bioperl 1.4
- Released by
- BIRNEY
- Version
- Release Date
- 2003-12-23
- Kwalitee
- 115.62
- Core Kwalitee
- 78.12
- LINKS
bioperl 1.4 Deleted
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
- has_security_doc
-
Add SECURITY(.pod|md). See Software::Security::Policy.
- security_doc_contains_contact
-
Add SECURITY(.pod|md) and add a contact address. See Software::Security::Policy.
- has_contributing_doc
-
Add CONTRIBUTING(.pod|md). See https://docs.github.com/en/communities/setting-up-your-project-for-healthy-contributions/setting-guidelines-for-repository-contributors.
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 |