::DB::EntrezGene, Bio::DB::Expression, Bio::DB::Expression::geo, Bio::DB::Failover, Bio::DB::Fasta, Bio::DB::FileCache, Bio::DB::Flat, Bio::DB::Flat::BDB, Bio::DB::Flat::BDB::embl, Bio::DB::Flat::BDB::fasta, Bio::DB::Flat::BDB::genbank, Bio::DB::Flat::BDB::swiss, Bio::DB::Flat::BDB::swissprot, Bio::DB::Flat::BinarySearch, Bio::DB::GDB, Bio::DB::GFF, Bio::DB::GFF::Adaptor::ace, Bio::DB::GFF::Adaptor::berkeleydb, Bio::DB::GFF::Adaptor::berkeleydb::iterator, Bio::DB::GFF::Adaptor::biofetch, Bio::DB::GFF::Adaptor::biofetch_oracle, Bio::DB::GFF::Adaptor::dbi, Bio::DB::GFF::Adaptor::dbi::caching_handle, Bio::DB::GFF::Adaptor::dbi::iterator, Bio::DB::GFF::Adaptor::dbi::mysql, Bio::DB::GFF::Adaptor::dbi::mysqlace, Bio::DB::GFF::Adaptor::dbi::mysqlcmap, Bio::DB::GFF::Adaptor::dbi::mysqlopt, Bio::DB::GFF::Adaptor::dbi::oracle, Bio::DB::GFF::Adaptor::dbi::oracleace, Bio::DB::GFF::Adaptor::dbi::pg, Bio::DB::GFF::Adaptor::dbi::pg_fts, Bio::DB::GFF::Adaptor::memory, Bio::DB::GFF::Adaptor::memory::feature_serializer, Bio::DB::GFF::Adaptor::memory::iterator, Bio::DB::GFF::Aggregator, Bio::DB::GFF::Aggregator::alignment, Bio::DB::GFF::Aggregator::clone, Bio::DB::GFF::Aggregator::coding, Bio::DB::GFF::Aggregator::match, Bio::DB::GFF::Aggregator::none, Bio::DB::GFF::Aggregator::processed_transcript, Bio::DB::GFF::Aggregator::so_transcript, Bio::DB::GFF::Aggregator::transcript, Bio::DB::GFF::Aggregator::ucsc_acembly, Bio::DB::GFF::Aggregator::ucsc_ensgene, Bio::DB::GFF::Aggregator::ucsc_genscan, Bio::DB::GFF::Aggregator::ucsc_refgene, Bio::DB::GFF::Aggregator::ucsc_sanger22, Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo, Bio::DB::GFF::Aggregator::ucsc_softberry, Bio::DB::GFF::Aggregator::ucsc_twinscan, Bio::DB::GFF::Aggregator::ucsc_unigene, Bio::DB::GFF::Featname, Bio::DB::GFF::Feature, Bio::DB::GFF::Homol, Bio::DB::GFF::RelSegment, Bio::DB::GFF::Segment, Bio::DB::GFF::Typename, Bio::DB::GFF::Util::Binning, Bio::DB::GFF::Util::Rearrange, Bio::DB::GenBank, Bio::DB::GenPept, Bio::DB::InMemoryCache, Bio::DB::LocationI, Bio::DB::MeSH, Bio::DB::NCBIHelper, Bio::DB::Query::GenBank, Bio::DB::Query::WebQuery, Bio::DB::QueryI, Bio::DB::RandomAccessI, Bio::DB::RefSeq, Bio::DB::ReferenceI, Bio::DB::Registry, Bio::DB::SeqFeature, Bio::DB::SeqFeature::NormalizedFeature, Bio::DB::SeqFeature::NormalizedFeatureI, Bio::DB::SeqFeature::NormalizedTableFeatureI, Bio::DB::SeqFeature::Segment, Bio::DB::SeqFeature::Store::DBI::Iterator, Bio::DB::SeqFeature::Store::DBI::mysql, Bio::DB::SeqFeature::Store::GFF3Loader, Bio::DB::SeqFeature::Store::bdb, Bio::DB::SeqFeature::Store::berkeleydb, Bio::DB::SeqFeature::Store::memory, Bio::DB::SeqHound, Bio::DB::SeqI, Bio::DB::SeqVersion, Bio::DB::SeqVersion::gi, Bio::DB::SwissProt, Bio::DB::Taxonomy, Bio::DB::Taxonomy::entrez, Bio::DB::Taxonomy::flatfile, Bio::DB::Taxonomy::list, Bio::DB::Universal, Bio::DB::UpdateableSeqI, Bio::DB::WebDBSeqI, Bio::DB::XEMBL, Bio::DB::XEMBLService, Bio::DBLinkContainerI, Bio::Das::FeatureTypeI, Bio::Das::SegmentI, Bio::DasI, Bio::DescribableI, Bio::Event::EventGeneratorI, Bio::Event::EventHandlerI, Bio::Expression::Contact, Bio::Expression::DataSet, Bio::Expression::FeatureGroup, Bio::Expression::FeatureGroup::FeatureGroupMas50, Bio::Expression::FeatureI, Bio::Expression::FeatureSet::FeatureSetMas50, Bio::Expression::Platform, Bio::Expression::ProbeI, Bio::Expression::Sample, Bio::Factory::AnalysisI, Bio::Factory::ApplicationFactoryI, Bio::Factory::DriverFactory, Bio::Factory::FTLocationFactory, Bio::Factory::HitFactoryI, Bio::Factory::LocationFactoryI, Bio::Factory::MapFactoryI, Bio::Factory::ObjectBuilderI, Bio::Factory::ObjectFactory, Bio::Factory::ObjectFactoryI, Bio::Factory::ResultFactoryI, Bio::Factory::SeqAnalysisParserFactory, Bio::Factory::SeqAnalysisParserFactoryI, Bio::Factory::SequenceFactoryI, Bio::Factory::SequenceProcessorI, Bio::Factory::SequenceStreamI, Bio::Factory::TreeFactoryI, Bio::FeatureHolderI, Bio::FeatureIO, Bio::FeatureIO::bed, Bio::FeatureIO::gff, Bio::FeatureIO::gtf, Bio::FeatureIO::interpro, Bio::FeatureIO::ptt, Bio::Graph::Edge, Bio::Graph::IO, Bio::Graph::IO::dip, Bio::Graph::IO::psi_xml, Bio::Graph::ProteinGraph, Bio::Graph::SimpleGraph, Bio::Graph::SimpleGraph::Traversal, Bio::Graphics, Bio::Graphics::ConfiguratorI, Bio::Graphics::Feature, Bio::Graphics::FeatureBase, Bio::Graphics::FeatureFile, Bio::Graphics::FeatureFile::Iterator, Bio::Graphics::Glyph, Bio::Graphics::Glyph::Factory, Bio::Graphics::Glyph::alignment, Bio::Graphics::Glyph::anchored_arrow, Bio::Graphics::Glyph::arrow, Bio::Graphics::Glyph::box, Bio::Graphics::Glyph::broken_line, Bio::Graphics::Glyph::cds, Bio::Graphics::Glyph::christmas_arrow, Bio::Graphics::Glyph::crossbox, Bio::Graphics::Glyph::dashed_line, Bio::Graphics::Glyph::diamond, Bio::Graphics::Glyph::dna, Bio::Graphics::Glyph::dot, Bio::Graphics::Glyph::dumbbell, Bio::Graphics::Glyph::ellipse, Bio::Graphics::Glyph::ex, Bio::Graphics::Glyph::extending_arrow, Bio::Graphics::Glyph::flag, Bio::Graphics::Glyph::gene, Bio::Graphics::Glyph::generic, Bio::Graphics::Glyph::graded_segments, Bio::Graphics::Glyph::group, Bio::Graphics::Glyph::heterogeneous_segments, Bio::Graphics::Glyph::image, Bio::Graphics::Glyph::lightning, Bio::Graphics::Glyph::line, Bio::Graphics::Glyph::merge_parts, Bio::Graphics::Glyph::merged_alignment, Bio::Graphics::Glyph::minmax, Bio::Graphics::Glyph::oval, Bio::Graphics::Glyph::pentagram, Bio::Graphics::Glyph::pinsertion, Bio::Graphics::Glyph::primers, Bio::Graphics::Glyph::processed_transcript, Bio::Graphics::Glyph::protein, Bio::Graphics::Glyph::ragged_ends, Bio::Graphics::Glyph::redgreen_box, Bio::Graphics::Glyph::redgreen_segment, Bio::Graphics::Glyph::repeating_shape, Bio::Graphics::Glyph::rndrect, Bio::Graphics::Glyph::ruler_arrow, Bio::Graphics::Glyph::saw_teeth, Bio::Graphics::Glyph::segmented_keyglyph, Bio::Graphics::Glyph::segments, Bio::Graphics::Glyph::so_transcript, Bio::Graphics::Glyph::span, Bio::Graphics::Glyph::splice_site, Bio::Graphics::Glyph::text_in_box, Bio::Graphics::Glyph::three_letters, Bio::Graphics::Glyph::tic_tac_toe, Bio::Graphics::Glyph::toomany, Bio::Graphics::Glyph::track, Bio::Graphics::Glyph::transcript, Bio::Graphics::Glyph::transcript2, Bio::Graphics::Glyph::translation, Bio::Graphics::Glyph::triangle, Bio::Graphics::Glyph::two_bolts, Bio::Graphics::Glyph::wave, Bio::Graphics::Glyph::weighted_arrow, Bio::Graphics::Glyph::whiskerplot, Bio::Graphics::Glyph::xyplot, Bio::Graphics::Panel, Bio::Graphics::Pictogram, Bio::Graphics::RendererI, Bio::Graphics::Util, Bio::IdCollectionI, Bio::IdentifiableI, Bio::Index::Abstract, Bio::Index::AbstractSeq, Bio::Index::Blast, Bio::Index::EMBL, Bio::Index::Fasta, Bio::Index::Fastq, Bio::Index::GenBank, Bio::Index::Hmmer, Bio::Index::Qual, Bio::Index::SwissPfam, Bio::Index::Swissprot, Bio::LiveSeq::AARange, Bio::LiveSeq::Chain, Bio::LiveSeq::ChainI, Bio::LiveSeq::DNA, Bio::LiveSeq::Exon, Bio::LiveSeq::Gene, Bio::LiveSeq::IO::BioPerl, Bio::LiveSeq::IO::Loader, Bio::LiveSeq::Intron, Bio::LiveSeq::Mutation, Bio::LiveSeq::Mutator, Bio::LiveSeq::Prim_Transcript, Bio::LiveSeq::Range, Bio::LiveSeq::Repeat_Region, Bio::LiveSeq::Repeat_Unit, Bio::LiveSeq::SeqI, Bio::LiveSeq::Transcript, Bio::LiveSeq::Translation, Bio::LocatableSeq, Bio::Location::Atomic, Bio::Location::AvWithinCoordPolicy, Bio::Location::CoordinatePolicyI, Bio::Location::Fuzzy, Bio::Location::FuzzyLocationI, Bio::Location::NarrowestCoordPolicy, Bio::Location::Simple, Bio::Location::Split, Bio::Location::SplitLocationI, Bio::Location::WidestCoordPolicy, Bio::LocationI, Bio::Map::Clone, Bio::Map::Contig, Bio::Map::CytoMap, Bio::Map::CytoMarker, Bio::Map::CytoPosition, Bio::Map::EntityI, Bio::Map::FPCMarker, Bio::Map::LinkageMap, Bio::Map::LinkagePosition, Bio::Map::MapI, Bio::Map::Mappable, Bio::Map::MappableI, Bio::Map::Marker, Bio::Map::MarkerI, Bio::Map::Microsatellite, Bio::Map::OrderedPosition, Bio::Map::OrderedPositionWithDistance, Bio::Map::Physical, Bio::Map::Position, Bio::Map::PositionHandler, Bio::Map::PositionHandlerI, Bio::Map::PositionI, Bio::Map::Relative, Bio::Map::RelativeI, Bio::Map::SimpleMap, Bio::MapIO, Bio::MapIO::fpc, Bio::MapIO::mapmaker, Bio::Matrix::Generic, Bio::Matrix::IO, Bio::Matrix::IO::phylip, Bio::Matrix::IO::scoring, Bio::Matrix::MatrixI, Bio::Matrix::PSM::IO, Bio::Matrix::PSM::IO::mast, Bio::Matrix::PSM::IO::masta, Bio::Matrix::PSM::IO::meme, Bio::Matrix::PSM::IO::psiblast, Bio::Matrix::PSM::IO::transfac, Bio::Matrix::PSM::InstanceSite, Bio::Matrix::PSM::InstanceSiteI, Bio::Matrix::PSM::ProtMatrix, Bio::Matrix::PSM::ProtPsm, Bio::Matrix::PSM::Psm, Bio::Matrix::PSM::PsmHeader, Bio::Matrix::PSM::PsmHeaderI, Bio::Matrix::PSM::PsmI, Bio::Matrix::PSM::SiteMatrix, Bio::Matrix::PSM::SiteMatrixI, Bio::Matrix::PhylipDist, Bio::Matrix::Scoring, Bio::Ontology::DocumentRegistry, Bio::Ontology::GOterm, Bio::Ontology::InterProTerm, Bio::Ontology::OBOEngine, Bio::Ontology::OBOterm, Bio::Ontology::Ontology, Bio::Ontology::OntologyEngineI, Bio::Ontology::OntologyI, Bio::Ontology::OntologyStore, Bio::Ontology::Path, Bio::Ontology::PathI, Bio::Ontology::Relationship, Bio::Ontology::RelationshipFactory, Bio::Ontology::RelationshipI, Bio::Ontology::RelationshipType, Bio::Ontology::SimpleGOEngine, Bio::Ontology::SimpleGOEngine::GraphAdaptor, Bio::Ontology::SimpleGOEngine::GraphAdaptor02, Bio::Ontology::SimpleOntologyEngine, Bio::Ontology::Term, Bio::Ontology::TermFactory, Bio::Ontology::TermI, Bio::OntologyIO, Bio::OntologyIO::Handlers::BaseSAXHandler, Bio::OntologyIO::Handlers::InterProHandler, Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler, Bio::OntologyIO::InterProParser, Bio::OntologyIO::dagflat, Bio::OntologyIO::goflat, Bio::OntologyIO::obo, Bio::OntologyIO::simplehierarchy, Bio::OntologyIO::soflat, Bio::Perl, Bio::Phenotype::Correlate, Bio::Phenotype::MeSH::Term, Bio::Phenotype::MeSH::Twig, Bio::Phenotype::Measure, Bio::Phenotype::OMIM::MiniMIMentry, Bio::Phenotype::OMIM::OMIMentry, Bio::Phenotype::OMIM::OMIMentryAllelicVariant, Bio::Phenotype::OMIM::OMIMparser, Bio::Phenotype::Phenotype, Bio::Phenotype::PhenotypeI, Bio::PopGen::Genotype, Bio::PopGen::GenotypeI, Bio::PopGen::HtSNP, Bio::PopGen::IO, Bio::PopGen::IO::csv, Bio::PopGen::IO::hapmap, Bio::PopGen::IO::phase, Bio::PopGen::IO::prettybase, Bio::PopGen::Individual, Bio::PopGen::IndividualI, Bio::PopGen::Marker, Bio::PopGen::MarkerI, Bio::PopGen::PopStats, Bio::PopGen::Population, Bio::PopGen::PopulationI, Bio::PopGen::Simulation::Coalescent, Bio::PopGen::Simulation::GeneticDrift, Bio::PopGen::Statistics, Bio::PopGen::TagHaplotype, Bio::PopGen::Utilities, Bio::PrimarySeq, Bio::PrimarySeqI, Bio::PullParserI, Bio::Range, Bio::RangeI, Bio::Restriction::Analysis, Bio::Restriction::Enzyme, Bio::Restriction::Enzyme::MultiCut, Bio::Restriction::Enzyme::MultiSite, Bio::Restriction::EnzymeCollection, Bio::Restriction::EnzymeI, Bio::Restriction::IO, Bio::Restriction::IO::bairoch, Bio::Restriction::IO::base, Bio::Restriction::IO::itype2, Bio::Restriction::IO::withrefm, Bio::Root::Exception, Bio::Root::HTTPget, Bio::Root::IO, Bio::Root::Root, Bio::Root::RootI, Bio::Root::Storable, Bio::Root::Version, Bio::Search::BlastStatistics, Bio::Search::BlastUtils, Bio::Search::DatabaseI, Bio::Search::GenericDatabase, Bio::Search::GenericStatistics, Bio::Search::HSP::BlastHSP, Bio::Search::HSP::FastaHSP, Bio::Search::HSP::GenericHSP, Bio::Search::HSP::HMMERHSP, Bio::Search::HSP::HSPFactory, Bio::Search::HSP::HSPI, Bio::Search::HSP::HmmpfamHSP, Bio::Search::HSP::PSLHSP, Bio::Search::HSP::PsiBlastHSP, Bio::Search::HSP::PullHSPI, Bio::Search::HSP::WABAHSP, Bio::Search::Hit::BlastHit, Bio::Search::Hit::Fasta, Bio::Search::Hit::GenericHit, Bio::Search::Hit::HMMERHit, Bio::Search::Hit::HitFactory, Bio::Search::Hit::HitI, Bio::Search::Hit::HmmpfamHit, Bio::Search::Hit::PsiBlastHit, Bio::Search::Hit::PullHitI, Bio::Search::Iteration::GenericIteration, Bio::Search::Iteration::IterationI, Bio::Search::Processor, Bio::Search::Result::BlastResult, Bio::Search::Result::GenericResult, Bio::Search::Result::HMMERResult, Bio::Search::Result::HmmpfamResult, Bio::Search::Result::PullResultI, Bio::Search::Result::ResultFactory, Bio::Search::Result::ResultI, Bio::Search::Result::WABAResult, Bio::Search::SearchUtils, Bio::Search::StatisticsI, Bio::SearchDist, Bio::SearchIO, Bio::SearchIO::EventHandlerI, Bio::SearchIO::FastHitEventBuilder, Bio::SearchIO::IteratedSearchResultEventBuilder, Bio::SearchIO::SearchResultEventBuilder, Bio::SearchIO::SearchWriterI, Bio::SearchIO::Writer::BSMLResultWriter, Bio::SearchIO::Writer::GbrowseGFF, Bio::SearchIO::Writer::HSPTableWriter, Bio::SearchIO::Writer::HTMLResultWriter, Bio::SearchIO::Writer::HitTableWriter, Bio::SearchIO::Writer::ResultTableWriter, Bio::SearchIO::Writer::TextResultWriter, Bio::SearchIO::axt, Bio::SearchIO::blast, Bio::SearchIO::blasttable, Bio::SearchIO::blastxml, Bio::SearchIO::exonerate, Bio::SearchIO::fasta, Bio::SearchIO::hmmer, Bio::SearchIO::hmmer_pull, Bio::SearchIO::megablast, Bio::SearchIO::psl, Bio::SearchIO::sim4, Bio::SearchIO::waba, Bio::SearchIO::wise, Bio::Seq, Bio::Seq::BaseSeqProcessor, Bio::Seq::EncodedSeq, Bio::Seq::LargeLocatableSeq, Bio::Seq::LargePrimarySeq, Bio::Seq::LargeSeq, Bio::Seq::LargeSeqI, Bio::Seq::Meta, Bio::Seq::Meta::Array, Bio::Seq::MetaI, Bio::Seq::PrimaryQual, Bio::Seq::PrimedSeq, Bio::Seq::QualI, Bio::Seq::Quality, Bio::Seq::RichSeq, Bio::Seq::RichSeqI, Bio::Seq::SeqBuilder, Bio::Seq::SeqFactory, Bio::Seq::SeqFastaSpeedFactory, Bio::Seq::SeqWithQuality, Bio::Seq::SequenceTrace, Bio::Seq::TraceI, Bio::SeqAnalysisParserI, Bio::SeqFeature::Annotated, Bio::SeqFeature::AnnotationAdaptor, Bio::SeqFeature::Collection, Bio::SeqFeature::CollectionI, Bio::SeqFeature::Computation, Bio::SeqFeature::FeaturePair, Bio::SeqFeature::Gene::Exon, Bio::SeqFeature::Gene::ExonI, Bio::SeqFeature::Gene::GeneStructure, Bio::SeqFeature::Gene::GeneStructureI, Bio::SeqFeature::Gene::Intron, Bio::SeqFeature::Gene::NC_Feature, Bio::SeqFeature::Gene::Poly_A_site, Bio::SeqFeature::Gene::Promoter, Bio::SeqFeature::Gene::Transcript, Bio::SeqFeature::Gene::TranscriptI, Bio::SeqFeature::Gene::UTR, Bio::SeqFeature::Generic, Bio::SeqFeature::PositionProxy, Bio::SeqFeature::Primer, Bio::SeqFeature::Similarity, Bio::SeqFeature::SimilarityPair, Bio::SeqFeature::Tools::FeatureNamer, Bio::SeqFeature::Tools::IDHandler, Bio::SeqFeature::Tools::TypeMapper, Bio::SeqFeature::Tools::Unflattener, Bio::SeqFeature::TypedSeqFeatureI, Bio::SeqFeatureI, Bio::SeqI, Bio::SeqIO, Bio::SeqIO::FTHelper, Bio::SeqIO::MultiFile, Bio::SeqIO::abi, Bio::SeqIO::ace, Bio::SeqIO::agave, Bio::SeqIO::alf, Bio::SeqIO::asciitree, Bio::SeqIO::bsml, Bio::SeqIO::bsml_sax, Bio::SeqIO::chadoxml, Bio::SeqIO::chaos, Bio::SeqIO::chaosxml, Bio::SeqIO::ctf, Bio::SeqIO::embl, Bio::SeqIO::entrezgene, Bio::SeqIO::excel, Bio::SeqIO::exp, Bio::SeqIO::fasta, Bio::SeqIO::fastq, Bio::SeqIO::game, Bio::SeqIO::game::featHandler, Bio::SeqIO::game::gameHandler, Bio::SeqIO::game::gameSubs, Bio::SeqIO::game::gameWriter, Bio::SeqIO::game::seqHandler, Bio::SeqIO::gcg, Bio::SeqIO::genbank, Bio::SeqIO::interpro, Bio::SeqIO::kegg, Bio::SeqIO::largefasta, Bio::SeqIO::lasergene, Bio::SeqIO::locuslink, Bio::SeqIO::metafasta, Bio::SeqIO::phd, Bio::SeqIO::pir, Bio::SeqIO::pln, Bio::SeqIO::qual, Bio::SeqIO::raw, Bio::SeqIO::scf, Bio::SeqIO::swiss, Bio::SeqIO::tab, Bio::SeqIO::table, Bio::SeqIO::tigr, Bio::SeqIO::tigrxml, Bio::SeqIO::tinyseq, Bio::SeqIO::ztr, Bio::SeqUtils, Bio::SimpleAlign, Bio::SimpleAnalysisI, Bio::Species, Bio::Structure::Atom, Bio::Structure::Chain, Bio::Structure::Entry, Bio::Structure::IO, Bio::Structure::IO::pdb, Bio::Structure::Model, Bio::Structure::Residue, Bio::Structure::SecStr::DSSP::Res, Bio::Structure::SecStr::STRIDE::Res, Bio::Structure::StructureI, Bio::Symbol::Alphabet, Bio::Symbol::AlphabetI, Bio::Symbol::DNAAlphabet, Bio::Symbol::ProteinAlphabet, Bio::Symbol::Symbol, Bio::Symbol::SymbolI, Bio::Taxon, Bio::Taxonomy, Bio::Taxonomy::FactoryI, Bio::Taxonomy::Node, Bio::Taxonomy::Taxon, Bio::Taxonomy::Tree, Bio::Tools::AlignFactory, Bio::Tools::Alignment::Consed, Bio::Tools::Alignment::Trim, Bio::Tools::Analysis::DNA::ESEfinder, Bio::Tools::Analysis::Protein::Domcut, Bio::Tools::Analysis::Protein::ELM, Bio::Tools::Analysis::Protein::GOR4, Bio::Tools::Analysis::Protein::HNN, Bio::Tools::Analysis::Protein::Mitoprot, Bio::Tools::Analysis::Protein::NetPhos, Bio::Tools::Analysis::Protein::Scansite, Bio::Tools::Analysis::Protein::Sopma, Bio::Tools::Analysis::SimpleAnalysisBase, Bio::Tools::AnalysisResult, Bio::Tools::BPbl2seq, Bio::Tools::BPlite, Bio::Tools::BPlite::HSP, Bio::Tools::BPlite::Iteration, Bio::Tools::BPlite::Sbjct, Bio::Tools::BPpsilite, Bio::Tools::Blat, Bio::Tools::CodonTable, Bio::Tools::Coil, Bio::Tools::ECnumber, Bio::Tools::EMBOSS::Palindrome, Bio::Tools::EPCR, Bio::Tools::ERPIN, Bio::Tools::ESTScan, Bio::Tools::Eponine, Bio::Tools::Est2Genome, Bio::Tools::Fgenesh, Bio::Tools::FootPrinter, Bio::Tools::GFF, Bio::Tools::Gel, Bio::Tools::Geneid, Bio::Tools::Genemark, Bio::Tools::Genewise, Bio::Tools::Genomewise, Bio::Tools::Genscan, Bio::Tools::Glimmer, Bio::Tools::Grail, Bio::Tools::HMM, Bio::Tools::HMMER::Domain, Bio::Tools::HMMER::Results, Bio::Tools::HMMER::Set, Bio::Tools::Hmmpfam, Bio::Tools::IUPAC, Bio::Tools::Lucy, Bio::Tools::MZEF, Bio::Tools::OddCodes, Bio::Tools::Phylo::Molphy, Bio::Tools::Phylo::Molphy::Result, Bio::Tools::Phylo::PAML, Bio::Tools::Phylo::PAML::ModelResult, Bio::Tools::Phylo::PAML::Result, Bio::Tools::Phylo::Phylip::ProtDist, Bio::Tools::Prediction::Exon, Bio::Tools::Prediction::Gene, Bio::Tools::Primer3, Bio::Tools::Primer::Assessor::Base, Bio::Tools::Primer::AssessorI, Bio::Tools::Primer::Feature, Bio::Tools::Primer::Pair, Bio::Tools::Prints, Bio::Tools::Profile, Bio::Tools::Promoterwise, Bio::Tools::PrositeScan, Bio::Tools::Pseudowise, Bio::Tools::QRNA, Bio::Tools::RNAMotif, Bio::Tools::RandomDistFunctions, Bio::Tools::RepeatMasker, Bio::Tools::RestrictionEnzyme, Bio::Tools::Run::GenericParameters, Bio::Tools::Run::ParametersI, Bio::Tools::Run::RemoteBlast, Bio::Tools::Run::StandAloneBlast, Bio::Tools::Run::WrapperBase, Bio::Tools::Seg, Bio::Tools::SeqPattern, Bio::Tools::SeqStats, Bio::Tools::SeqWords, Bio::Tools::SiRNA::Ruleset::saigo, Bio::Tools::SiRNA::Ruleset::tuschl, Bio::Tools::Sigcleave, Bio::Tools::Signalp, Bio::Tools::Sim4::Exon, Bio::Tools::Sim4::Results, Bio::Tools::Spidey::Exon, Bio::Tools::Spidey::Results, Bio::Tools::Tmhmm, Bio::Tools::dpAlign, Bio::Tools::ipcress, Bio::Tools::isPcr, Bio::Tools::pICalculator, Bio::Tools::pSW, Bio::Tools::tRNAscanSE, Bio::Tree::AlleleNode, Bio::Tree::Compatible, Bio::Tree::DistanceFactory, Bio::Tree::Draw::Cladogram, Bio::Tree::Node, Bio::Tree::NodeI, Bio::Tree::NodeNHX, Bio::Tree::RandomFactory, Bio::Tree::Statistics, Bio::Tree::Tree, Bio::Tree::TreeFunctionsI, Bio::Tree::TreeI, Bio::TreeIO, Bio::TreeIO::TreeEventBuilder, Bio::TreeIO::cluster, Bio::TreeIO::lintree, Bio::TreeIO::newick, Bio::TreeIO::nexus, Bio::TreeIO::nhx, Bio::TreeIO::pag, Bio::TreeIO::svggraph, Bio::TreeIO::tabtree, Bio::UpdateableSeqI, Bio::Variation::AAChange, Bio::Variation::AAReverseMutate, Bio::Variation::Allele, Bio::Variation::DNAMutation, Bio::Variation::IO, Bio::Variation::IO::flat, Bio::Variation::IO::xml, Bio::Variation::RNAChange, Bio::Variation::SNP, Bio::Variation::SeqDiff, Bio::Variation::VariantI, Bio::WebAgent

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Error:

• Bio::Tools::AnalysisResult

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