Kwalitee Issues

has_meta_yml

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

main_module_version_matches_dist_version

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

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 (838) does not match dist (842):
  • Missing in MANIFEST: Bio/DB/Makefile.PL, MANIFEST.SKIP, Makefile.PL, bioperl.lisp

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,bioperl.lisp

no_pod_errors

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

Error: *** ERROR: Can't have a 0 in =over 0 at line 329 in file bioperl-1.0.1/Bio/Root/Object.pm *** ERROR: empty =head2 at line 153 in file bioperl-1.0.1/Bio/Species.pm *** ERROR: Can't have a 0 in =over 0 at line 82 in file bioperl-1.0.1/Bio/Tools/Blast/HSP.pm

prereq_matches_use

List all used modules in META.yml requires

Error:

  • Bio::DB::GFF::Aggregator
  • Bio::Index::AbstractSeq
  • Bio::Root::RootI
  • DBI
  • GD
  • HTML::Parser
  • HTTP::Request::Common
  • HTTP::Response
  • IO::String
  • LWP
  • LWP::UserAgent
  • SOAP::Lite
  • Text::Shellwords
  • XML::DOM
  • XML::Handler::Subs
  • XML::Parser
  • XML::Parser::PerlSAX
  • XML::Twig
  • XML::Writer

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::DB::Flat, Bio::DB::XEMBLService, Bio::DasSegmentI, Bio::Root::Xref, Bio::Search::BlastUtils, Bio::SearchIO::SearchWriterI, Bio::SeqIO::game::seqHandler

consistent_version

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

Error: 0.01,0.011,0.014,0.02,0.04,0.041,0.043,0.05,0.09,0.1,0.10,0.15,0.2,0.20,0.30,0.50,0.60,0.8,1,1.0,1.00,1.000001,1.01,1.03,1.04,1.1,1.2,1.3,1.4,1.40,1.5,1.6,1.8,1.9,2.3,2.4,2.42,2.7,3.3,4.44,5.2

has_meta_json

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

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.

no_stdin_for_prompting

Use the prompt() method from ExtUtils::MakeMaker/Module::Build.

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::Glyph::wormbase_transcript
  • Bio::Graphics::Panel

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/AlignIO.pm, Bio/AlignIO/bl2seq.pm, Bio/AlignIO/clustalw.pm, Bio/AlignIO/emboss.pm, Bio/AlignIO/fasta.pm, Bio/AlignIO/mase.pm, Bio/AlignIO/mega.pm, Bio/AlignIO/meme.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/AnalysisParserI.pm, Bio/AnalysisResultI.pm, Bio/Annotation.pm, Bio/Annotation/Collection.pm, Bio/Annotation/Comment.pm, Bio/Annotation/DBLink.pm, Bio/Annotation/Reference.pm, Bio/Annotation/SimpleValue.pm, Bio/Annotation/TypeManager.pm, Bio/AnnotationCollectionI.pm, Bio/AnnotationI.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/DB/Ace.pm, Bio/DB/Biblio/biofetch.pm, Bio/DB/Biblio/soap.pm, Bio/DB/BiblioI.pm, Bio/DB/BioFetch.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/OBDAIndex.pm, Bio/DB/GDB.pm, Bio/DB/GFF.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/mysqlopt.pm, Bio/DB/GFF/Adaptor/memory.pm, Bio/DB/GFF/Adaptor/memory_iterator.pm, Bio/DB/GFF/Aggregator/alignment.pm, Bio/DB/GFF/Aggregator/clone.pm, Bio/DB/GFF/Aggregator.pm, Bio/DB/GFF/Aggregator/none.pm, Bio/DB/GFF/Aggregator/transcript.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/NCBIHelper.pm, Bio/DB/RandomAccessI.pm, Bio/DB/RefSeq.pm, Bio/DB/Registry.pm, Bio/DB/SeqI.pm, Bio/DB/SwissProt.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/DasI.pm, Bio/DasSegmentI.pm, Bio/Event/EventGeneratorI.pm, Bio/Event/EventHandlerI.pm, Bio/Factory/ApplicationFactoryI.pm, Bio/Factory/BlastHitFactory.pm, Bio/Factory/BlastResultFactory.pm, Bio/Factory/DriverFactory.pm, Bio/Factory/EMBOSS.pm, Bio/Factory/HitFactoryI.pm, Bio/Factory/MapFactoryI.pm, Bio/Factory/ResultFactoryI.pm, Bio/Factory/SeqAnalysisParserFactory.pm, Bio/Factory/SeqAnalysisParserFactoryI.pm, Bio/Factory/TreeFactoryI.pm, Bio/Graphics.pm, Bio/Graphics/Feature.pm, Bio/Graphics/FeatureFile.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/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/line.pm, Bio/Graphics/Glyph/oval.pm, Bio/Graphics/Glyph/pinsertion.pm, Bio/Graphics/Glyph/primers.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/toomany.pm, Bio/Graphics/Glyph/track.pm, Bio/Graphics/Glyph/transcript.pm, Bio/Graphics/Glyph/transcript2.pm, Bio/Graphics/Glyph/triangle.pm, Bio/Graphics/Glyph/wormbase_transcript.pm, Bio/Graphics/Panel.pm, Bio/Index/Abstract.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/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/Perl.pm, Bio/PrimarySeq.pm, Bio/PrimarySeqI.pm, Bio/Range.pm, Bio/RangeI.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/Utilities.pm, Bio/Root/Vector.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/GenericHSP.pm, Bio/Search/HSP/HSPI.pm, Bio/Search/Hit/BlastHit.pm, Bio/Search/Hit/Fasta.pm, Bio/Search/Hit/GenericHit.pm, Bio/Search/Hit/HitI.pm, Bio/Search/Result/BlastResult.pm, Bio/Search/Result/GenericResult.pm, Bio/Search/Result/ResultI.pm, Bio/SearchDist.pm, Bio/SearchIO.pm, Bio/SearchIO/EventHandlerI.pm, Bio/SearchIO/SearchResultEventBuilder.pm, Bio/SearchIO/SearchWriterI.pm, Bio/SearchIO/Writer/HSPTableWriter.pm, Bio/SearchIO/Writer/HTMLResultWriter.pm, Bio/SearchIO/Writer/HitTableWriter.pm, Bio/SearchIO/Writer/ResultTableWriter.pm, Bio/SearchIO/blast.pm, Bio/SearchIO/blastxml.pm, Bio/SearchIO/fasta.pm, Bio/SearchIO/psiblast.pm, Bio/Seq.pm, Bio/Seq/LargePrimarySeq.pm, Bio/Seq/LargeSeq.pm, Bio/Seq/PrimaryQual.pm, Bio/Seq/QualI.pm, Bio/Seq/RichSeq.pm, Bio/Seq/RichSeqI.pm, Bio/Seq/SeqWithQuality.pm, Bio/SeqAnalysisParserI.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/Similarity.pm, Bio/SeqFeature/SimilarityPair.pm, Bio/SeqFeatureI.pm, Bio/SeqI.pm, Bio/SeqIO.pm, Bio/SeqIO/FTHelper.pm, Bio/SeqIO/MultiFile.pm, Bio/SeqIO/ace.pm, Bio/SeqIO/bsml.pm, Bio/SeqIO/embl.pm, Bio/SeqIO/fasta.pm, Bio/SeqIO/fastq.pm, Bio/SeqIO/game.pm, Bio/SeqIO/game/featureHandler.pm, Bio/SeqIO/game/idHandler.pm, Bio/SeqIO/game/seqHandler.pm, Bio/SeqIO/gcg.pm, Bio/SeqIO/genbank.pm, Bio/SeqIO/largefasta.pm, Bio/SeqIO/phd.pm, Bio/SeqIO/pir.pm, Bio/SeqIO/qual.pm, Bio/SeqIO/raw.pm, Bio/SeqIO/scf.pm, Bio/SeqIO/swiss.pm, Bio/SeqUtils.pm, Bio/SimpleAlign.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/Tools/AlignFactory.pm, Bio/Tools/Alignment/Consed.pm, Bio/Tools/Alignment/Trim.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/CodonTable.pm, Bio/Tools/EPCR.pm, Bio/Tools/ESTScan.pm, Bio/Tools/GFF.pm, Bio/Tools/Gel.pm, Bio/Tools/Genemark.pm, Bio/Tools/Genscan.pm, Bio/Tools/Grail.pm, Bio/Tools/HMMER/Domain.pm, Bio/Tools/HMMER/Results.pm, Bio/Tools/HMMER/Set.pm, Bio/Tools/IUPAC.pm, Bio/Tools/Lucy.pm, Bio/Tools/MZEF.pm, Bio/Tools/OddCodes.pm, Bio/Tools/Prediction/Exon.pm, Bio/Tools/Prediction/Gene.pm, Bio/Tools/RestrictionEnzyme.pm, Bio/Tools/Run/Alignment/Clustalw.pm, Bio/Tools/Run/Alignment/TCoffee.pm, Bio/Tools/Run/EMBOSSApplication.pm, Bio/Tools/Run/RemoteBlast.pm, Bio/Tools/Run/StandAloneBlast.pm, Bio/Tools/SeqAnal.pm, Bio/Tools/SeqPattern.pm, Bio/Tools/SeqStats.pm, Bio/Tools/SeqWords.pm, Bio/Tools/Sigcleave.pm, Bio/Tools/Sim4/Exon.pm, Bio/Tools/Sim4/Results.pm, Bio/Tools/StateMachine/IOStateMachine.pm, Bio/Tools/WWW.pm, Bio/Tools/pSW.pm, Bio/Tree/AlleleNode.pm, Bio/Tree/Node.pm, Bio/Tree/NodeI.pm, Bio/Tree/RandomFactory.pm, Bio/Tree/Statistics.pm, Bio/Tree/Tree.pm, Bio/Tree/TreeI.pm, Bio/TreeIO.pm, Bio/TreeIO/TreeEventBuilder.pm, Bio/TreeIO/newick.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/SeqDiff.pm, Bio/Variation/VariantI.pm, Bio/Root/RootI.pm, Bio/Index/AbstractSeq.pm, Bio/Tools/StateMachine/AbstractStateMachine.pm

use_warnings

Add 'use warnings' (or its equivalents) to all modules (this will require perl > 5.6), 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::AlignIO, Bio::AlignIO::bl2seq, Bio::AlignIO::clustalw, Bio::AlignIO::emboss, Bio::AlignIO::fasta, Bio::AlignIO::mase, Bio::AlignIO::mega, Bio::AlignIO::meme, 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::AnalysisParserI, Bio::AnalysisResultI, Bio::Annotation, Bio::Annotation::Collection, Bio::Annotation::Comment, Bio::Annotation::DBLink, Bio::Annotation::Reference, Bio::Annotation::SimpleValue, Bio::Annotation::TypeManager, Bio::AnnotationCollectionI, Bio::AnnotationI, 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::DB::Ace, Bio::DB::Biblio::biofetch, Bio::DB::Biblio::soap, Bio::DB::BiblioI, Bio::DB::BioFetch, 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::OBDAIndex, Bio::DB::GDB, Bio::DB::GFF, 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::mysqlopt, Bio::DB::GFF::Adaptor::memory, Bio::DB::GFF::Adaptor::memory_iterator, Bio::DB::GFF::Aggregator::alignment, Bio::DB::GFF::Aggregator::clone, Bio::DB::GFF::Aggregator::mutant, Bio::DB::GFF::Aggregator::none, Bio::DB::GFF::Aggregator::transcript, 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::NCBIHelper, Bio::DB::RandomAccessI, Bio::DB::RefSeq, Bio::DB::Registry, Bio::DB::SeqI, Bio::DB::SwissProt, Bio::DB::Universal, Bio::DB::UpdateableSeqI, Bio::DB::WebDBSeqI, Bio::DB::XEMBL, Bio::DB::XEMBLService, Bio::DBLinkContainerI, Bio::DasI, Bio::DasSegmentI, Bio::Event::EventGeneratorI, Bio::Event::EventHandlerI, Bio::Factory::ApplicationFactoryI, Bio::Factory::BlastHitFactory, Bio::Factory::BlastResultFactory, Bio::Factory::DriverFactory, Bio::Factory::EMBOSS, Bio::Factory::HitFactoryI, Bio::Factory::MapFactoryI, Bio::Factory::ResultFactoryI, Bio::Factory::SeqAnalysisParserFactory, Bio::Factory::SeqAnalysisParserFactoryI, Bio::Factory::TreeFactoryI, 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::extending_arrow, 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::ruler_arrow, 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::Glyph::wormbase_transcript, Bio::Graphics::Panel, Bio::Index::Abstract, 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::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::Perl, Bio::PrimarySeq, Bio::PrimarySeqI, Bio::Range, Bio::RangeI, 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::Utilities, Bio::Root::Vector, Bio::Root::Xref, Bio::Search::BlastUtils, Bio::Search::DatabaseI, Bio::Search::GenericDatabase, Bio::Search::HSP::BlastHSP, Bio::Search::HSP::GenericHSP, Bio::Search::HSP::HSPI, Bio::Search::Hit::BlastHit, Bio::Search::Hit::Fasta, Bio::Search::Hit::GenericHit, Bio::Search::Hit::HitI, Bio::Search::Result::BlastResult, Bio::Search::Result::GenericResult, Bio::Search::Result::ResultI, Bio::SearchDist, Bio::SearchIO, Bio::SearchIO::EventHandlerI, Bio::SearchIO::SearchResultEventBuilder, Bio::SearchIO::SearchWriterI, Bio::SearchIO::Writer::HSPTableWriter, Bio::SearchIO::Writer::HTMLResultWriter, Bio::SearchIO::Writer::HitTableWriter, Bio::SearchIO::Writer::ResultTableWriter, Bio::SearchIO::blast, Bio::SearchIO::blastxml, Bio::SearchIO::fasta, Bio::SearchIO::psiblast, Bio::Seq, Bio::Seq::LargePrimarySeq, Bio::Seq::LargeSeq, Bio::Seq::PrimaryQual, Bio::Seq::QualI, Bio::Seq::RichSeq, Bio::Seq::RichSeqI, Bio::Seq::SeqWithQuality, Bio::SeqAnalysisParserI, 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::Similarity, Bio::SeqFeature::SimilarityPair, Bio::SeqFeatureI, Bio::SeqI, Bio::SeqIO, Bio::SeqIO::FTHelper, Bio::SeqIO::MultiFile, Bio::SeqIO::ace, Bio::SeqIO::bsml, Bio::SeqIO::embl, Bio::SeqIO::fasta, Bio::SeqIO::fastq, Bio::SeqIO::game, Bio::SeqIO::game::featureHandler, Bio::SeqIO::game::idHandler, Bio::SeqIO::game::seqHandler, Bio::SeqIO::gcg, Bio::SeqIO::genbank, Bio::SeqIO::largefasta, Bio::SeqIO::phd, Bio::SeqIO::pir, Bio::SeqIO::qual, Bio::SeqIO::raw, Bio::SeqIO::scf, Bio::SeqIO::swiss, Bio::SeqUtils, Bio::SimpleAlign, 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::Tools::AlignFactory, Bio::Tools::Alignment::Consed, Bio::Tools::Alignment::Trim, 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::CodonTable, Bio::Tools::EPCR, Bio::Tools::ESTScan, Bio::Tools::GFF, Bio::Tools::Gel, Bio::Tools::Genemark, Bio::Tools::Genscan, Bio::Tools::Grail, Bio::Tools::HMMER::Domain, Bio::Tools::HMMER::Results, Bio::Tools::HMMER::Set, Bio::Tools::IUPAC, Bio::Tools::Lucy, Bio::Tools::MZEF, Bio::Tools::OddCodes, Bio::Tools::Prediction::Exon, Bio::Tools::Prediction::Gene, Bio::Tools::RestrictionEnzyme, Bio::Tools::Run::Alignment::Clustalw, Bio::Tools::Run::Alignment::TCoffee, Bio::Tools::Run::EMBOSSApplication, Bio::Tools::Run::RemoteBlast, Bio::Tools::Run::StandAloneBlast, Bio::Tools::SeqAnal, Bio::Tools::SeqPattern, Bio::Tools::SeqStats, Bio::Tools::SeqWords, Bio::Tools::Sigcleave, Bio::Tools::Sim4::Exon, Bio::Tools::Sim4::Results, Bio::Tools::StateMachine::IOStateMachine, Bio::Tools::WWW, Bio::Tools::pSW, Bio::Tree::AlleleNode, Bio::Tree::Node, Bio::Tree::NodeI, Bio::Tree::RandomFactory, Bio::Tree::Statistics, Bio::Tree::Tree, Bio::Tree::TreeI, Bio::TreeIO, Bio::TreeIO::TreeEventBuilder, Bio::TreeIO::newick, 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::SeqDiff, Bio::Variation::VariantI, Foo, MyShinyNewIndexer, SimpleStateMachine

Modules

Name Abstract Version View
Bio::Align::AlignI An interface for describing sequence alignments. 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 sequence input/output 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::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::AnalysisParserI Generic analysis output parser interface metacpan
Bio::AnalysisResultI Interface for analysis result objects metacpan
Bio::Annotation A generic object for annotations. 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::Reference Specialised DBLink object for Literature References metacpan
Bio::Annotation::SimpleValue A simple scalar metacpan
Bio::Annotation::TypeManager Manages types for annotation collections metacpan
Bio::AnnotationCollectionI Interface for annotation collections metacpan
Bio::AnnotationI Annotation interface metacpan
Bio::Biblio A Bibliographic Query Service module 1.5 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 1.8 metacpan
Bio::Biblio::IO::medlinexml A converter of XML files with MEDLINE citations 1.3 metacpan
Bio::Biblio::IO::pubmed2ref A converter of a raw hash to PUBMED citations 1.1 metacpan
Bio::Biblio::IO::pubmedxml A converter of XML files with PUBMED citations 1.2 metacpan
Bio::Biblio::Journal Representation of a journal metacpan
Bio::Biblio::JournalArticle Representation of a journal article metacpan
Bio::Biblio::MedlineArticle 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::DB::Ace Database object interface to ACeDB servers metacpan
Bio::DB::Biblio::biofetch A BioFetch-based access to a bibliographic citation retrieval 1.1 metacpan
Bio::DB::Biblio::soap A SOAP-based access to a bibliographic query service 1.1 metacpan
Bio::DB::BiblioI An interface to a Bibliographic Query Service 1.1 metacpan
Bio::DB::BioFetch Database object interface to BioFetch retrieval 1.0 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 1.03 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 metacpan
Bio::DB::Flat::BDB::fasta metacpan
Bio::DB::Flat::OBDAIndex Binary 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 1.03 metacpan
Bio::DB::GFF::Adaptor::dbi Database adaptor for DBI (SQL) databases 0.30 metacpan
Bio::DB::GFF::Adaptor::dbi::caching_handle Cache for database handles 1 metacpan
Bio::DB::GFF::Adaptor::dbi::iterator metacpan
Bio::DB::GFF::Adaptor::dbi::mysql Database adaptor for a specific mysql schema 0.50 metacpan
Bio::DB::GFF::Adaptor::dbi::mysqlopt Optimized Bio::DB::GFF adaptor for mysql 0.8 metacpan
Bio::DB::GFF::Adaptor::memory 0.02 metacpan
Bio::DB::GFF::Adaptor::memory_iterator metacpan
Bio::DB::GFF::Aggregator::alignment Alignment aggregator 0.15 metacpan
Bio::DB::GFF::Aggregator::clone Clone aggregator 0.20 metacpan
Bio::DB::GFF::Aggregator::none No aggregation 0.10 metacpan
Bio::DB::GFF::Aggregator::transcript Transcript aggregator 0.10 metacpan
Bio::DB::GFF::Featname The name of a feature metacpan
Bio::DB::GFF::Feature A relative segment identified by a feature type 0.60 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 0.30 metacpan
Bio::DB::GFF::Segment Simple DNA segment object 0.30 metacpan
Bio::DB::GFF::Typename The name of a feature type 1.1 metacpan
Bio::DB::GFF::Util::Binning metacpan
Bio::DB::GFF::Util::Rearrange 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::NCBIHelper A collection of routines useful for queries to NCBI 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::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::DasI DAS-style access to a feature database metacpan
Bio::Event::EventGeneratorI This interface describes the basic event generator class. metacpan
Bio::Event::EventHandlerI An Event Handler Interface metacpan
Bio::Factory::ApplicationFactoryI Interface class for Application Factories metacpan
Bio::Factory::BlastHitFactory Factory for Bio::Search::Hit::BlastHit objects metacpan
Bio::Factory::BlastResultFactory Factory for Bio::Search::Result::BlastResult objects metacpan
Bio::Factory::DriverFactory Base class for factory classes loading drivers metacpan
Bio::Factory::EMBOSS EMBOSS appliaction factory class metacpan
Bio::Factory::HitFactoryI Interface for an object that builds Bio::Search::Hit::HitI objects metacpan
Bio::Factory::MapFactoryI A Factory for getting markers 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::TreeFactoryI Factory Interface for getting and writing trees from/to a data stream metacpan
Bio::Graphics Generate GD images of Bio::Seq objects 1.04 metacpan
Bio::Graphics::Feature A simple feature object for use with Bio::Graphics::Panel 1.40 metacpan
Bio::Graphics::FeatureFile A set of Bio::Graphics features, stored in a file 1.01 metacpan
Bio::Graphics::Glyph Base class for Bio::Graphics::Glyph objects 1.01 metacpan
Bio::Graphics::Glyph::Factory metacpan
Bio::Graphics::Glyph::alignment The "alignment" glyph metacpan
Bio::Graphics::Glyph::anchored_arrow The "anchored_arrow" glyph 1.01 metacpan
Bio::Graphics::Glyph::arrow metacpan
Bio::Graphics::Glyph::box The "box" glyph metacpan
Bio::Graphics::Glyph::crossbox The "crossbox" glyph metacpan
Bio::Graphics::Glyph::diamond The "diamond" glyph metacpan
Bio::Graphics::Glyph::dna 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::line The "line" 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::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 1.00 metacpan
Bio::Graphics::Glyph::span The "span" 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 1.2 metacpan
Bio::Graphics::Glyph::triangle The "triangle" glyph metacpan
Bio::Graphics::Glyph::wormbase_transcript The "wormbase_transcript" glyph metacpan
Bio::Graphics::Panel Generate GD images of Bio::Seq objects 1.01 metacpan
Bio::Index::Abstract Abstract interface for indexing a flat file metacpan
Bio::Index::Blast Indexes Blast reports and supports retrieval based on query accession(s) 0.1 metacpan
Bio::Index::EMBL Interface for indexing (multiple) EMBL/Swissprot .dat files (ie flat file embl/swissprot format). 0.1 metacpan
Bio::Index::Fasta Interface for indexing (multiple) fasta files 0.2 metacpan
Bio::Index::Fastq Interface for indexing (multiple) fastq files 0.2 metacpan
Bio::Index::GenBank Interface for indexing (multiple) GenBank .seq files (ie flat file GenBank format). 0.1 metacpan
Bio::Index::SwissPfam Interface for indexing swisspfam files 0.1 metacpan
Bio::Index::Swissprot Interface for indexing (multiple) Swissprot .dat files (ie flat file swissprot format). 0.1 metacpan
Bio::LiveSeq::AARange AARange abstract class for LiveSeq 1.8 metacpan
Bio::LiveSeq::Chain DoubleChain DataStructure for Perl 2.7 metacpan
Bio::LiveSeq::ChainI Double linked chain data structure 1.9 metacpan
Bio::LiveSeq::DNA DNA object for LiveSeq 1.4 metacpan
Bio::LiveSeq::Exon Range abstract class for LiveSeq 1.1 metacpan
Bio::LiveSeq::Gene Range abstract class for LiveSeq 2.3 metacpan
Bio::LiveSeq::IO::BioPerl Loader for LiveSeq from EMBL entries with BioPerl 2.42 metacpan
Bio::LiveSeq::IO::Loader Parent Loader for LiveSeq 4.44 metacpan
Bio::LiveSeq::IO::SRS Loader for LiveSeq from EMBL entries with SRS 2.4 metacpan
Bio::LiveSeq::Intron Range abstract class for LiveSeq 1 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 1 metacpan
Bio::LiveSeq::Range Range abstract class for LiveSeq 1.6 metacpan
Bio::LiveSeq::Repeat_Region Repeat_Region class for LiveSeq 1 metacpan
Bio::LiveSeq::Repeat_Unit Repeat_Unit class for LiveSeq 1 metacpan
Bio::LiveSeq::SeqI Abstract sequence interface class for LiveSeq 3.3 metacpan
Bio::LiveSeq::Transcript Transcript class for LiveSeq 5.2 metacpan
Bio::LiveSeq::Translation Translation class for LiveSeq 1.8 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::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 1 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::Perl Functional access to BioPerl for people who don't know objects metacpan
Bio::PrimarySeq Bioperl lightweight Sequence Object metacpan
Bio::PrimarySeqI Interface definition for a Bio::PrimarySeq metacpan
Bio::Range Pure perl RangeI implementation metacpan
Bio::RangeI Range interface metacpan
Bio::Root::Err 0.041 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. 0.043 metacpan
Bio::Root::Object A core Perl 5 object. 0.041 metacpan
Bio::Root::Root Hash-based implementation of Bio::Root::RootI 1 metacpan
Bio::Root::Utilities General-purpose utility module 0.05 metacpan
Bio::Root::Vector Interface for managing linked lists of Perl5 objects. 0.04 metacpan
Bio::Root::Xref A generic cross-reference object. 0.01 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::GenericHSP DESCRIPTION of Object metacpan
Bio::Search::HSP::HSPI Interface for a High Scoring Pair in a similarity search result metacpan
Bio::Search::Hit::BlastHit Bioperl BLAST Hit object 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::HitI Interface for a hit in a similarity search result metacpan
Bio::Search::Result::BlastResult A top-level BLAST Report object metacpan
Bio::Search::Result::GenericResult Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results. metacpan
Bio::Search::Result::ResultI Abstract interface to Search Result 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::SearchResultEventBuilder Event Handler for SearchIO events. metacpan
Bio::SearchIO::SearchWriterI Interface for outputting parsed Search results 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::blast Event generator for event based parsing of blast reports metacpan
Bio::SearchIO::blastxml A SearchIO implementation of NCBI Blast XML parsing. metacpan
Bio::SearchIO::fasta A SearchIO parser for FASTA results metacpan
Bio::SearchIO::psiblast Parser for traditional BLAST and PSI-BLAST reports metacpan
Bio::Seq Sequence object, with features 1.000001 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::PrimaryQual Bioperl lightweight Quality Object 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 RichSeq interface, mainly for database orientated sequences metacpan
Bio::Seq::SeqWithQuality Bioperl object packaging a sequence with its quality metacpan
Bio::SeqAnalysisParserI Sequence analysis output parser interface 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 DESCRIPTION of Object 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 transcription unit metacpan
Bio::SeqFeature::Generic Generic SeqFeature metacpan
Bio::SeqFeature::PositionProxy 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::SeqFeatureI Abstract interface of a Sequence Feature metacpan
Bio::SeqI Abstract Interface of Sequence (with features) 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::ace ace sequence input/output stream metacpan
Bio::SeqIO::bsml BSML sequence input/output stream metacpan
Bio::SeqIO::embl EMBL 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 Parses GAME XML 0.1 and higher into and out of Bio::Seq objects. metacpan
Bio::SeqIO::game::featureHandler GAME helper via PerlSAX helper. metacpan
Bio::SeqIO::game::idHandler GAME helper via PerlSAX helper. metacpan
Bio::SeqIO::game::seqHandler GAME helper via PerlSAX helper. metacpan
Bio::SeqIO::gcg GCG sequence input/output stream metacpan
Bio::SeqIO::genbank metacpan
Bio::SeqIO::largefasta method i/o on very large fasta sequence files metacpan
Bio::SeqIO::phd .phd file input/output stream metacpan
Bio::SeqIO::pir PIR 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::SeqUtils Additional methods for PrimarySeq objects metacpan
Bio::SimpleAlign 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::Tools::AlignFactory Base object for alignment factories metacpan
Bio::Tools::Alignment::Consed A module to work with objects from consed .ace files 0.60 metacpan
Bio::Tools::Alignment::Trim A kludge to do specialized trimming of sequence based on quality. 0.01 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 metacpan
Bio::Tools::BPlite::Sbjct A Blast Subject (database search Hit) metacpan
Bio::Tools::BPpsilite metacpan
Bio::Tools::Blast 0.09 metacpan
Bio::Tools::Blast::HSP metacpan
Bio::Tools::Blast::HTML metacpan
Bio::Tools::Blast::Sbjct metacpan
Bio::Tools::CodonTable Bioperl codon table object metacpan
Bio::Tools::EPCR Parse ePCR output and make features metacpan
Bio::Tools::ESTScan Results of one ESTScan run metacpan
Bio::Tools::GFF A Bio::SeqAnalysisParserI compliant GFF format parser metacpan
Bio::Tools::Gel Calculates relative electrophoretic migration distances metacpan
Bio::Tools::Genemark Results of one Genemark run metacpan
Bio::Tools::Genscan Results of one Genscan run metacpan
Bio::Tools::Grail Results of one Grail run 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::IUPAC metacpan
Bio::Tools::Lucy Object for analyzing the output from Lucy, a vector and quality trimming program from TIGR 0.01 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::Prediction::Exon A predicted exon feature metacpan
Bio::Tools::Prediction::Gene a predicted gene structure feature metacpan
Bio::Tools::RestrictionEnzyme Bioperl object for a restriction endonuclease (cuts DNA at specific locations) metacpan
Bio::Tools::Run::Alignment::Clustalw Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the Clustalw program metacpan
Bio::Tools::Run::Alignment::TCoffee Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the TCoffee program metacpan
Bio::Tools::Run::EMBOSSApplication class for EMBOSS Applications 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) metacpan
Bio::Tools::SeqAnal 0.011 metacpan
Bio::Tools::SeqPattern 0.011 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::Sigcleave 0.01 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::StateMachine::IOStateMachine IO-based implementation of AbstractStateMachine metacpan
Bio::Tools::WWW 0.014 metacpan
Bio::Tools::pSW pairwise Smith Waterman object metacpan
Bio::Tree::AlleleNode DESCRIPTION of Object metacpan
Bio::Tree::Node A Simple Tree Node metacpan
Bio::Tree::NodeI Interface describing a Tree Node 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::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::newick TreeIO implementation for parsing Newick/New Hampshire/PHYLIP format. metacpan
Bio::UpdateableSeqI Descendant of Bio::SeqI that allows updates metacpan
Bio::Variation::AAChange Sequence change class for polypeptides 1 metacpan
Bio::Variation::AAReverseMutate point mutation and codon information from single amino acid changes 1 metacpan
Bio::Variation::Allele Sequence object with allele-specific attributes 1 metacpan
Bio::Variation::DNAMutation DNA level mutation class 1 metacpan
Bio::Variation::IO Handler for sequence variation IO Formats 1 metacpan
Bio::Variation::IO::flat flat file sequence variation input/output stream 1 metacpan
Bio::Variation::IO::xml XML sequence variation input/output stream 1.1 metacpan
Bio::Variation::RNAChange Sequence change class for RNA level 1 metacpan
Bio::Variation::SeqDiff Container class for mutation/variant descriptions 1 metacpan
Bio::Variation::VariantI Sequence Change SeqFeature abstract class 1 metacpan

Provides

Name File View
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::Adaptor::dbi::faux_sth Bio/DB/GFF/Adaptor/dbi/caching_handle.pm metacpan
Bio::DB::GFF::Aggregator Bio/DB/GFF/Aggregator.pm metacpan
Bio::DB::GFF::ID_Iterator Bio/DB/GFF.pm metacpan
Bio::Index::AbstractSeq Bio/Index/AbstractSeq.pm metacpan
Bio::PrimarySeq::Fasta Bio/DB/Fasta.pm metacpan
Bio::Root::RootI Bio/Root/RootI.pm metacpan
Bio::Tools::StateMachine::AbstractStateMachine Bio/Tools/StateMachine/AbstractStateMachine.pm metacpan

Other Files

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