Kwalitee Issues

has_meta_yml

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

no_files_to_be_skipped

Fix MANIFEST.SKIP or use an authoring tool which respects MANIFEST.SKIP. Note that each entry in MANIFEST.SKIP is a regular expression. You may need to add appropriate meta characters not to ignore necessary stuff.

Error: Bio/DB/Makefile.PL,MANIFEST.SKIP,Makefile.PL,Makefile.old,bioperl.lisp,doc/faq/faq.html,doc/howto/html/Flat_Databases.html,doc/howto/html/Graphics-HOWTO.html,doc/howto/html/OBDA_Access.html,doc/howto/html/PAML.html,doc/howto/html/SearchIO.html,doc/howto/html/SeqIO.html,doc/howto/html/SimpleWebAnalysis.html,t/data/neighbor.dist

manifest_matches_dist

Run a proper command ("make manifest" or "./Build manifest", maybe with a force option), or use a distribution builder to generate the MANIFEST. Or update MANIFEST manually.

Error:

  • MANIFEST (1403) does not match dist (1417):
  • Missing in MANIFEST: Bio/DB/Makefile.PL, MANIFEST.SKIP, Makefile.PL, Makefile.old, bioperl.lisp, doc/faq/faq.html, doc/howto/html/Flat_Databases.html, doc/howto/html/Graphics-HOWTO.html, doc/howto/html/OBDA_Access.html, doc/howto/html/PAML.html, doc/howto/html/SearchIO.html, doc/howto/html/SeqIO.html, doc/howto/html/SimpleWebAnalysis.html, t/data/neighbor.dist

use_strict

Add 'use strict' (or its equivalents) to all modules, or convince us that your favorite module is well-known enough and people can easily see the modules are strictly written.

Error: Bio::CodonUsage::IO, Bio::DB::CUTG, Bio::DB::Flat, Bio::DB::XEMBLService, Bio::Graphics::FeatureFile::Iterator, Bio::Matrix::PSM::SiteMatrixI, Bio::Phenotype::PhenotypeI, Bio::Root::Xref, Bio::Search::BlastUtils, Bio::SearchIO::SearchWriterI, Bio::SearchIO::Writer::GbrowseGFF, Bio::SeqIO::game, Bio::Tools::Primer::Assessor::Base, Bio::Tools::Primer::AssessorI.pm, Bio::Tools::Primer::Feature, Bio::Tools::Primer::Pair, Bio::Tools::dpAlign

prereq_matches_use

List all used modules in META.yml requires

Error:

  • Ace
  • Class::MakeMethods::Emulator::MethodMaker
  • DBI
  • GD
  • Graph::Directed
  • HTTP::Request::Common
  • HTTP::Response
  • LWP
  • LWP::UserAgent
  • SOAP::Lite
  • SVG
  • SVG::Graph
  • SVG::Graph::Data
  • SVG::Graph::Data::Node
  • SVG::Graph::Data::Tree
  • Text::Shellwords
  • Tree::DAG_Node
  • URI
  • URI::Escape
  • XML::DOM
  • XML::Handler::Subs
  • XML::Parser
  • XML::Parser::PerlSAX
  • XML::Twig
  • XML::Writer

main_module_version_matches_dist_version

Make sure that the main module name and version are the same of the distribution.

no_pod_errors

Remove the POD errors. You can check for POD errors automatically by including Test::Pod to your test suite.

Error: bioperl-1.4/Bio/Restriction/Enzyme.pm -- Around line 818: =cut found outside a pod block. Skipping to next block. bioperl-1.4/Bio/Root/Object.pm -- Around line 328: Can't have a 0 in =over 0 bioperl-1.4/Bio/Tools/Blast/HSP.pm -- Around line 82: Can't have a 0 in =over 0 bioperl-1.4/Bio/Tools/Geneid.pm -- Around line 36: Non-ASCII character seen before =encoding in 'Guigó'. Assuming CP1252 bioperl-1.4/Bio/Tools/GuessSeqFormat.pm -- Around line 214: Non-ASCII character seen before =encoding in 'Kähäri,'. Assuming CP1252

has_meta_json

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

proper_libs

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/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/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/prodom.pm, Bio/AlignIO/psi.pm, Bio/AlignIO/selex.pm, Bio/AlignIO/stockholm.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/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/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/soap.pm, Bio/DB/BiblioI.pm, Bio/DB/BioFetch.pm, Bio/DB/CUTG.pm, Bio/DB/DBFetch.pm, Bio/DB/EMBL.pm, Bio/DB/Failover.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/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/iterator.pm, Bio/DB/GFF/Adaptor/dbi/mysql.pm, Bio/DB/GFF/Adaptor/dbi/mysqlace.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/memory.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/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/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/InMemoryCache.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/Registry.pm, Bio/DB/SeqI.pm, Bio/DB/SwissProt.pm, Bio/DB/Taxonomy.pm, Bio/DB/Taxonomy/entrez.pm, Bio/DB/Taxonomy/flatfile.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/FeatureGroup.pm, Bio/Expression/FeatureGroup/FeatureGroupMas50.pm, Bio/Expression/FeatureI.pm, Bio/Expression/FeatureSet/FeatureSetMas50.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/Graphics.pm, Bio/Graphics/ConfiguratorI.pm, Bio/Graphics/Feature.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/cds.pm, Bio/Graphics/Glyph/crossbox.pm, Bio/Graphics/Glyph/diamond.pm, Bio/Graphics/Glyph/dna.pm, Bio/Graphics/Glyph/dot.pm, Bio/Graphics/Glyph/ellipse.pm, Bio/Graphics/Glyph/ex.pm, Bio/Graphics/Glyph/extending_arrow.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/line.pm, Bio/Graphics/Glyph/minmax.pm, Bio/Graphics/Glyph/oval.pm, Bio/Graphics/Glyph/pinsertion.pm, Bio/Graphics/Glyph/primers.pm, Bio/Graphics/Glyph/processed_transcript.pm, Bio/Graphics/Glyph/redgreen_box.pm, Bio/Graphics/Glyph/redgreen_segment.pm, Bio/Graphics/Glyph/rndrect.pm, Bio/Graphics/Glyph/ruler_arrow.pm, Bio/Graphics/Glyph/segmented_keyglyph.pm, Bio/Graphics/Glyph/segments.pm, Bio/Graphics/Glyph/span.pm, Bio/Graphics/Glyph/splice_site.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/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/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/IO/SRS.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/CytoMap.pm, Bio/Map/CytoMarker.pm, Bio/Map/CytoPosition.pm, Bio/Map/LinkageMap.pm, Bio/Map/LinkagePosition.pm, Bio/Map/MapI.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/Position.pm, Bio/Map/PositionI.pm, Bio/Map/SimpleMap.pm, Bio/MapIO.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/meme.pm, Bio/Matrix/PSM/IO/transfac.pm, Bio/Matrix/PSM/InstanceSite.pm, Bio/Matrix/PSM/InstanceSiteI.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/GOterm.pm, Bio/Ontology/InterProTerm.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/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/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/IO.pm, Bio/PopGen/IO/csv.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/PrimarySeq.pm, Bio/PrimarySeqI.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/Err.pm, Bio/Root/Exception.pm, Bio/Root/Global.pm, Bio/Root/HTTPget.pm, Bio/Root/IO.pm, Bio/Root/IOManager.pm, Bio/Root/Object.pm, Bio/Root/Root.pm, Bio/Root/RootI.pm, Bio/Root/Storable.pm, Bio/Root/Utilities.pm, Bio/Root/Vector.pm, Bio/Root/Version.pm, Bio/Root/Xref.pm, Bio/Search/BlastUtils.pm, Bio/Search/DatabaseI.pm, Bio/Search/GenericDatabase.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/PSLHSP.pm, Bio/Search/HSP/PsiBlastHSP.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/PsiBlastHit.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/ResultFactory.pm, Bio/Search/Result/ResultI.pm, Bio/Search/Result/WABAResult.pm, Bio/Search/SearchUtils.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/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/LargePrimarySeq.pm, Bio/Seq/LargeSeq.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/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/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/TypeMapper.pm, Bio/SeqFeature/Tools/Unflattener.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/alf.pm, Bio/SeqIO/asciitree.pm, Bio/SeqIO/bsml.pm, Bio/SeqIO/chadoxml.pm, Bio/SeqIO/ctf.pm, Bio/SeqIO/embl.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/kegg.pm, Bio/SeqIO/largefasta.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/swiss.pm, Bio/SeqIO/tab.pm, Bio/SeqIO/tigr.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/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/Blast.pm, Bio/Tools/Blast/HSP.pm, Bio/Tools/Blast/HTML.pm, Bio/Tools/Blast/Sbjct.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/ESTScan.pm, Bio/Tools/Eponine.pm, Bio/Tools/Est2Genome.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/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/RandomDistFunctions.pm, Bio/Tools/RepeatMasker.pm, Bio/Tools/RestrictionEnzyme.pm, Bio/Tools/Run/RemoteBlast.pm, Bio/Tools/Run/StandAloneBlast.pm, Bio/Tools/Run/WrapperBase.pm, Bio/Tools/Seg.pm, Bio/Tools/SeqAnal.pm, Bio/Tools/SeqPattern.pm, Bio/Tools/SeqStats.pm, Bio/Tools/SeqWords.pm, Bio/Tools/SiRNA.pm, Bio/Tools/Sigcleave.pm, Bio/Tools/Signalp.pm, Bio/Tools/Sim4/Exon.pm, Bio/Tools/Sim4/Results.pm, Bio/Tools/Tmhmm.pm, Bio/Tools/WWW.pm, Bio/Tools/dpAlign.pm, Bio/Tools/pICalculator.pm, Bio/Tools/pSW.pm, Bio/Tree/AlleleNode.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/lintree.pm, Bio/TreeIO/newick.pm, Bio/TreeIO/nexus.pm, Bio/TreeIO/nhx.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

meta_yml_has_license

Define the license if you are using in Build.PL. If you are using MakeMaker (Makefile.PL) you should upgrade to ExtUtils::MakeMaker version 6.31.

use_warnings

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::StatisticsI, Bio::Align::Utilities, Bio::AlignIO, Bio::AlignIO::bl2seq, Bio::AlignIO::clustalw, Bio::AlignIO::emboss, Bio::AlignIO::fasta, 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::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::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::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::soap, Bio::DB::BiblioI, Bio::DB::BioFetch, Bio::DB::CUTG, Bio::DB::DBFetch, Bio::DB::EMBL, 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::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::mysqlopt, Bio::DB::GFF::Adaptor::dbi::oracle, Bio::DB::GFF::Adaptor::dbi::oracleace, Bio::DB::GFF::Adaptor::dbi::pg, Bio::DB::GFF::Adaptor::memory, 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::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::MeSH, Bio::DB::NCBIHelper, Bio::DB::Query::GenBank, Bio::DB::Query::WebQuery, Bio::DB::QueryI, Bio::DB::RandomAccessI, Bio::DB::RefSeq, Bio::DB::Registry, Bio::DB::SeqI, Bio::DB::SwissProt, Bio::DB::Taxonomy, Bio::DB::Taxonomy::entrez, Bio::DB::Taxonomy::flatfile, 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::FeatureGroup, Bio::Expression::FeatureGroup::FeatureGroupMas50, Bio::Expression::FeatureI, Bio::Expression::FeatureSet::FeatureSetMas50, 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::Graphics, Bio::Graphics::ConfiguratorI, Bio::Graphics::Feature, 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::cds, Bio::Graphics::Glyph::crossbox, Bio::Graphics::Glyph::diamond, Bio::Graphics::Glyph::dna, Bio::Graphics::Glyph::dot, Bio::Graphics::Glyph::ellipse, Bio::Graphics::Glyph::ex, Bio::Graphics::Glyph::extending_arrow, Bio::Graphics::Glyph::generic, Bio::Graphics::Glyph::graded_segments, Bio::Graphics::Glyph::group, Bio::Graphics::Glyph::heterogeneous_segments, Bio::Graphics::Glyph::line, Bio::Graphics::Glyph::minmax, Bio::Graphics::Glyph::oval, Bio::Graphics::Glyph::pinsertion, Bio::Graphics::Glyph::primers, Bio::Graphics::Glyph::processed_transcript, Bio::Graphics::Glyph::redgreen_box, Bio::Graphics::Glyph::redgreen_segment, Bio::Graphics::Glyph::rndrect, Bio::Graphics::Glyph::ruler_arrow, Bio::Graphics::Glyph::segmented_keyglyph, Bio::Graphics::Glyph::segments, Bio::Graphics::Glyph::span, Bio::Graphics::Glyph::splice_site, 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::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::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::IO::SRS, 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::CytoMap, Bio::Map::CytoMarker, Bio::Map::CytoPosition, Bio::Map::LinkageMap, Bio::Map::LinkagePosition, Bio::Map::MapI, Bio::Map::MappableI, Bio::Map::Marker, Bio::Map::MarkerI, Bio::Map::Microsatellite, Bio::Map::OrderedPosition, Bio::Map::OrderedPositionWithDistance, Bio::Map::Position, Bio::Map::PositionI, Bio::Map::SimpleMap, Bio::MapIO, 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::meme, Bio::Matrix::PSM::IO::transfac, Bio::Matrix::PSM::InstanceSite, Bio::Matrix::PSM::InstanceSiteI, 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::GOterm, Bio::Ontology::InterProTerm, 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::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::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::IO, Bio::PopGen::IO::csv, 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::PrimarySeq, Bio::PrimarySeqI, 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::Err, Bio::Root::Exception, Bio::Root::Global, Bio::Root::HTTPget, Bio::Root::IO, Bio::Root::IOManager, Bio::Root::Object, Bio::Root::Root, Bio::Root::RootI, Bio::Root::Storable, Bio::Root::Utilities, Bio::Root::Vector, Bio::Root::Version, Bio::Root::Xref, Bio::Search::BlastUtils, Bio::Search::DatabaseI, Bio::Search::GenericDatabase, 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::PSLHSP, Bio::Search::HSP::PsiBlastHSP, 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::PsiBlastHit, 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::ResultFactory, Bio::Search::Result::ResultI, Bio::Search::Result::WABAResult, Bio::Search::SearchUtils, 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::megablast, Bio::SearchIO::psl, Bio::SearchIO::sim4, Bio::SearchIO::waba, Bio::SearchIO::wise, Bio::Seq, Bio::Seq::BaseSeqProcessor, Bio::Seq::EncodedSeq, Bio::Seq::LargePrimarySeq, Bio::Seq::LargeSeq, Bio::Seq::Meta, Bio::Seq::Meta::Array, Bio::Seq::MetaI, Bio::Seq::PrimaryQual, Bio::Seq::PrimedSeq, Bio::Seq::QualI, 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::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::TypeMapper, Bio::SeqFeature::Tools::Unflattener, Bio::SeqFeatureI, Bio::SeqI, Bio::SeqIO, Bio::SeqIO::FTHelper, Bio::SeqIO::MultiFile, Bio::SeqIO::abi, Bio::SeqIO::ace, Bio::SeqIO::alf, Bio::SeqIO::asciitree, Bio::SeqIO::bsml, Bio::SeqIO::chadoxml, Bio::SeqIO::ctf, Bio::SeqIO::embl, 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::kegg, Bio::SeqIO::largefasta, 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::tigr, 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::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::Blast, Bio::Tools::Blast::HSP, Bio::Tools::Blast::HTML, Bio::Tools::Blast::Sbjct, Bio::Tools::Blat, Bio::Tools::CodonTable, Bio::Tools::Coil, Bio::Tools::ECnumber, Bio::Tools::EMBOSS::Palindrome, Bio::Tools::EPCR, Bio::Tools::ESTScan, Bio::Tools::Eponine, Bio::Tools::Est2Genome, 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::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.pm, 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::RandomDistFunctions, Bio::Tools::RepeatMasker, Bio::Tools::RestrictionEnzyme, Bio::Tools::Run::RemoteBlast, Bio::Tools::Run::StandAloneBlast, Bio::Tools::Run::WrapperBase, Bio::Tools::Seg, Bio::Tools::SeqAnal, Bio::Tools::SeqPattern, Bio::Tools::SeqStats, Bio::Tools::SeqWords, Bio::Tools::Sigcleave, Bio::Tools::Signalp, Bio::Tools::Sim4::Exon, Bio::Tools::Sim4::Results, Bio::Tools::Tmhmm, Bio::Tools::WWW, Bio::Tools::dpAlign, Bio::Tools::pICalculator, Bio::Tools::pSW, Bio::Tree::AlleleNode, 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::lintree, Bio::TreeIO::newick, Bio::TreeIO::nexus, Bio::TreeIO::nhx, 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

no_unauthorized_packages

Ask the owner of the distribution (the one who released it first, or the one who is designated in x_authority) to give you a (co-)maintainer's permission.

Error:

  • Bio::Graphics
  • Bio::Graphics::Feature
  • Bio::Graphics::FeatureFile
  • 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::crossbox
  • Bio::Graphics::Glyph::diamond
  • Bio::Graphics::Glyph::dna
  • Bio::Graphics::Glyph::dot
  • Bio::Graphics::Glyph::ellipse
  • Bio::Graphics::Glyph::ex
  • Bio::Graphics::Glyph::generic
  • Bio::Graphics::Glyph::graded_segments
  • Bio::Graphics::Glyph::group
  • Bio::Graphics::Glyph::line
  • Bio::Graphics::Glyph::oval
  • Bio::Graphics::Glyph::pinsertion
  • Bio::Graphics::Glyph::primers
  • Bio::Graphics::Glyph::rndrect
  • Bio::Graphics::Glyph::segmented_keyglyph
  • Bio::Graphics::Glyph::segments
  • Bio::Graphics::Glyph::span
  • Bio::Graphics::Glyph::toomany
  • Bio::Graphics::Glyph::track
  • Bio::Graphics::Glyph::transcript
  • Bio::Graphics::Glyph::transcript2
  • Bio::Graphics::Glyph::triangle
  • Bio::Graphics::Panel
  • Bio::Tools::AnalysisResult

test_prereq_matches_use

List all modules used in the test suite in META.yml test_requires

Error:

  • Error

consistent_version

Split the distribution, or fix the version numbers to make them consistent (use the highest version number to avoid version downgrade).

Error: 0.50,1.4

Modules

Name Abstract Version View
Bio::Align::AlignI An interface for describing sequence alignments. metacpan
Bio::Align::DNAStatistics Calculate some statistics for a DNA alignment metacpan
Bio::Align::PairwiseStatistics Base statistic object for Pairwise Alignments metacpan
Bio::Align::StatisticsI Calculate some statistics for an alignment metacpan
Bio::Align::Utilities A collection of utilities regarding converting and manipulating alignment objects metacpan
Bio::AlignIO Handler for AlignIO Formats metacpan
Bio::AlignIO::bl2seq bl2seq sequence input/output stream metacpan
Bio::AlignIO::clustalw clustalw sequence input/output stream metacpan
Bio::AlignIO::emboss Parse EMBOSS alignment output (from applications water and needle) metacpan
Bio::AlignIO::fasta FastA MSA Sequence input/output stream metacpan
Bio::AlignIO::maf Multipla Alignment Format sequence input stream metacpan
Bio::AlignIO::mase mase sequence input/output stream metacpan
Bio::AlignIO::mega Parse and Create MEGA format data files metacpan
Bio::AlignIO::meme meme sequence input/output stream metacpan
Bio::AlignIO::metafasta Metafasta MSA Sequence input/output stream metacpan
Bio::AlignIO::msf msf sequence input/output stream metacpan
Bio::AlignIO::nexus NEXUS format sequence input/output stream metacpan
Bio::AlignIO::pfam pfam sequence input/output stream metacpan
Bio::AlignIO::phylip PHYLIP format sequence input/output stream metacpan
Bio::AlignIO::prodom prodom sequence input/output stream metacpan
Bio::AlignIO::psi Read/Write PSI-BLAST profile alignment files metacpan
Bio::AlignIO::selex selex sequence input/output stream metacpan
Bio::AlignIO::stockholm stockholm sequence input/output stream metacpan
Bio::AnalysisI An interface to any (local or remote) analysis tool metacpan
Bio::AnalysisParserI Generic analysis output parser interface metacpan
Bio::AnalysisResultI Interface for analysis result objects metacpan
Bio::AnnotatableI the base interface an annotatable object must implement metacpan
Bio::Annotation::AnnotationFactory Instantiates a new Bio::AnnotationI (or derived class) through a factory metacpan
Bio::Annotation::Collection Default Perl implementation of AnnotationCollectionI metacpan
Bio::Annotation::Comment A comment object, holding text metacpan
Bio::Annotation::DBLink DESCRIPTION of Object metacpan
Bio::Annotation::OntologyTerm An ontology term adapted to AnnotationI metacpan
Bio::Annotation::Reference Specialised DBLink object for Literature References metacpan
Bio::Annotation::SimpleValue A simple scalar metacpan
Bio::Annotation::StructuredValue A scalar with embedded structured information metacpan
Bio::Annotation::TypeManager Manages types for annotation collections metacpan
Bio::AnnotationCollectionI Interface for annotation collections metacpan
Bio::AnnotationI Annotation interface metacpan
Bio::Assembly::Contig Perl module to hold and manipulate sequence assembly contigs. metacpan
Bio::Assembly::ContigAnalysis metacpan
Bio::Assembly::IO Handler for Assembly::IO Formats metacpan
Bio::Assembly::IO::ace module to load phrap ACE files. metacpan
Bio::Assembly::IO::phrap driver to load phrap.out files. metacpan
Bio::Assembly::Scaffold Perl module to hold and manipulate sequence assembly data. metacpan
Bio::Assembly::ScaffoldI Abstract Inteface of Sequence Assemblies metacpan
Bio::Biblio A Bibliographic Query Service module metacpan
Bio::Biblio::Article Representation of a general article metacpan
Bio::Biblio::BiblioBase An abstract base for other biblio classes metacpan
Bio::Biblio::Book Representation of a book metacpan
Bio::Biblio::BookArticle Representation of a book article metacpan
Bio::Biblio::IO Handling the bibliographic references metacpan
Bio::Biblio::IO::medline2ref A converter of a raw hash to MEDLINE citations metacpan
Bio::Biblio::IO::medlinexml A converter of XML files with MEDLINE citations metacpan
Bio::Biblio::IO::pubmed2ref A converter of a raw hash to PUBMED citations metacpan
Bio::Biblio::IO::pubmedxml A converter of XML files with PUBMED citations metacpan
Bio::Biblio::Journal Representation of a journal metacpan
Bio::Biblio::JournalArticle Representation of a journal article metacpan
Bio::Biblio::MedlineArticle Representation of a MEDLINE article metacpan
Bio::Biblio::MedlineBook Representation of a MEDLINE book metacpan
Bio::Biblio::MedlineBookArticle Representation of a MEDLINE book article metacpan
Bio::Biblio::MedlineJournal Representation of a MEDLINE journal metacpan
Bio::Biblio::MedlineJournalArticle Representation of a MEDLINE journal article metacpan
Bio::Biblio::Organisation Representation of an organisation metacpan
Bio::Biblio::Patent Representation of a patent metacpan
Bio::Biblio::Person Representation of a person metacpan
Bio::Biblio::Proceeding Representation of a conference proceeding metacpan
Bio::Biblio::Provider Representation of a general provider metacpan
Bio::Biblio::PubmedArticle Representation of a PUBMED article metacpan
Bio::Biblio::PubmedBookArticle Representation of a PUBMED book article metacpan
Bio::Biblio::PubmedJournalArticle Representation of a PUBMED journal article metacpan
Bio::Biblio::Ref Representation of a bibliographic reference metacpan
Bio::Biblio::Service Representation of a provider of type service metacpan
Bio::Biblio::TechReport Representation of a technical report metacpan
Bio::Biblio::Thesis Representation of thesis metacpan
Bio::Biblio::WebResource Representation of a web resource metacpan
Bio::Cluster::ClusterFactory Instantiates a new Bio::ClusterI (or derived class) through a factory metacpan
Bio::Cluster::FamilyI Family Interface metacpan
Bio::Cluster::SequenceFamily Sequence Family object metacpan
Bio::Cluster::UniGene UniGene object metacpan
Bio::Cluster::UniGeneI abstract interface of UniGene object metacpan
Bio::ClusterI Cluster Interface metacpan
Bio::ClusterIO Handler for Cluster Formats metacpan
Bio::ClusterIO::dbsnp dbSNP input stream metacpan
Bio::ClusterIO::unigene UniGene input stream metacpan
Bio::CodonUsage::IO for reading and writing codon usage tables to file metacpan
Bio::CodonUsage::Table for access to the Codon usage Database at http://www.kazusa.or.jp/codon. metacpan
Bio::Coordinate::Chain Mapping locations through a chain of coordinate mappers metacpan
Bio::Coordinate::Collection Noncontinuous match between two coordinate sets metacpan
Bio::Coordinate::ExtrapolatingPair Continuous match between two coordinate sets metacpan
Bio::Coordinate::GeneMapper transformations between gene related coordinate systems metacpan
Bio::Coordinate::Graph Finds shortest path between nodes in a graph metacpan
Bio::Coordinate::MapperI Interface describing coordinate mappers metacpan
Bio::Coordinate::Pair Continuous match between two coordinate sets metacpan
Bio::Coordinate::Result Results from coordinate transformation metacpan
Bio::Coordinate::Result::Gap Another name for Bio::Location::Simple metacpan
Bio::Coordinate::Result::Match Another name for Bio::Location::Simple metacpan
Bio::Coordinate::ResultI Interface to identify coordinate mapper results metacpan
Bio::Coordinate::Utils Additional methods to create Bio::Coordinate objects metacpan
Bio::DB::Ace Database object interface to ACeDB servers metacpan
Bio::DB::Biblio::biofetch A BioFetch-based access to a bibliographic citation retrieval metacpan
Bio::DB::Biblio::soap A SOAP-based access to a bibliographic query service metacpan
Bio::DB::BiblioI An interface to a Bibliographic Query Service metacpan
Bio::DB::BioFetch Database object interface to BioFetch retrieval metacpan
Bio::DB::CUTG for access to the Codon usage Database at http://www.kazusa.or.jp/codon. metacpan
Bio::DB::DBFetch Database object for retrieving using the dbfetch script metacpan
Bio::DB::EMBL Database object interface for EMBL entry retrieval metacpan
Bio::DB::Failover A Bio::DB::RandomAccessI compliant class which wraps a priority list of DBs metacpan
Bio::DB::Fasta Fast indexed access to a directory of fasta files metacpan
Bio::DB::FileCache In file cache for BioSeq objects metacpan
Bio::DB::Flat Interface for indexed flat files metacpan
Bio::DB::Flat::BDB Interface for BioHackathon standard BDB-indexed flat file metacpan
Bio::DB::Flat::BDB::embl embl adaptor for Open-bio standard BDB-indexed flat file metacpan
Bio::DB::Flat::BDB::fasta fasta adaptor for Open-bio standard BDB-indexed flat file metacpan
Bio::DB::Flat::BDB::genbank genbank adaptor for Open-bio standard BDB-indexed flat file metacpan
Bio::DB::Flat::BDB::swiss swissprot adaptor for Open-bio standard BDB-indexed flat file metacpan
Bio::DB::Flat::BDB::swissprot swissprot adaptor for Open-bio standard BDB-indexed flat file metacpan
Bio::DB::Flat::BinarySearch BinarySearch search indexing system for sequence files metacpan
Bio::DB::GDB Database object interface to GDB HTTP query metacpan
Bio::DB::GFF Storage and retrieval of sequence annotation data metacpan
Bio::DB::GFF::Adaptor::ace ace interface (for multiple inheritance) metacpan
Bio::DB::GFF::Adaptor::biofetch Cache BioFetch objects in a Bio::DB::GFF database metacpan
Bio::DB::GFF::Adaptor::biofetch_oracle metacpan
Bio::DB::GFF::Adaptor::dbi Database adaptor for DBI (SQL) databases metacpan
Bio::DB::GFF::Adaptor::dbi::caching_handle Cache for database handles metacpan
Bio::DB::GFF::Adaptor::dbi::iterator iterator for Bio::DB::GFF::Adaptor::dbi metacpan
Bio::DB::GFF::Adaptor::dbi::mysql Database adaptor for a specific mysql schema metacpan
Bio::DB::GFF::Adaptor::dbi::mysqlace Unholy union between mysql GFF database and acedb database metacpan
Bio::DB::GFF::Adaptor::dbi::mysqlopt Deprecated database adaptor metacpan
Bio::DB::GFF::Adaptor::dbi::oracle Database adaptor for a specific oracle schema metacpan
Bio::DB::GFF::Adaptor::dbi::oracleace Unholy union between oracle GFF database and acedb database metacpan
Bio::DB::GFF::Adaptor::dbi::pg Database adaptor for a specific postgres schema metacpan
Bio::DB::GFF::Adaptor::memory metacpan
Bio::DB::GFF::Adaptor::memory_iterator iterator for Bio::DB::GFF::Adaptor::memory metacpan
Bio::DB::GFF::Aggregator Aggregate GFF groups into composite features metacpan
Bio::DB::GFF::Aggregator::alignment Alignment aggregator metacpan
Bio::DB::GFF::Aggregator::clone Clone aggregator metacpan
Bio::DB::GFF::Aggregator::coding The Coding Region Aggregator metacpan
Bio::DB::GFF::Aggregator::match Match aggregator metacpan
Bio::DB::GFF::Aggregator::none No aggregation metacpan
Bio::DB::GFF::Aggregator::processed_transcript Sequence Ontology Transcript metacpan
Bio::DB::GFF::Aggregator::transcript Transcript aggregator metacpan
Bio::DB::GFF::Aggregator::ucsc_acembly UCSC acembly aggregator metacpan
Bio::DB::GFF::Aggregator::ucsc_ensgene UCSC ensGene aggregator metacpan
Bio::DB::GFF::Aggregator::ucsc_genscan UCSC genscan aggregator metacpan
Bio::DB::GFF::Aggregator::ucsc_refgene UCSC refGene aggregator metacpan
Bio::DB::GFF::Aggregator::ucsc_sanger22 UCSC sanger22 aggregator metacpan
Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo UCSC sanger22pseudo aggregator metacpan
Bio::DB::GFF::Aggregator::ucsc_softberry UCSC softberry aggregator metacpan
Bio::DB::GFF::Aggregator::ucsc_twinscan UCSC twinscan aggregator metacpan
Bio::DB::GFF::Aggregator::ucsc_unigene UCSC UniGene aggregator metacpan
Bio::DB::GFF::Featname The name of a feature metacpan
Bio::DB::GFF::Feature A relative segment identified by a feature type metacpan
Bio::DB::GFF::Homol A segment of DNA that is homologous to another metacpan
Bio::DB::GFF::RelSegment Sequence segment with relative coordinate support metacpan
Bio::DB::GFF::Segment Simple DNA segment object metacpan
Bio::DB::GFF::Typename The name of a feature type metacpan
Bio::DB::GFF::Util::Binning binning utility for Bio::DB::GFF index metacpan
Bio::DB::GFF::Util::Rearrange rearrange utility metacpan
Bio::DB::GenBank Database object interface to GenBank metacpan
Bio::DB::GenPept Database object interface to GenPept metacpan
Bio::DB::InMemoryCache Abstract interface for a sequence database metacpan
Bio::DB::MeSH Term retrieval from a Web MeSH database metacpan
Bio::DB::NCBIHelper A collection of routines useful for queries to NCBI databases. metacpan
Bio::DB::Query::GenBank Build a GenBank Entrez Query metacpan
Bio::DB::Query::WebQuery Helper class for web-based sequence queryies metacpan
Bio::DB::QueryI Object Interface to queryable sequence databases metacpan
Bio::DB::RandomAccessI Abstract interface for a sequence database metacpan
Bio::DB::RefSeq Database object interface for RefSeq retrieval metacpan
Bio::DB::Registry Access to the Open Bio Database Access registry scheme metacpan
Bio::DB::SeqI Abstract Interface for Sequence databases metacpan
Bio::DB::SwissProt Database object interface to SwissProt retrieval metacpan
Bio::DB::Taxonomy Access to a taxonomy database metacpan
Bio::DB::Taxonomy::entrez Taxonomy Entrez driver metacpan
Bio::DB::Taxonomy::flatfile An implementation of Bio::DB::Taxonomy which uses local flat files metacpan
Bio::DB::Universal Artificial database that delegates to specific databases metacpan
Bio::DB::UpdateableSeqI An interface for writing to a database of sequences. metacpan
Bio::DB::WebDBSeqI Object Interface to generalize Web Databases for retrieving sequences metacpan
Bio::DB::XEMBL Database object interface for XEMBL entry retrieval metacpan
Bio::DB::XEMBLService SOAP service definition for XEMBL metacpan
Bio::DBLinkContainerI Abstract interface for any object wanting to use database cross references metacpan
Bio::Das::FeatureTypeI Simple interface to Sequence Ontology feature types metacpan
Bio::Das::SegmentI DAS-style access to a feature database metacpan
Bio::DasI DAS-style access to a feature database metacpan
Bio::DescribableI interface for objects with human readable names and descriptions metacpan
Bio::Event::EventGeneratorI This interface describes the basic event generator class. metacpan
Bio::Event::EventHandlerI An Event Handler Interface metacpan
Bio::Expression::FeatureGroup a set of DNA/RNA features. ISA Bio::Expression::FeatureI metacpan
Bio::Expression::FeatureGroup::FeatureGroupMas50 metacpan
Bio::Expression::FeatureI an interface class for DNA/RNA features metacpan
Bio::Expression::FeatureSet::FeatureSetMas50 metacpan
Bio::Factory::AnalysisI An interface to analysis tool factory metacpan
Bio::Factory::ApplicationFactoryI Interface class for Application Factories metacpan
Bio::Factory::DriverFactory Base class for factory classes loading drivers metacpan
Bio::Factory::FTLocationFactory A FeatureTable Location Parser metacpan
Bio::Factory::HitFactoryI Interface for an object that builds Bio::Search::Hit::HitI objects metacpan
Bio::Factory::LocationFactoryI DESCRIPTION of Interface metacpan
Bio::Factory::MapFactoryI A Factory for getting markers metacpan
Bio::Factory::ObjectBuilderI Interface for an object builder metacpan
Bio::Factory::ObjectFactory Instantiates a new Bio::Root::RootI (or derived class) through a factory metacpan
Bio::Factory::ObjectFactoryI A General object creator factory metacpan
Bio::Factory::ResultFactoryI Interface for an object that builds Bio::Search::Result::ResultI objects metacpan
Bio::Factory::SeqAnalysisParserFactory class capable of creating SeqAnalysisParserI compliant parsers metacpan
Bio::Factory::SeqAnalysisParserFactoryI interface describing objects capable of creating SeqAnalysisParserI compliant parsers metacpan
Bio::Factory::SequenceFactoryI This interface allows for generic building of sequences in factories which create sequences (like SeqIO) metacpan
Bio::Factory::SequenceProcessorI Interface for chained sequence processing algorithms metacpan
Bio::Factory::SequenceStreamI Interface describing the basics of a Sequence Stream. metacpan
Bio::Factory::TreeFactoryI Factory Interface for getting and writing trees from/to a data stream metacpan
Bio::FeatureHolderI the base interface an object with features must implement metacpan
Bio::Graphics Generate GD images of Bio::Seq objects metacpan
Bio::Graphics::ConfiguratorI A sectioned map of configuration options (a map of maps), with a default section. Intended to augment existing tag->value semantics (ie. of Bio::AnnotationCollectionI) for object-representation information (eg. foreground color), and for general interface preferences (eg. image width in gbrowse). metacpan
Bio::Graphics::Feature A simple feature object for use with Bio::Graphics::Panel metacpan
Bio::Graphics::FeatureFile A set of Bio::Graphics features, stored in a file metacpan
Bio::Graphics::FeatureFile::Iterator Iterator across a Bio::Graphics::FeatureFile metacpan
Bio::Graphics::Glyph Base class for Bio::Graphics::Glyph objects metacpan
Bio::Graphics::Glyph::Factory Factory for Bio::Graphics::Glyph objects metacpan
Bio::Graphics::Glyph::alignment The "alignment" glyph metacpan
Bio::Graphics::Glyph::anchored_arrow The "anchored_arrow" glyph metacpan
Bio::Graphics::Glyph::arrow The "ruler_arrow" glyph metacpan
Bio::Graphics::Glyph::box The "box" glyph metacpan
Bio::Graphics::Glyph::cds The "cds" glyph metacpan
Bio::Graphics::Glyph::crossbox The "crossbox" glyph metacpan
Bio::Graphics::Glyph::diamond The "diamond" glyph metacpan
Bio::Graphics::Glyph::dna The "dna" glyph metacpan
Bio::Graphics::Glyph::dot The "dot" glyph metacpan
Bio::Graphics::Glyph::ellipse The "ellipse" glyph metacpan
Bio::Graphics::Glyph::ex metacpan
Bio::Graphics::Glyph::extending_arrow The "extending arrow" glyph metacpan
Bio::Graphics::Glyph::generic The "generic" glyph metacpan
Bio::Graphics::Glyph::graded_segments The "graded_segments" glyph metacpan
Bio::Graphics::Glyph::group The "group" glyph metacpan
Bio::Graphics::Glyph::heterogeneous_segments The "heterogeneous_segments" glyph metacpan
Bio::Graphics::Glyph::line The "line" glyph metacpan
Bio::Graphics::Glyph::minmax The minmax glyph metacpan
Bio::Graphics::Glyph::oval The "oval" glyph metacpan
Bio::Graphics::Glyph::pinsertion The "Drosophila P-element Insertion" glyph metacpan
Bio::Graphics::Glyph::primers The "STS primers" glyph metacpan
Bio::Graphics::Glyph::processed_transcript The sequence ontology transcript glyph metacpan
Bio::Graphics::Glyph::redgreen_box The "redgreen_box" glyph metacpan
Bio::Graphics::Glyph::redgreen_segment metacpan
Bio::Graphics::Glyph::rndrect The "round rect" glyph metacpan
Bio::Graphics::Glyph::ruler_arrow metacpan
Bio::Graphics::Glyph::segmented_keyglyph The "segmented_keyglyph" glyph metacpan
Bio::Graphics::Glyph::segments The "segments" glyph metacpan
Bio::Graphics::Glyph::span The "span" glyph metacpan
Bio::Graphics::Glyph::splice_site The "splice_site" glyph metacpan
Bio::Graphics::Glyph::toomany The "too many to show" glyph metacpan
Bio::Graphics::Glyph::track The "track" glyph metacpan
Bio::Graphics::Glyph::transcript The "transcript" glyph metacpan
Bio::Graphics::Glyph::transcript2 The "transcript2" glyph metacpan
Bio::Graphics::Glyph::translation The "6-frame translation" glyph metacpan
Bio::Graphics::Glyph::triangle The "triangle" glyph metacpan
Bio::Graphics::Glyph::xyplot The xyplot glyph metacpan
Bio::Graphics::Panel Generate GD images of Bio::Seq objects metacpan
Bio::Graphics::Pictogram metacpan
Bio::Graphics::RendererI A renderer for the Bio::Graphics class that renders Bio::SeqFeature::CollectionI objects onto Bio::Graphics::Panels using configuration information provided by a Bio::Graphics::ConfiguratorI. metacpan
Bio::Graphics::Util metacpan
Bio::IdCollectionI metacpan
Bio::IdentifiableI interface for objects with identifiers metacpan
Bio::Index::Abstract Abstract interface for indexing a flat file metacpan
Bio::Index::AbstractSeq Base class for AbstractSeq s metacpan
Bio::Index::Blast Indexes Blast reports and supports retrieval based on query accession(s) metacpan
Bio::Index::EMBL Interface for indexing (multiple) EMBL/Swissprot .dat files (ie flat file embl/swissprot format). metacpan
Bio::Index::Fasta Interface for indexing (multiple) fasta files metacpan
Bio::Index::Fastq Interface for indexing (multiple) fastq files metacpan
Bio::Index::GenBank Interface for indexing (multiple) GenBank .seq files (ie flat file GenBank format). metacpan
Bio::Index::SwissPfam Interface for indexing swisspfam files metacpan
Bio::Index::Swissprot Interface for indexing (multiple) Swissprot .dat files (ie flat file swissprot format). metacpan
Bio::LiveSeq::AARange AARange abstract class for LiveSeq metacpan
Bio::LiveSeq::Chain DoubleChain DataStructure for Perl metacpan
Bio::LiveSeq::ChainI Double linked chain data structure metacpan
Bio::LiveSeq::DNA DNA object for LiveSeq metacpan
Bio::LiveSeq::Exon Range abstract class for LiveSeq metacpan
Bio::LiveSeq::Gene Range abstract class for LiveSeq metacpan
Bio::LiveSeq::IO::BioPerl Loader for LiveSeq from EMBL entries with BioPerl metacpan
Bio::LiveSeq::IO::Loader Parent Loader for LiveSeq metacpan
Bio::LiveSeq::IO::SRS Loader for LiveSeq from EMBL entries with SRS metacpan
Bio::LiveSeq::Intron Range abstract class for LiveSeq metacpan
Bio::LiveSeq::Mutation Mutation event descriptor class metacpan
Bio::LiveSeq::Mutator Package mutating LiveSequences metacpan
Bio::LiveSeq::Prim_Transcript Prim_Transcript class for LiveSeq metacpan
Bio::LiveSeq::Range Range abstract class for LiveSeq metacpan
Bio::LiveSeq::Repeat_Region Repeat_Region class for LiveSeq metacpan
Bio::LiveSeq::Repeat_Unit Repeat_Unit class for LiveSeq metacpan
Bio::LiveSeq::SeqI Abstract sequence interface class for LiveSeq metacpan
Bio::LiveSeq::Transcript Transcript class for LiveSeq metacpan
Bio::LiveSeq::Translation Translation class for LiveSeq metacpan
Bio::LocatableSeq A Sequence object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq. metacpan
Bio::Location::Atomic Implementation of a Atomic Location on a Sequence metacpan
Bio::Location::AvWithinCoordPolicy class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise metacpan
Bio::Location::CoordinatePolicyI Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location metacpan
Bio::Location::Fuzzy Implementation of a Location on a Sequence which has unclear start and/or end locations metacpan
Bio::Location::FuzzyLocationI Abstract interface of a Location on a Sequence which has unclear start/end location metacpan
Bio::Location::NarrowestCoordPolicy class implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range metacpan
Bio::Location::Simple Implementation of a Simple Location on a Sequence metacpan
Bio::Location::Split Implementation of a Location on a Sequence which has multiple locations (start/end points) metacpan
Bio::Location::SplitLocationI metacpan
Bio::Location::WidestCoordPolicy class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable range metacpan
Bio::LocationI Abstract interface of a Location on a Sequence metacpan
Bio::Map::CytoMap A Bio::MapI compliant map implementation handling cytogenic bands metacpan
Bio::Map::CytoMarker An object representing a marker. metacpan
Bio::Map::CytoPosition Marker class with cytogenetic band storing attributes metacpan
Bio::Map::LinkageMap A representation of a genetic linkage map. metacpan
Bio::Map::LinkagePosition Create a Position for a Marker that will be placed on a Bio::Map::LinkageMap metacpan
Bio::Map::MapI Interface for describing Map objects in bioperl metacpan
Bio::Map::MappableI An object that can be placed in a map metacpan
Bio::Map::Marker An central map object representing a generic marker that can have multiple location in several maps. metacpan
Bio::Map::MarkerI Interface for basic marker functionality metacpan
Bio::Map::Microsatellite An object representing a Microsatellite marker. metacpan
Bio::Map::OrderedPosition Abstracts the notion of a member of an ordered list of markers. Each marker is a certain distance from the one in the ordered list before it. metacpan
Bio::Map::OrderedPositionWithDistance Abstracts the notion of a member of an ordered list of markers. Each marker is a certain distance from the one in the ordered list before it. metacpan
Bio::Map::Position A single position of a Marker in a Map metacpan
Bio::Map::PositionI Abstracts the notion of a position having a value in the context of a marker and a Map metacpan
Bio::Map::SimpleMap A MapI implementation handling the basics of a Map metacpan
Bio::MapIO A Map Factory object metacpan
Bio::MapIO::mapmaker A Mapmaker Map reader metacpan
Bio::Matrix::Generic metacpan
Bio::Matrix::IO A factory for Matrix parsing metacpan
Bio::Matrix::IO::phylip A parser for PHYLIP distance matricies metacpan
Bio::Matrix::IO::scoring A parser for PAM/BLOSUM matricies metacpan
Bio::Matrix::MatrixI An interface for describing a Matrix metacpan
Bio::Matrix::PSM::IO PSM parser metacpan
Bio::Matrix::PSM::IO::mast PSM mast parser implementation metacpan
Bio::Matrix::PSM::IO::meme metacpan
Bio::Matrix::PSM::IO::transfac metacpan
Bio::Matrix::PSM::InstanceSite A PSM site occurance metacpan
Bio::Matrix::PSM::InstanceSiteI InstanceSite interface, holds an instance of a PSM metacpan
Bio::Matrix::PSM::Psm handle combination of site matricies metacpan
Bio::Matrix::PSM::PsmHeader PSM mast parser implementation metacpan
Bio::Matrix::PSM::PsmHeaderI metacpan
Bio::Matrix::PSM::PsmI abstract interface to handler of site matricies metacpan
Bio::Matrix::PSM::SiteMatrix SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) metacpan
Bio::Matrix::PSM::SiteMatrixI SiteMatrix interface, holds a position scoring matrix (or position weight matrix) metacpan
Bio::Matrix::PhylipDist A Phylip Distance Matrix object metacpan
Bio::Matrix::Scoring Object which can hold scoring matrix information metacpan
Bio::Ontology::GOterm metacpan
Bio::Ontology::InterProTerm metacpan
Bio::Ontology::Ontology standard implementation of an Ontology metacpan
Bio::Ontology::OntologyEngineI metacpan
Bio::Ontology::OntologyI Interface for an ontology implementation metacpan
Bio::Ontology::OntologyStore A repository of ontologies metacpan
Bio::Ontology::Path metacpan
Bio::Ontology::PathI metacpan
Bio::Ontology::Relationship metacpan
Bio::Ontology::RelationshipFactory Instantiates a new Bio::Ontology::RelationshipI (or derived class) through a factory metacpan
Bio::Ontology::RelationshipI metacpan
Bio::Ontology::RelationshipType metacpan
Bio::Ontology::SimpleGOEngine metacpan
Bio::Ontology::SimpleOntologyEngine metacpan
Bio::Ontology::Term metacpan
Bio::Ontology::TermFactory Instantiates a new Bio::Ontology::TermI (or derived class) through a factory metacpan
Bio::Ontology::TermI metacpan
Bio::OntologyIO Parser factory for Ontology formats metacpan
Bio::OntologyIO::Handlers::BaseSAXHandler metacpan
Bio::OntologyIO::Handlers::InterProHandler metacpan
Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler metacpan
Bio::OntologyIO::InterProParser metacpan
Bio::OntologyIO::dagflat metacpan
Bio::OntologyIO::goflat metacpan
Bio::OntologyIO::simplehierarchy metacpan
Bio::OntologyIO::soflat metacpan
Bio::Perl Functional access to BioPerl for people who don't know objects metacpan
Bio::Phenotype::Correlate metacpan
Bio::Phenotype::MeSH::Term A MeSH term metacpan
Bio::Phenotype::MeSH::Twig Context for a MeSH term metacpan
Bio::Phenotype::Measure metacpan
Bio::Phenotype::OMIM::MiniMIMentry metacpan
Bio::Phenotype::OMIM::OMIMentry metacpan
Bio::Phenotype::OMIM::OMIMentryAllelicVariant metacpan
Bio::Phenotype::OMIM::OMIMparser metacpan
Bio::Phenotype::Phenotype metacpan
Bio::Phenotype::PhenotypeI metacpan
Bio::PopGen::Genotype An implementation of a genotype which is an allele container metacpan
Bio::PopGen::GenotypeI A marker and alleles for a specific individual metacpan
Bio::PopGen::IO Input individual,marker,allele information metacpan
Bio::PopGen::IO::csv metacpan
Bio::PopGen::IO::prettybase Extract individual allele data from PrettyBase format metacpan
Bio::PopGen::Individual An implementation of an Individual who has Genotype or Sequence Results metacpan
Bio::PopGen::IndividualI An individual who has Genotype or Sequence Results metacpan
Bio::PopGen::Marker A genetic marker which one uses to generate genotypes metacpan
Bio::PopGen::MarkerI A Population Genetic conceptual marker metacpan
Bio::PopGen::PopStats A collection of methods for calculating statistics about a population or sets of populations metacpan
Bio::PopGen::Population A population of individuals metacpan
Bio::PopGen::PopulationI Interface for Populations metacpan
Bio::PopGen::Simulation::Coalescent A Coalescent simulation factory metacpan
Bio::PopGen::Simulation::GeneticDrift A simple genetic drift simulation metacpan
Bio::PopGen::Statistics Population Genetics statistical tests metacpan
Bio::PrimarySeq Bioperl lightweight Sequence Object metacpan
Bio::PrimarySeqI metacpan
Bio::Range Pure perl RangeI implementation metacpan
Bio::RangeI Range interface metacpan
Bio::Restriction::Analysis cutting sequences with restriction enzymes metacpan
Bio::Restriction::Enzyme A single restriction endonuclease (cuts DNA at specific locations) metacpan
Bio::Restriction::Enzyme::MultiCut A single restriction endonuclease metacpan
Bio::Restriction::Enzyme::MultiSite A single restriction endonuclease metacpan
Bio::Restriction::EnzymeCollection Set of restriction endonucleases metacpan
Bio::Restriction::EnzymeI Interface class for restriction endonuclease metacpan
Bio::Restriction::IO Handler for sequence variation IO Formats metacpan
Bio::Restriction::IO::bairoch bairoch enzyme set metacpan
Bio::Restriction::IO::base base enzyme set metacpan
Bio::Restriction::IO::itype2 itype2 enzyme set metacpan
Bio::Restriction::IO::withrefm withrefm enzyme set metacpan
Bio::Root::Err Exception class for Perl 5 objects metacpan
Bio::Root::Exception Generic exception objects for Bioperl metacpan
Bio::Root::Global Global variables and utility functions metacpan
Bio::Root::HTTPget module for fallback HTTP get operations when LWP:: is unavailable metacpan
Bio::Root::IO module providing several methods often needed when dealing with file IO metacpan
Bio::Root::IOManager Input and output manager for Perl5 objects. metacpan
Bio::Root::Object A core Perl 5 object. metacpan
Bio::Root::Root Hash-based implementation of Bio::Root::RootI metacpan
Bio::Root::RootI Abstract interface to root object code metacpan
Bio::Root::Storable object serialisation methods metacpan
Bio::Root::Utilities General-purpose utility module metacpan
Bio::Root::Vector Interface for managing linked lists of Perl5 objects. metacpan
Bio::Root::Version provide global, distribution-level versioning 1.4 metacpan
Bio::Root::Xref A generic cross-reference object. metacpan
Bio::Search::BlastUtils Utility functions for Bio::Search:: BLAST objects metacpan
Bio::Search::DatabaseI Interface for a database used in a sequence search metacpan
Bio::Search::GenericDatabase Generic implementation of Bio::Search::DatabaseI metacpan
Bio::Search::HSP::BlastHSP Bioperl BLAST High-Scoring Pair object metacpan
Bio::Search::HSP::FastaHSP HSP object for FASTA specific data metacpan
Bio::Search::HSP::GenericHSP A "Generic" implementation of a High Scoring Pair metacpan
Bio::Search::HSP::HMMERHSP A HSP object for HMMER results metacpan
Bio::Search::HSP::HSPFactory A factory to create Bio::Search::HSP::HSPI objects metacpan
Bio::Search::HSP::HSPI Interface for a High Scoring Pair in a similarity search result metacpan
Bio::Search::HSP::PSLHSP A HSP for PSL output metacpan
Bio::Search::HSP::PsiBlastHSP Bioperl BLAST High-Scoring Pair object metacpan
Bio::Search::HSP::WABAHSP HSP object suitable for describing WABA alignments metacpan
Bio::Search::Hit::BlastHit Blast-specific subclass of Bio::Search::Hit::GenericHit metacpan
Bio::Search::Hit::Fasta Hit object specific for Fasta-generated hits metacpan
Bio::Search::Hit::GenericHit A generic implementation of the Bio::Search::Hit::HitI interface metacpan
Bio::Search::Hit::HMMERHit A Hit module for HMMER hits metacpan
Bio::Search::Hit::HitFactory A factory to create Bio::Search::Hit::HitI objects metacpan
Bio::Search::Hit::HitI Interface for a hit in a similarity search result metacpan
Bio::Search::Hit::PsiBlastHit Bioperl BLAST Hit object metacpan
Bio::Search::Iteration::GenericIteration A generic implementation of the Bio::Search::Iteration::IterationI interface. metacpan
Bio::Search::Iteration::IterationI Abstract interface to an iteration from an iterated search result, such as PSI-BLAST. metacpan
Bio::Search::Processor DESCRIPTION of Object metacpan
Bio::Search::Result::BlastResult Blast-specific subclass of Bio::Search::Result::GenericResult metacpan
Bio::Search::Result::GenericResult Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results. metacpan
Bio::Search::Result::HMMERResult A Result object for HMMER results metacpan
Bio::Search::Result::ResultFactory A factory to create Bio::Search::Result::ResultI objects metacpan
Bio::Search::Result::ResultI Abstract interface to Search Result objects metacpan
Bio::Search::Result::WABAResult Result object for WABA alignment output metacpan
Bio::Search::SearchUtils Utility functions for Bio::Search:: objects metacpan
Bio::SearchDist A perl wrapper around Sean Eddy's histogram object metacpan
Bio::SearchIO Driver for parsing Sequence Database Searches (Blast,FASTA,...) metacpan
Bio::SearchIO::EventHandlerI An abstract Event Handler for Search Result parsing metacpan
Bio::SearchIO::FastHitEventBuilder Event Handler for SearchIO events. metacpan
Bio::SearchIO::IteratedSearchResultEventBuilder Event Handler for SearchIO events. metacpan
Bio::SearchIO::SearchResultEventBuilder Event Handler for SearchIO events. metacpan
Bio::SearchIO::SearchWriterI Interface for outputting parsed Search results metacpan
Bio::SearchIO::Writer::BSMLResultWriter DESCRIPTION of Object metacpan
Bio::SearchIO::Writer::GbrowseGFF Interface for outputting parsed search results in Gbrowse GFF format metacpan
Bio::SearchIO::Writer::HSPTableWriter Tab-delimited data for Bio::Search::HSP::HSPI objects metacpan
Bio::SearchIO::Writer::HTMLResultWriter Object to implement writing a Bio::Search::ResultI in HTML. metacpan
Bio::SearchIO::Writer::HitTableWriter Tab-delimited data for Bio::Search::Hit::HitI objects metacpan
Bio::SearchIO::Writer::ResultTableWriter Outputs tab-delimited data for each Bio::Search::Result::ResultI object. metacpan
Bio::SearchIO::Writer::TextResultWriter Object to implement writing a Bio::Search::ResultI in Text. metacpan
Bio::SearchIO::axt a parser for axt format reports metacpan
Bio::SearchIO::blast Event generator for event based parsing of blast reports metacpan
Bio::SearchIO::blasttable Driver module for SearchIO for parsing NCBI -m 8/9 format metacpan
Bio::SearchIO::blastxml A SearchIO implementation of NCBI Blast XML parsing. metacpan
Bio::SearchIO::exonerate parser for Exonerate metacpan
Bio::SearchIO::fasta A SearchIO parser for FASTA results metacpan
Bio::SearchIO::hmmer A parser for HMMER output (hmmpfam, hmmsearch) metacpan
Bio::SearchIO::megablast a driver module for Bio::SearchIO to parse megablast reports (format 0) metacpan
Bio::SearchIO::psl A parser for PSL output (UCSC) metacpan
Bio::SearchIO::sim4 parser for Sim4 alignments metacpan
Bio::SearchIO::waba SearchIO parser for Jim Kent WABA program alignment output metacpan
Bio::SearchIO::wise Parsing of wise output as alignments metacpan
Bio::Seq Sequence object, with features metacpan
Bio::Seq::BaseSeqProcessor Base implementation for a SequenceProcessor metacpan
Bio::Seq::EncodedSeq subtype of L<Bio::LocatableSeq|Bio::LocatableSeq> to store DNA that encodes a protein metacpan
Bio::Seq::LargePrimarySeq PrimarySeq object that stores sequence as files in the tempdir (as found by File::Temp) or the default method in Bio::Root::Root metacpan
Bio::Seq::LargeSeq SeqI compliant object that stores sequence as files in /tmp metacpan
Bio::Seq::Meta metacpan
Bio::Seq::Meta::Array array-based generic implementation of a sequence class with residue-based meta information metacpan
Bio::Seq::MetaI Interface for sequence objects with residue-based meta information metacpan
Bio::Seq::PrimaryQual Bioperl lightweight Quality Object metacpan
Bio::Seq::PrimedSeq A representation of a sequence and two primers flanking a target region for amplification metacpan
Bio::Seq::QualI Interface definition for a Bio::Seq::Qual metacpan
Bio::Seq::RichSeq Module implementing a sequence created from a rich sequence database entry metacpan
Bio::Seq::RichSeqI interface for sequences from rich data sources, mostly databases metacpan
Bio::Seq::SeqBuilder Configurable object builder for sequence stream parsers metacpan
Bio::Seq::SeqFactory Instantiates a new Bio::PrimarySeqI (or derived class) through a factory metacpan
Bio::Seq::SeqFastaSpeedFactory metacpan
Bio::Seq::SeqWithQuality Bioperl object packaging a sequence with its quality metacpan
Bio::Seq::SequenceTrace Bioperl object packaging a sequence with its trace metacpan
Bio::Seq::TraceI Interface definition for a Bio::Seq::Trace metacpan
Bio::SeqAnalysisParserI Sequence analysis output parser interface metacpan
Bio::SeqFeature::AnnotationAdaptor integrates SeqFeatureIs annotation metacpan
Bio::SeqFeature::Collection A container class for SeqFeatures suitable for performing operations such as finding features within a range, that match a certain feature type, etc. metacpan
Bio::SeqFeature::CollectionI An interface for a collection of SeqFeatureI objects. metacpan
Bio::SeqFeature::Computation Computation SeqFeature metacpan
Bio::SeqFeature::FeaturePair hold pair feature information e.g. blast hits metacpan
Bio::SeqFeature::Gene::Exon a feature representing an exon metacpan
Bio::SeqFeature::Gene::ExonI Interface for a feature representing an exon metacpan
Bio::SeqFeature::Gene::GeneStructure A feature representing an arbitrarily complex structure of a gene metacpan
Bio::SeqFeature::Gene::GeneStructureI metacpan
Bio::SeqFeature::Gene::Intron DESCRIPTION of Object metacpan
Bio::SeqFeature::Gene::NC_Feature metacpan
Bio::SeqFeature::Gene::Poly_A_site metacpan
Bio::SeqFeature::Gene::Promoter Describes a promotor metacpan
Bio::SeqFeature::Gene::Transcript A feature representing a transcript metacpan
Bio::SeqFeature::Gene::TranscriptI Interface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site. metacpan
Bio::SeqFeature::Gene::UTR A feature representing an untranslated region that is part of a transcriptional unit metacpan
Bio::SeqFeature::Generic Generic SeqFeature metacpan
Bio::SeqFeature::PositionProxy handle features when truncation/revcom sequences span a feature metacpan
Bio::SeqFeature::Primer Primer Generic SeqFeature metacpan
Bio::SeqFeature::SiRNA::Oligo Perl object for small inhibitory RNAs. metacpan
Bio::SeqFeature::SiRNA::Pair Perl object for small inhibitory RNA (SiRNA) oligo pairs metacpan
Bio::SeqFeature::Similarity A sequence feature based on similarity metacpan
Bio::SeqFeature::SimilarityPair Sequence feature based on the similarity of two sequences. metacpan
Bio::SeqFeature::Tools::TypeMapper maps $seq_feature->primary_tag metacpan
Bio::SeqFeature::Tools::Unflattener turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy metacpan
Bio::SeqFeatureI Abstract interface of a Sequence Feature metacpan
Bio::SeqI metacpan
Bio::SeqIO Handler for SeqIO Formats metacpan
Bio::SeqIO::FTHelper Helper class for Embl/Genbank feature tables metacpan
Bio::SeqIO::MultiFile Treating a set of files as a single input stream metacpan
Bio::SeqIO::abi abi trace sequence input/output stream metacpan
Bio::SeqIO::ace ace sequence input/output stream metacpan
Bio::SeqIO::alf alf trace sequence input/output stream metacpan
Bio::SeqIO::asciitree asciitree sequence input/output stream metacpan
Bio::SeqIO::bsml BSML sequence input/output stream metacpan
Bio::SeqIO::chadoxml chadoxml sequence input/output stream metacpan
Bio::SeqIO::ctf ctf trace sequence input/output stream metacpan
Bio::SeqIO::embl EMBL sequence input/output stream metacpan
Bio::SeqIO::exp exp trace sequence input/output stream metacpan
Bio::SeqIO::fasta fasta sequence input/output stream metacpan
Bio::SeqIO::fastq fastq sequence input/output stream metacpan
Bio::SeqIO::game a class for parsing and writing game-XML metacpan
Bio::SeqIO::game::featHandler a class for handling feature elements metacpan
Bio::SeqIO::game::gameHandler PerlSAX handler for game-XML metacpan
Bio::SeqIO::game::gameSubs a base class for game-XML parsing metacpan
Bio::SeqIO::game::gameWriter a class for writing game-XML metacpan
Bio::SeqIO::game::seqHandler a class for handling game-XML sequences metacpan
Bio::SeqIO::gcg GCG sequence input/output stream metacpan
Bio::SeqIO::genbank metacpan
Bio::SeqIO::kegg KEGG sequence input/output stream metacpan
Bio::SeqIO::largefasta method i/o on very large fasta sequence files metacpan
Bio::SeqIO::locuslink DESCRIPTION of Object metacpan
Bio::SeqIO::metafasta metafasta sequence input/output stream metacpan
Bio::SeqIO::phd .phd file input/output stream metacpan
Bio::SeqIO::pir PIR sequence input/output stream metacpan
Bio::SeqIO::pln pln trace sequence input/output stream metacpan
Bio::SeqIO::qual metacpan
Bio::SeqIO::raw raw sequence file input/output stream metacpan
Bio::SeqIO::scf .scf file input/output stream metacpan
Bio::SeqIO::swiss Swissprot sequence input/output stream metacpan
Bio::SeqIO::tab nearly raw sequence file input/output stream. Reads/writes id"\t"sequence"\n" metacpan
Bio::SeqIO::tigr TIGR XML sequence input/output stream metacpan
Bio::SeqIO::ztr ztr trace sequence input/output stream metacpan
Bio::SeqUtils Additional methods for PrimarySeq objects metacpan
Bio::SimpleAlign Multiple alignments held as a set of sequences metacpan
Bio::SimpleAnalysisI A simple interface to any (local or remote) analysis tool metacpan
Bio::Species Generic species object metacpan
Bio::Structure::Atom Bioperl structure Object, describes an Atom metacpan
Bio::Structure::Chain Bioperl structure Object, describes a chain metacpan
Bio::Structure::Entry Bioperl structure Object, describes the whole entry metacpan
Bio::Structure::IO Handler for Structure Formats metacpan
Bio::Structure::IO::pdb PDB input/output stream metacpan
Bio::Structure::Model Bioperl structure Object, describes a Model metacpan
Bio::Structure::Residue Bioperl structure Object, describes a Residue metacpan
Bio::Structure::SecStr::DSSP::Res Module for parsing/accessing dssp output metacpan
Bio::Structure::SecStr::STRIDE::Res Module for parsing/accessing stride output metacpan
Bio::Structure::StructureI Abstract Interface for a Structure objects metacpan
Bio::Symbol::Alphabet DESCRIPTION of Object metacpan
Bio::Symbol::AlphabetI A Symbol Alphabet metacpan
Bio::Symbol::DNAAlphabet A ready made DNA alphabet metacpan
Bio::Symbol::ProteinAlphabet A ready made Protein alphabet metacpan
Bio::Symbol::Symbol A biological symbol metacpan
Bio::Symbol::SymbolI Interface for a Symbol metacpan
Bio::Taxonomy representing Taxonomy. metacpan
Bio::Taxonomy::FactoryI interface to define how to access NCBI Taxonoy metacpan
Bio::Taxonomy::Node A node in a represented taxonomy metacpan
Bio::Taxonomy::Taxon Generic Taxonomic Entity object metacpan
Bio::Taxonomy::Tree An Organism Level Implementation of TreeI interface. metacpan
Bio::Tools::AlignFactory Base object for alignment factories metacpan
Bio::Tools::Alignment::Consed A module to work with objects from consed .ace files metacpan
Bio::Tools::Alignment::Trim A kludge to do specialized trimming of sequence based on quality. metacpan
Bio::Tools::Analysis::DNA::ESEfinder a wrapper around ESEfinder server metacpan
Bio::Tools::Analysis::Protein::Domcut a wrapper around Domcut server metacpan
Bio::Tools::Analysis::Protein::ELM metacpan
Bio::Tools::Analysis::Protein::GOR4 a wrapper around GOR4 protein secondary structure prediction server metacpan
Bio::Tools::Analysis::Protein::HNN a wrapper around HNN protein secondary structure prediction server metacpan
Bio::Tools::Analysis::Protein::Mitoprot a wrapper around Mitoprot server metacpan
Bio::Tools::Analysis::Protein::NetPhos a wrapper around NetPhos server metacpan
Bio::Tools::Analysis::Protein::Scansite a wrapper around the Scansite server metacpan
Bio::Tools::Analysis::Protein::Sopma a wrapper around Sopma protein secondary structure prediction server metacpan
Bio::Tools::Analysis::SimpleAnalysisBase abstact superclass for SimpleAnalysis implementations metacpan
Bio::Tools::AnalysisResult Base class for analysis result objects and parsers metacpan
Bio::Tools::BPbl2seq Lightweight BLAST parser for pair-wise sequence alignment using the BLAST algorithm. metacpan
Bio::Tools::BPlite Lightweight BLAST parser metacpan
Bio::Tools::BPlite::HSP Blast report High Scoring Pair (HSP) metacpan
Bio::Tools::BPlite::Iteration object for parsing single iteration of a PSIBLAST report metacpan
Bio::Tools::BPlite::Sbjct A Blast Subject (database search Hit) metacpan
Bio::Tools::BPpsilite Lightweight BLAST parser for (iterated) psiblast reports metacpan
Bio::Tools::Blast Bioperl BLAST sequence analysis object metacpan
Bio::Tools::Blast::HSP Bioperl BLAST High-Scoring Segment Pair object metacpan
Bio::Tools::Blast::HTML Bioperl Utility module for HTML formatting Blast reports metacpan
Bio::Tools::Blast::Sbjct Bioperl BLAST "Hit" object metacpan
Bio::Tools::Blat metacpan
Bio::Tools::CodonTable Bioperl codon table object metacpan
Bio::Tools::Coil metacpan
Bio::Tools::ECnumber metacpan
Bio::Tools::EMBOSS::Palindrome parse EMBOSS palindrome output metacpan
Bio::Tools::EPCR Parse ePCR output and make features metacpan
Bio::Tools::ESTScan Results of one ESTScan run metacpan
Bio::Tools::Eponine Results of one Eponine run metacpan
Bio::Tools::Est2Genome Parse est2genome output, makes simple Bio::SeqFeature::Generic objects metacpan
Bio::Tools::FootPrinter DESCRIPTION of Object metacpan
Bio::Tools::GFF A Bio::SeqAnalysisParserI compliant GFF format parser metacpan
Bio::Tools::Gel Calculates relative electrophoretic migration distances metacpan
Bio::Tools::Geneid Results of one geneid run metacpan
Bio::Tools::Genemark Results of one Genemark run metacpan
Bio::Tools::Genewise Results of one Genewise run metacpan
Bio::Tools::Genomewise Results of one Genomewise run metacpan
Bio::Tools::Genscan Results of one Genscan run metacpan
Bio::Tools::Glimmer A parser for GLIMMER gene predictions metacpan
Bio::Tools::Grail Results of one Grail run metacpan
Bio::Tools::GuessSeqFormat Module for determining the sequence format of the contents of a file, a string, or through a filehandle. metacpan
Bio::Tools::HMMER::Domain One particular domain hit from HMMER metacpan
Bio::Tools::HMMER::Results Object representing HMMER output results metacpan
Bio::Tools::HMMER::Set Set of identical domains from HMMER matches metacpan
Bio::Tools::Hmmpfam metacpan
Bio::Tools::IUPAC Generates unique Seq objects from an ambiguous Seq object metacpan
Bio::Tools::Lucy Object for analyzing the output from Lucy, a vector and quality trimming program from TIGR metacpan
Bio::Tools::MZEF Results of one MZEF run metacpan
Bio::Tools::OddCodes Object holding alternative alphabet coding for one protein sequence metacpan
Bio::Tools::Phylo::Molphy DESCRIPTION of Object metacpan
Bio::Tools::Phylo::Molphy::Result DESCRIPTION of Object metacpan
Bio::Tools::Phylo::PAML Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00 metacpan
Bio::Tools::Phylo::PAML::ModelResult A container for NSSite Model Result from PAML metacpan
Bio::Tools::Phylo::PAML::Result A PAML result set object metacpan
Bio::Tools::Phylo::Phylip::ProtDist DESCRIPTION of Object metacpan
Bio::Tools::Prediction::Exon A predicted exon feature metacpan
Bio::Tools::Prediction::Gene a predicted gene structure feature metacpan
Bio::Tools::Primer3 Create input for and work with the output from the program primer3 metacpan
Bio::Tools::Primer::Assessor::Base base class for common assessor things metacpan
Bio::Tools::Primer::Feature position of a single primer metacpan
Bio::Tools::Primer::Pair two primers on left and right side metacpan
Bio::Tools::Prints Parser for FingerPRINTScanII program metacpan
Bio::Tools::Profile parse Profile output metacpan
Bio::Tools::Promoterwise DESCRIPTION of Object metacpan
Bio::Tools::PrositeScan Parser for ps_scan result metacpan
Bio::Tools::Pseudowise Results of one Pseudowise run metacpan
Bio::Tools::QRNA A Parser for qrna output metacpan
Bio::Tools::RandomDistFunctions A set of routines useful for generating random data in different distributions metacpan
Bio::Tools::RepeatMasker DESCRIPTION of Object metacpan
Bio::Tools::RestrictionEnzyme Bioperl object for a restriction endonuclease (cuts DNA at specific locations) metacpan
Bio::Tools::Run::RemoteBlast Object for remote execution of the NCBI Blast via HTTP metacpan
Bio::Tools::Run::StandAloneBlast Object for the local execution of the NCBI Blast program suite (blastall, blastpgp, bl2seq). There is experimental support for WU-Blast. metacpan
Bio::Tools::Run::WrapperBase A Base object for wrappers around executables metacpan
Bio::Tools::Seg parse Seg output (filter low complexity protein sequence) metacpan
Bio::Tools::SeqAnal Bioperl sequence analysis base class. metacpan
Bio::Tools::SeqPattern Bioperl object for a sequence pattern or motif metacpan
Bio::Tools::SeqStats Object holding statistics for one particular sequence metacpan
Bio::Tools::SeqWords Object holding n-mer statistics for one sequence metacpan
Bio::Tools::SiRNA metacpan
Bio::Tools::Sigcleave Bioperl object for sigcleave analysis metacpan
Bio::Tools::Signalp metacpan
Bio::Tools::Sim4::Exon A single exon determined by an alignment metacpan
Bio::Tools::Sim4::Results Results of one Sim4 run metacpan
Bio::Tools::Tmhmm parse TmHMM output (transmembrane HMM) metacpan
Bio::Tools::WWW Bioperl manager for web resources related to biology. metacpan
Bio::Tools::dpAlign Perl extension to do pairwise dynamic programming sequence alignment 0.50 metacpan
Bio::Tools::pICalculator metacpan
Bio::Tools::pSW pairwise Smith Waterman object metacpan
Bio::Tree::AlleleNode A Node with Alleles attached metacpan
Bio::Tree::Node A Simple Tree Node metacpan
Bio::Tree::NodeI Interface describing a Tree Node metacpan
Bio::Tree::NodeNHX A Simple Tree Node with support for NHX tags metacpan
Bio::Tree::RandomFactory TreeFactory for generating Random Trees metacpan
Bio::Tree::Statistics Calculate certain statistics for a Tree metacpan
Bio::Tree::Tree An Implementation of TreeI interface. metacpan
Bio::Tree::TreeFunctionsI Decorated Interface implementing basic Tree exploration methods metacpan
Bio::Tree::TreeI A Tree object suitable for lots of things, designed originally for Phylogenetic Trees. metacpan
Bio::TreeIO Parser for Tree files metacpan
Bio::TreeIO::TreeEventBuilder Build Bio::Tree::Tree's and Bio::Tree::Node's from Events metacpan
Bio::TreeIO::lintree Parser for lintree output trees metacpan
Bio::TreeIO::newick TreeIO implementation for parsing Newick/New Hampshire/PHYLIP format. metacpan
Bio::TreeIO::nexus A TreeIO driver module for parsing Nexus tree output from PAUP metacpan
Bio::TreeIO::nhx TreeIO implementation for parsing Newick/New Hampshire eXtendend (NHX) format. metacpan
Bio::TreeIO::svggraph A simple output format that converts a Tree object to an SVG output metacpan
Bio::TreeIO::tabtree A simple output format which displays a tree as an ASCII drawing metacpan
Bio::UpdateableSeqI Descendant of Bio::SeqI that allows updates metacpan
Bio::Variation::AAChange Sequence change class for polypeptides metacpan
Bio::Variation::AAReverseMutate point mutation and codon information from single amino acid changes metacpan
Bio::Variation::Allele Sequence object with allele-specific attributes metacpan
Bio::Variation::DNAMutation DNA level mutation class metacpan
Bio::Variation::IO Handler for sequence variation IO Formats metacpan
Bio::Variation::IO::flat flat file sequence variation input/output stream metacpan
Bio::Variation::IO::xml XML sequence variation input/output stream metacpan
Bio::Variation::RNAChange Sequence change class for RNA level metacpan
Bio::Variation::SNP submitted SNP metacpan
Bio::Variation::SeqDiff Container class for mutation/variant descriptions metacpan
Bio::Variation::VariantI Sequence Change SeqFeature abstract class metacpan
Bio::WebAgent A base class for Web (any protocol) access metacpan

Provides

Name File View
Bio::AnalysisI::JobI Bio/AnalysisI.pm metacpan
Bio::DB::Fasta::Stream Bio/DB/Fasta.pm metacpan
Bio::DB::GFF::Adaptor::dbi::faux_dbh Bio/DB/GFF/Adaptor/dbi/caching_handle.pm metacpan
Bio::DB::GFF::ID_Iterator Bio/DB/GFF.pm metacpan
Bio::PrimarySeq::Fasta Bio/DB/Fasta.pm metacpan

Other Files

Bio/DB/MANIFEST metacpan
Bio/DB/Makefile.PL metacpan
Changes metacpan
MANIFEST metacpan
Makefile.PL metacpan
README metacpan