BioPerl 1.5.9_4
- Released by
- CJFIELDS
- Version
- Release Date
- 2009-01-22
- Kwalitee
- 137.5
- Core Kwalitee
- 87.5
- LINKS
BioPerl 1.5.9_4 Deleted
Kwalitee Issues
- buildtool_not_executable
-
Change the permissions of Build.PL/Makefile.PL to not-executable.
- 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::SeqFeature::NormalizedFeatureI, Bio::DB::SeqFeature::NormalizedTableFeatureI, Bio::DB::SeqFeature::Store::DBI::Iterator, Bio::Location::Split, Bio::Matrix::PSM::SiteMatrixI, Bio::MolEvol::CodonModel, Bio::Phenotype::PhenotypeI, Bio::Search::BlastUtils, Bio::SearchIO::SearchWriterI, Bio::SearchIO::XML::BlastHandler, Bio::SearchIO::XML::PsiBlastHandler, Bio::SearchIO::cross_match, Bio::SeqIO::game, Bio::Tools::EUtilities::Link::UrlLink, Bio::Tools::HMM, Bio::Tools::Primer::Assessor::Base, Bio::Tools::Primer::AssessorI, Bio::Tools::Primer::Feature, Bio::Tools::Primer::Pair, Bio::Tools::dpAlign
- 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-1.5.9._4/Bio/Tools/Geneid.pm -- Around line 36: Non-ASCII character seen before =encoding in 'Guigó'. Assuming CP1252 BioPerl-1.5.9._4/Bio/Tools/GuessSeqFormat.pm -- Around line 213: Non-ASCII character seen before =encoding in 'Kähäri,'. Assuming CP1252 BioPerl-1.5.9._4/Bio/Tools/Run/WrapperBase.pm -- Around line 169: Non-ASCII character seen before =encoding in 'NB:ÃThis'. Assuming CP1252 BioPerl-1.5.9._4/Bio/Tree/Statistics.pm -- Around line 198: Non-ASCII character seen before =encoding in 'deï¬ning'. Assuming UTF-8
- 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/ProteinStatistics.pm, Bio/Align/StatisticsI.pm, Bio/Align/Utilities.pm, Bio/AlignIO.pm, Bio/AlignIO/Handler/GenericAlignHandler.pm, Bio/AlignIO/arp.pm, Bio/AlignIO/bl2seq.pm, Bio/AlignIO/clustalw.pm, Bio/AlignIO/emboss.pm, Bio/AlignIO/fasta.pm, Bio/AlignIO/largemultifasta.pm, Bio/AlignIO/maf.pm, Bio/AlignIO/mase.pm, Bio/AlignIO/mega.pm, Bio/AlignIO/meme.pm, Bio/AlignIO/metafasta.pm, Bio/AlignIO/msf.pm, Bio/AlignIO/nexus.pm, Bio/AlignIO/pfam.pm, Bio/AlignIO/phylip.pm, Bio/AlignIO/po.pm, Bio/AlignIO/proda.pm, Bio/AlignIO/prodom.pm, Bio/AlignIO/psi.pm, Bio/AlignIO/selex.pm, Bio/AlignIO/stockholm.pm, Bio/AlignIO/xmfa.pm, Bio/AnalysisI.pm, Bio/AnalysisI.pm, Bio/AnalysisParserI.pm, Bio/AnalysisResultI.pm, Bio/AnnotatableI.pm, Bio/Annotation/AnnotationFactory.pm, Bio/Annotation/Collection.pm, Bio/Annotation/Comment.pm, Bio/Annotation/DBLink.pm, Bio/Annotation/OntologyTerm.pm, Bio/Annotation/Reference.pm, Bio/Annotation/Relation.pm, Bio/Annotation/SimpleValue.pm, Bio/Annotation/StructuredValue.pm, Bio/Annotation/TagTree.pm, Bio/Annotation/Target.pm, Bio/Annotation/Tree.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/IO/tigr.pm, Bio/Assembly/Scaffold.pm, Bio/Assembly/ScaffoldI.pm, Bio/Assembly/Singlet.pm, Bio/Assembly/Tools/ContigSpectrum.pm, Bio/Biblio.pm, Bio/Biblio/Article.pm, Bio/Biblio/BiblioBase.pm, Bio/Biblio/Book.pm, Bio/Biblio/BookArticle.pm, Bio/Biblio/IO.pm, Bio/Biblio/IO/medline2ref.pm, Bio/Biblio/IO/medlinexml.pm, Bio/Biblio/IO/pubmed2ref.pm, Bio/Biblio/IO/pubmedxml.pm, Bio/Biblio/Journal.pm, Bio/Biblio/JournalArticle.pm, Bio/Biblio/MedlineArticle.pm, Bio/Biblio/MedlineBook.pm, Bio/Biblio/MedlineBookArticle.pm, Bio/Biblio/MedlineJournal.pm, Bio/Biblio/MedlineJournalArticle.pm, Bio/Biblio/Organisation.pm, Bio/Biblio/Patent.pm, Bio/Biblio/Person.pm, Bio/Biblio/Proceeding.pm, Bio/Biblio/Provider.pm, Bio/Biblio/PubmedArticle.pm, Bio/Biblio/PubmedBookArticle.pm, Bio/Biblio/PubmedJournalArticle.pm, Bio/Biblio/Ref.pm, Bio/Biblio/Service.pm, Bio/Biblio/TechReport.pm, Bio/Biblio/Thesis.pm, Bio/Biblio/WebResource.pm, Bio/Cluster/ClusterFactory.pm, Bio/Cluster/FamilyI.pm, Bio/Cluster/SequenceFamily.pm, Bio/Cluster/UniGene.pm, Bio/Cluster/UniGeneI.pm, Bio/ClusterI.pm, Bio/ClusterIO.pm, Bio/ClusterIO/dbsnp.pm, Bio/ClusterIO/unigene.pm, Bio/CodonUsage/IO.pm, Bio/CodonUsage/Table.pm, Bio/Coordinate/Chain.pm, Bio/Coordinate/Collection.pm, Bio/Coordinate/ExtrapolatingPair.pm, Bio/Coordinate/GeneMapper.pm, Bio/Coordinate/Graph.pm, Bio/Coordinate/MapperI.pm, Bio/Coordinate/Pair.pm, Bio/Coordinate/Result.pm, Bio/Coordinate/Result/Gap.pm, Bio/Coordinate/Result/Match.pm, Bio/Coordinate/ResultI.pm, Bio/Coordinate/Utils.pm, Bio/DB/Ace.pm, Bio/DB/Biblio/biofetch.pm, Bio/DB/Biblio/eutils.pm, Bio/DB/Biblio/soap.pm, Bio/DB/BiblioI.pm, Bio/DB/BioFetch.pm, Bio/DB/CUTG.pm, Bio/DB/DBFetch.pm, Bio/DB/EMBL.pm, Bio/DB/EUtilities.pm, Bio/DB/EntrezGene.pm, Bio/DB/Expression.pm, Bio/DB/Expression/geo.pm, Bio/DB/Failover.pm, Bio/DB/Fasta.pm, Bio/DB/Fasta.pm, Bio/DB/FileCache.pm, Bio/DB/Flat.pm, Bio/DB/Flat/BDB.pm, Bio/DB/Flat/BDB/embl.pm, Bio/DB/Flat/BDB/fasta.pm, Bio/DB/Flat/BDB/genbank.pm, Bio/DB/Flat/BDB/swiss.pm, Bio/DB/Flat/BinarySearch.pm, Bio/DB/GFF.pm, Bio/DB/GFF/Adaptor/ace.pm, Bio/DB/GFF/Adaptor/berkeleydb.pm, Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm, Bio/DB/GFF/Adaptor/biofetch.pm, Bio/DB/GFF/Adaptor/biofetch_oracle.pm, Bio/DB/GFF/Adaptor/dbi.pm, Bio/DB/GFF/Adaptor/dbi/caching_handle.pm, Bio/DB/GFF/Adaptor/dbi/caching_handle.pm, Bio/DB/GFF/Adaptor/dbi/iterator.pm, Bio/DB/GFF/Adaptor/dbi/mysql.pm, Bio/DB/GFF/Adaptor/dbi/mysqlace.pm, Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm, Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm, Bio/DB/GFF/Adaptor/dbi/oracle.pm, Bio/DB/GFF/Adaptor/dbi/oracleace.pm, Bio/DB/GFF/Adaptor/dbi/pg.pm, Bio/DB/GFF/Adaptor/dbi/pg_fts.pm, Bio/DB/GFF/Adaptor/memory.pm, Bio/DB/GFF/Adaptor/memory/feature_serializer.pm, Bio/DB/GFF/Adaptor/memory/iterator.pm, Bio/DB/GFF/Aggregator.pm, Bio/DB/GFF/Aggregator/alignment.pm, Bio/DB/GFF/Aggregator/clone.pm, Bio/DB/GFF/Aggregator/coding.pm, Bio/DB/GFF/Aggregator/gene.pm, Bio/DB/GFF/Aggregator/match.pm, Bio/DB/GFF/Aggregator/none.pm, Bio/DB/GFF/Aggregator/orf.pm, Bio/DB/GFF/Aggregator/processed_transcript.pm, Bio/DB/GFF/Aggregator/so_transcript.pm, Bio/DB/GFF/Aggregator/transcript.pm, Bio/DB/GFF/Aggregator/ucsc_acembly.pm, Bio/DB/GFF/Aggregator/ucsc_ensgene.pm, Bio/DB/GFF/Aggregator/ucsc_genscan.pm, Bio/DB/GFF/Aggregator/ucsc_refgene.pm, Bio/DB/GFF/Aggregator/ucsc_sanger22.pm, Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm, Bio/DB/GFF/Aggregator/ucsc_softberry.pm, Bio/DB/GFF/Aggregator/ucsc_twinscan.pm, Bio/DB/GFF/Aggregator/ucsc_unigene.pm, Bio/DB/GFF/Featname.pm, Bio/DB/GFF/Feature.pm, Bio/DB/GFF/Homol.pm, Bio/DB/GFF.pm, Bio/DB/GFF/RelSegment.pm, Bio/DB/GFF/Segment.pm, Bio/DB/GFF/Typename.pm, Bio/DB/GFF/Util/Binning.pm, Bio/DB/GFF/Util/Rearrange.pm, Bio/DB/GenBank.pm, Bio/DB/GenPept.pm, Bio/DB/GenericWebAgent.pm, Bio/DB/HIV.pm, Bio/DB/HIV/HIVAnnotProcessor.pm, Bio/DB/HIV/HIVQueryHelper.pm, Bio/DB/InMemoryCache.pm, Bio/DB/LocationI.pm, Bio/DB/MeSH.pm, Bio/DB/NCBIHelper.pm, Bio/DB/Qual.pm, Bio/DB/Qual.pm, Bio/DB/Query/GenBank.pm, Bio/DB/Query/HIVQuery.pm, Bio/DB/Query/WebQuery.pm, Bio/DB/QueryI.pm, Bio/DB/RandomAccessI.pm, Bio/DB/RefSeq.pm, Bio/DB/ReferenceI.pm, Bio/DB/Registry.pm, Bio/DB/SeqFeature.pm, Bio/DB/SeqFeature/NormalizedFeature.pm, Bio/DB/SeqFeature/NormalizedFeatureI.pm, Bio/DB/SeqFeature/NormalizedTableFeatureI.pm, Bio/DB/SeqFeature/Segment.pm, Bio/DB/SeqFeature/Store.pm, Bio/DB/SeqFeature/Store/DBI/Iterator.pm, Bio/DB/SeqFeature/Store/DBI/mysql.pm, Bio/DB/SeqFeature/Store/FeatureFileLoader.pm, Bio/DB/SeqFeature/Store/GFF2Loader.pm, Bio/DB/SeqFeature/Store/GFF3Loader.pm, Bio/DB/SeqFeature/Store/LoadHelper.pm, Bio/DB/SeqFeature/Store/Loader.pm, Bio/DB/SeqFeature/Store/bdb.pm, Bio/DB/SeqFeature/Store/berkeleydb.pm, Bio/DB/SeqFeature/Store/berkeleydb.pm, Bio/DB/SeqFeature/Store/memory.pm, Bio/DB/SeqFeature/Store/memory.pm, Bio/DB/SeqHound.pm, Bio/DB/SeqI.pm, Bio/DB/SeqVersion.pm, Bio/DB/SeqVersion/gi.pm, Bio/DB/SwissProt.pm, Bio/DB/TFBS.pm, Bio/DB/TFBS/transfac_pro.pm, Bio/DB/Taxonomy.pm, Bio/DB/Taxonomy/entrez.pm, Bio/DB/Taxonomy/flatfile.pm, Bio/DB/Taxonomy/list.pm, Bio/DB/Universal.pm, Bio/DB/UpdateableSeqI.pm, Bio/DB/WebDBSeqI.pm, Bio/DBLinkContainerI.pm, Bio/Das/FeatureTypeI.pm, Bio/Das/SegmentI.pm, Bio/DasI.pm, Bio/DescribableI.pm, Bio/Event/EventGeneratorI.pm, Bio/Event/EventHandlerI.pm, Bio/Expression/Contact.pm, Bio/Expression/DataSet.pm, Bio/Expression/FeatureGroup.pm, Bio/Expression/FeatureGroup/FeatureGroupMas50.pm, Bio/Expression/FeatureI.pm, Bio/Expression/FeatureSet/FeatureSetMas50.pm, Bio/Expression/Platform.pm, Bio/Expression/ProbeI.pm, Bio/Expression/Sample.pm, Bio/Factory/AnalysisI.pm, Bio/Factory/ApplicationFactoryI.pm, Bio/Factory/DriverFactory.pm, Bio/Factory/FTLocationFactory.pm, Bio/Factory/LocationFactoryI.pm, Bio/Factory/MapFactoryI.pm, Bio/Factory/ObjectBuilderI.pm, Bio/Factory/ObjectFactory.pm, Bio/Factory/ObjectFactoryI.pm, Bio/Factory/SeqAnalysisParserFactory.pm, Bio/Factory/SeqAnalysisParserFactoryI.pm, Bio/Factory/SequenceFactoryI.pm, Bio/Factory/SequenceProcessorI.pm, Bio/Factory/SequenceStreamI.pm, Bio/Factory/TreeFactoryI.pm, Bio/FeatureHolderI.pm, Bio/FeatureIO.pm, Bio/FeatureIO/bed.pm, Bio/FeatureIO/gff.pm, Bio/FeatureIO/gtf.pm, Bio/FeatureIO/interpro.pm, Bio/FeatureIO/ptt.pm, Bio/FeatureIO/vecscreen_simple.pm, Bio/HandlerBaseI.pm, Bio/IdCollectionI.pm, Bio/IdentifiableI.pm, Bio/Index/Abstract.pm, Bio/Index/AbstractSeq.pm, Bio/Index/Blast.pm, Bio/Index/BlastTable.pm, Bio/Index/EMBL.pm, Bio/Index/Fasta.pm, Bio/Index/Fastq.pm, Bio/Index/GenBank.pm, Bio/Index/Hmmer.pm, Bio/Index/Qual.pm, Bio/Index/Stockholm.pm, Bio/Index/SwissPfam.pm, Bio/Index/Swissprot.pm, Bio/LiveSeq/AARange.pm, Bio/LiveSeq/Chain.pm, Bio/LiveSeq/ChainI.pm, Bio/LiveSeq/DNA.pm, Bio/LiveSeq/Exon.pm, Bio/LiveSeq/Gene.pm, Bio/LiveSeq/IO/BioPerl.pm, Bio/LiveSeq/IO/Loader.pm, Bio/LiveSeq/Intron.pm, Bio/LiveSeq/Mutation.pm, Bio/LiveSeq/Mutator.pm, Bio/LiveSeq/Prim_Transcript.pm, Bio/LiveSeq/Range.pm, Bio/LiveSeq/Repeat_Region.pm, Bio/LiveSeq/Repeat_Unit.pm, Bio/LiveSeq/SeqI.pm, Bio/LiveSeq/Transcript.pm, Bio/LiveSeq/Translation.pm, Bio/LocatableSeq.pm, Bio/Location/Atomic.pm, Bio/Location/AvWithinCoordPolicy.pm, Bio/Location/CoordinatePolicyI.pm, Bio/Location/Fuzzy.pm, Bio/Location/FuzzyLocationI.pm, Bio/Location/NarrowestCoordPolicy.pm, Bio/Location/Simple.pm, Bio/Location/Split.pm, Bio/Location/SplitLocationI.pm, Bio/Location/WidestCoordPolicy.pm, Bio/LocationI.pm, Bio/Map/Clone.pm, Bio/Map/Contig.pm, Bio/Map/CytoMap.pm, Bio/Map/CytoMarker.pm, Bio/Map/CytoPosition.pm, Bio/Map/EntityI.pm, Bio/Map/FPCMarker.pm, Bio/Map/Gene.pm, Bio/Map/GeneMap.pm, Bio/Map/GenePosition.pm, Bio/Map/GeneRelative.pm, Bio/Map/LinkageMap.pm, Bio/Map/LinkagePosition.pm, Bio/Map/MapI.pm, Bio/Map/Mappable.pm, Bio/Map/MappableI.pm, Bio/Map/Marker.pm, Bio/Map/MarkerI.pm, Bio/Map/Microsatellite.pm, Bio/Map/OrderedPosition.pm, Bio/Map/OrderedPositionWithDistance.pm, Bio/Map/Physical.pm, Bio/Map/Position.pm, Bio/Map/PositionHandler.pm, Bio/Map/PositionHandlerI.pm, Bio/Map/PositionI.pm, Bio/Map/PositionWithSequence.pm, Bio/Map/Prediction.pm, Bio/Map/Relative.pm, Bio/Map/RelativeI.pm, Bio/Map/SimpleMap.pm, Bio/Map/TranscriptionFactor.pm, Bio/MapIO.pm, Bio/MapIO/fpc.pm, Bio/MapIO/mapmaker.pm, Bio/Matrix/Generic.pm, Bio/Matrix/IO.pm, Bio/Matrix/IO/mlagan.pm, Bio/Matrix/IO/phylip.pm, Bio/Matrix/IO/scoring.pm, Bio/Matrix/MatrixI.pm, Bio/Matrix/Mlagan.pm, Bio/Matrix/PSM/IO.pm, Bio/Matrix/PSM/IO/mast.pm, Bio/Matrix/PSM/IO/masta.pm, Bio/Matrix/PSM/IO/meme.pm, Bio/Matrix/PSM/IO/psiblast.pm, Bio/Matrix/PSM/IO/transfac.pm, Bio/Matrix/PSM/InstanceSite.pm, Bio/Matrix/PSM/InstanceSiteI.pm, Bio/Matrix/PSM/ProtMatrix.pm, Bio/Matrix/PSM/ProtPsm.pm, Bio/Matrix/PSM/Psm.pm, Bio/Matrix/PSM/PsmHeader.pm, Bio/Matrix/PSM/PsmHeaderI.pm, Bio/Matrix/PSM/PsmI.pm, Bio/Matrix/PSM/SiteMatrix.pm, Bio/Matrix/PSM/SiteMatrixI.pm, Bio/Matrix/PhylipDist.pm, Bio/Matrix/Scoring.pm, Bio/MolEvol/CodonModel.pm, Bio/Ontology/DocumentRegistry.pm, Bio/Ontology/GOterm.pm, Bio/Ontology/InterProTerm.pm, Bio/Ontology/OBOEngine.pm, Bio/Ontology/OBOterm.pm, Bio/Ontology/Ontology.pm, Bio/Ontology/OntologyEngineI.pm, Bio/Ontology/OntologyI.pm, Bio/Ontology/OntologyStore.pm, Bio/Ontology/Path.pm, Bio/Ontology/PathI.pm, Bio/Ontology/Relationship.pm, Bio/Ontology/RelationshipFactory.pm, Bio/Ontology/RelationshipI.pm, Bio/Ontology/RelationshipType.pm, Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm, Bio/Ontology/SimpleGOEngine/GraphAdaptor02.pm, Bio/Ontology/SimpleOntologyEngine.pm, Bio/Ontology/Term.pm, Bio/Ontology/TermFactory.pm, Bio/Ontology/TermI.pm, Bio/OntologyIO.pm, Bio/OntologyIO/Handlers/BaseSAXHandler.pm, Bio/OntologyIO/Handlers/InterProHandler.pm, Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm, Bio/OntologyIO/InterProParser.pm, Bio/OntologyIO/dagflat.pm, Bio/OntologyIO/goflat.pm, Bio/OntologyIO/obo.pm, Bio/OntologyIO/simplehierarchy.pm, Bio/OntologyIO/soflat.pm, Bio/ParameterBaseI.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/PhyloNetwork.pm, Bio/PhyloNetwork/Factory.pm, Bio/PhyloNetwork/FactoryX.pm, Bio/PhyloNetwork/GraphViz.pm, Bio/PhyloNetwork/RandomFactory.pm, Bio/PhyloNetwork/TreeFactory.pm, Bio/PhyloNetwork/TreeFactoryMulti.pm, Bio/PhyloNetwork/TreeFactoryX.pm, Bio/PhyloNetwork/muVector.pm, Bio/PopGen/Genotype.pm, Bio/PopGen/GenotypeI.pm, Bio/PopGen/HtSNP.pm, Bio/PopGen/IO.pm, Bio/PopGen/IO/csv.pm, Bio/PopGen/IO/hapmap.pm, Bio/PopGen/IO/phase.pm, Bio/PopGen/IO/prettybase.pm, Bio/PopGen/Individual.pm, Bio/PopGen/IndividualI.pm, Bio/PopGen/Marker.pm, Bio/PopGen/MarkerI.pm, Bio/PopGen/PopStats.pm, Bio/PopGen/Population.pm, Bio/PopGen/PopulationI.pm, Bio/PopGen/Simulation/Coalescent.pm, Bio/PopGen/Simulation/GeneticDrift.pm, Bio/PopGen/Statistics.pm, Bio/PopGen/TagHaplotype.pm, Bio/PopGen/Utilities.pm, Bio/PrimarySeq.pm, Bio/DB/Fasta.pm, Bio/PrimarySeqI.pm, Bio/PullParserI.pm, Bio/Range.pm, Bio/RangeI.pm, Bio/Restriction/Analysis.pm, Bio/Restriction/Enzyme.pm, Bio/Restriction/Enzyme/MultiCut.pm, Bio/Restriction/Enzyme/MultiSite.pm, Bio/Restriction/EnzymeCollection.pm, Bio/Restriction/EnzymeI.pm, Bio/Restriction/IO.pm, Bio/Restriction/IO/bairoch.pm, Bio/Restriction/IO/base.pm, Bio/Restriction/IO/itype2.pm, Bio/Restriction/IO/prototype.pm, Bio/Restriction/IO/withrefm.pm, Bio/Root/Build.pm, Bio/Root/Exception.pm, Bio/Root/HTTPget.pm, Bio/Root/IO.pm, Bio/Root/Root.pm, Bio/Root/RootI.pm, Bio/Root/Storable.pm, Bio/Root/Test.pm, Bio/Root/Test/Warn.pm, Bio/Root/Utilities.pm, Bio/Root/Version.pm, Bio/Search/BlastStatistics.pm, Bio/Search/BlastUtils.pm, Bio/Search/DatabaseI.pm, Bio/Search/GenericDatabase.pm, Bio/Search/GenericStatistics.pm, Bio/Search/HSP/BlastHSP.pm, Bio/Search/HSP/BlastPullHSP.pm, Bio/Search/HSP/FastaHSP.pm, Bio/Search/HSP/GenericHSP.pm, Bio/Search/HSP/HMMERHSP.pm, Bio/Search/HSP/HSPFactory.pm, Bio/Search/HSP/HSPI.pm, Bio/Search/HSP/HmmpfamHSP.pm, Bio/Search/HSP/ModelHSP.pm, Bio/Search/HSP/PSLHSP.pm, Bio/Search/HSP/PsiBlastHSP.pm, Bio/Search/HSP/PullHSPI.pm, Bio/Search/HSP/WABAHSP.pm, Bio/Search/Hit/BlastHit.pm, Bio/Search/Hit/BlastPullHit.pm, Bio/Search/Hit/Fasta.pm, Bio/Search/Hit/GenericHit.pm, Bio/Search/Hit/HMMERHit.pm, Bio/Search/Hit/HitFactory.pm, Bio/Search/Hit/HitI.pm, Bio/Search/Hit/HmmpfamHit.pm, Bio/Search/Hit/ModelHit.pm, Bio/Search/Hit/PsiBlastHit.pm, Bio/Search/Hit/PullHitI.pm, Bio/Search/Iteration/GenericIteration.pm, Bio/Search/Iteration/IterationI.pm, Bio/Search/Processor.pm, Bio/Search/Result/BlastPullResult.pm, Bio/Search/Result/BlastResult.pm, Bio/Search/Result/CrossMatchResult.pm, Bio/Search/Result/GenericResult.pm, Bio/Search/Result/HMMERResult.pm, Bio/Search/Result/HmmpfamResult.pm, Bio/Search/Result/PullResultI.pm, Bio/Search/Result/ResultFactory.pm, Bio/Search/Result/ResultI.pm, Bio/Search/Result/WABAResult.pm, Bio/Search/SearchUtils.pm, Bio/Search/StatisticsI.pm, Bio/SearchDist.pm, Bio/SearchIO.pm, Bio/SearchIO/EventHandlerI.pm, Bio/SearchIO/FastHitEventBuilder.pm, Bio/SearchIO/IteratedSearchResultEventBuilder.pm, Bio/SearchIO/SearchResultEventBuilder.pm, Bio/SearchIO/SearchWriterI.pm, Bio/SearchIO/Writer/BSMLResultWriter.pm, Bio/SearchIO/Writer/GbrowseGFF.pm, Bio/SearchIO/Writer/HSPTableWriter.pm, Bio/SearchIO/Writer/HTMLResultWriter.pm, Bio/SearchIO/Writer/HitTableWriter.pm, Bio/SearchIO/Writer/ResultTableWriter.pm, Bio/SearchIO/Writer/TextResultWriter.pm, Bio/SearchIO/XML/BlastHandler.pm, Bio/SearchIO/XML/PsiBlastHandler.pm, Bio/SearchIO/axt.pm, Bio/SearchIO/blast.pm, Bio/SearchIO/blast_pull.pm, Bio/SearchIO/blasttable.pm, Bio/SearchIO/blastxml.pm, Bio/SearchIO/cross_match.pm, Bio/SearchIO/erpin.pm, Bio/SearchIO/exonerate.pm, Bio/SearchIO/fasta.pm, Bio/SearchIO/hmmer.pm, Bio/SearchIO/hmmer_pull.pm, Bio/SearchIO/infernal.pm, Bio/SearchIO/megablast.pm, Bio/SearchIO/psl.pm, Bio/SearchIO/rnamotif.pm, Bio/SearchIO/sim4.pm, Bio/SearchIO/waba.pm, Bio/SearchIO/wise.pm, Bio/Seq.pm, Bio/Seq/BaseSeqProcessor.pm, Bio/Seq/EncodedSeq.pm, Bio/Seq/LargeLocatableSeq.pm, Bio/Seq/LargePrimarySeq.pm, Bio/Seq/LargeSeq.pm, Bio/Seq/LargeSeqI.pm, Bio/Seq/Meta.pm, Bio/Seq/Meta/Array.pm, Bio/Seq/MetaI.pm, Bio/Seq/PrimaryQual.pm, Bio/DB/Qual.pm, Bio/Seq/PrimedSeq.pm, Bio/Seq/QualI.pm, Bio/Seq/Quality.pm, Bio/Seq/RichSeq.pm, Bio/Seq/RichSeqI.pm, Bio/Seq/SeqBuilder.pm, Bio/Seq/SeqFactory.pm, Bio/Seq/SeqFastaSpeedFactory.pm, Bio/Seq/SeqWithQuality.pm, Bio/Seq/SequenceTrace.pm, Bio/Seq/TraceI.pm, Bio/SeqAnalysisParserI.pm, Bio/SeqEvolution/DNAPoint.pm, Bio/SeqEvolution/EvolutionI.pm, Bio/SeqEvolution/Factory.pm, Bio/SeqFeature/Annotated.pm, Bio/SeqFeature/AnnotationAdaptor.pm, Bio/SeqFeature/Collection.pm, Bio/SeqFeature/CollectionI.pm, Bio/SeqFeature/Computation.pm, Bio/SeqFeature/FeaturePair.pm, Bio/SeqFeature/Gene/Exon.pm, Bio/SeqFeature/Gene/ExonI.pm, Bio/SeqFeature/Gene/GeneStructure.pm, Bio/SeqFeature/Gene/GeneStructureI.pm, Bio/SeqFeature/Gene/Intron.pm, Bio/SeqFeature/Gene/NC_Feature.pm, Bio/SeqFeature/Gene/Poly_A_site.pm, Bio/SeqFeature/Gene/Promoter.pm, Bio/SeqFeature/Gene/Transcript.pm, Bio/SeqFeature/Gene/TranscriptI.pm, Bio/SeqFeature/Gene/UTR.pm, Bio/SeqFeature/Generic.pm, Bio/SeqFeature/Lite.pm, Bio/SeqFeature/PositionProxy.pm, Bio/SeqFeature/Primer.pm, Bio/SeqFeature/SiRNA/Oligo.pm, Bio/SeqFeature/SiRNA/Pair.pm, Bio/SeqFeature/Similarity.pm, Bio/SeqFeature/SimilarityPair.pm, Bio/SeqFeature/Tools/FeatureNamer.pm, Bio/SeqFeature/Tools/IDHandler.pm, Bio/SeqFeature/Tools/TypeMapper.pm, Bio/SeqFeature/Tools/Unflattener.pm, Bio/SeqFeature/TypedSeqFeatureI.pm, Bio/SeqFeatureI.pm, Bio/SeqI.pm, Bio/SeqIO.pm, Bio/SeqIO/FTHelper.pm, Bio/SeqIO/Handler/GenericRichSeqHandler.pm, Bio/SeqIO/MultiFile.pm, Bio/SeqIO/abi.pm, Bio/SeqIO/ace.pm, Bio/SeqIO/agave.pm, Bio/SeqIO/alf.pm, Bio/SeqIO/asciitree.pm, Bio/SeqIO/bsml.pm, Bio/SeqIO/bsml_sax.pm, Bio/SeqIO/chadoxml.pm, Bio/SeqIO/chaos.pm, Bio/SeqIO/chaosxml.pm, Bio/SeqIO/ctf.pm, Bio/SeqIO/embl.pm, Bio/SeqIO/embldriver.pm, Bio/SeqIO/entrezgene.pm, Bio/SeqIO/excel.pm, Bio/SeqIO/exp.pm, Bio/SeqIO/fasta.pm, Bio/SeqIO/fastq.pm, Bio/SeqIO/flybase_chadoxml.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/gbdriver.pm, Bio/SeqIO/gcg.pm, Bio/SeqIO/genbank.pm, Bio/SeqIO/interpro.pm, Bio/SeqIO/kegg.pm, Bio/SeqIO/largefasta.pm, Bio/SeqIO/lasergene.pm, Bio/SeqIO/locuslink.pm, Bio/SeqIO/metafasta.pm, Bio/SeqIO/phd.pm, Bio/SeqIO/pir.pm, Bio/SeqIO/pln.pm, Bio/SeqIO/qual.pm, Bio/SeqIO/raw.pm, Bio/SeqIO/scf.pm, Bio/SeqIO/strider.pm, Bio/SeqIO/swiss.pm, Bio/SeqIO/swissdriver.pm, Bio/SeqIO/tab.pm, Bio/SeqIO/table.pm, Bio/SeqIO/tigr.pm, Bio/SeqIO/tigrxml.pm, Bio/SeqIO/tinyseq.pm, Bio/SeqIO/tinyseq/tinyseqHandler.pm, Bio/SeqIO/ztr.pm, Bio/SeqUtils.pm, Bio/SimpleAlign.pm, Bio/SimpleAnalysisI.pm, Bio/Species.pm, Bio/Structure/Atom.pm, Bio/Structure/Chain.pm, Bio/Structure/Entry.pm, Bio/Structure/IO.pm, Bio/Structure/IO/pdb.pm, Bio/Structure/Model.pm, Bio/Structure/Residue.pm, Bio/Structure/SecStr/DSSP/Res.pm, Bio/Structure/SecStr/STRIDE/Res.pm, Bio/Structure/StructureI.pm, Bio/Symbol/Alphabet.pm, Bio/Symbol/AlphabetI.pm, Bio/Symbol/DNAAlphabet.pm, Bio/Symbol/ProteinAlphabet.pm, Bio/Symbol/Symbol.pm, Bio/Symbol/SymbolI.pm, Bio/Taxon.pm, Bio/Taxonomy.pm, Bio/Taxonomy/FactoryI.pm, Bio/Taxonomy/Node.pm, Bio/Taxonomy/Taxon.pm, Bio/Taxonomy/Tree.pm, Bio/Tools/AlignFactory.pm, Bio/Tools/Alignment/Consed.pm, Bio/Tools/Alignment/Trim.pm, Bio/Tools/Analysis/DNA/ESEfinder.pm, Bio/Tools/Analysis/Protein/Domcut.pm, Bio/Tools/Analysis/Protein/ELM.pm, Bio/Tools/Analysis/Protein/GOR4.pm, Bio/Tools/Analysis/Protein/HNN.pm, Bio/Tools/Analysis/Protein/Mitoprot.pm, Bio/Tools/Analysis/Protein/NetPhos.pm, Bio/Tools/Analysis/Protein/Scansite.pm, Bio/Tools/Analysis/Protein/Sopma.pm, Bio/Tools/Analysis/SimpleAnalysisBase.pm, Bio/Tools/AnalysisResult.pm, Bio/Tools/Blat.pm, Bio/Tools/CodonTable.pm, Bio/Tools/Coil.pm, Bio/Tools/ECnumber.pm, Bio/Tools/EMBOSS/Palindrome.pm, Bio/Tools/EPCR.pm, Bio/Tools/ERPIN.pm, Bio/Tools/ESTScan.pm, Bio/Tools/EUtilities.pm, Bio/Tools/EUtilities/EUtilDataI.pm, Bio/Tools/EUtilities/EUtilParameters.pm, Bio/Tools/EUtilities/Cookie.pm, Bio/Tools/EUtilities/HistoryI.pm, Bio/Tools/EUtilities/Info.pm, Bio/Tools/EUtilities/Info/FieldInfo.pm, Bio/Tools/EUtilities/Info/LinkInfo.pm, Bio/Tools/EUtilities/Link.pm, Bio/Tools/EUtilities/Link/LinkSet.pm, Bio/Tools/EUtilities/Link/UrlLink.pm, Bio/Tools/EUtilities/Query.pm, Bio/Tools/EUtilities/Query/GlobalQuery.pm, Bio/Tools/EUtilities/Summary.pm, Bio/Tools/EUtilities/Summary/DocSum.pm, Bio/Tools/EUtilities/Summary/Item.pm, Bio/Tools/Eponine.pm, Bio/Tools/Est2Genome.pm, Bio/Tools/Fgenesh.pm, Bio/Tools/FootPrinter.pm, Bio/Tools/GFF.pm, Bio/Tools/Gel.pm, Bio/Tools/Geneid.pm, Bio/Tools/Genemark.pm, Bio/Tools/Genewise.pm, Bio/Tools/Genomewise.pm, Bio/Tools/Genscan.pm, Bio/Tools/Glimmer.pm, Bio/Tools/Grail.pm, Bio/Tools/GuessSeqFormat.pm, Bio/Tools/HMM.pm, Bio/Tools/HMMER/Domain.pm, Bio/Tools/HMMER/Results.pm, Bio/Tools/HMMER/Set.pm, Bio/Tools/Hmmpfam.pm, Bio/Tools/IUPAC.pm, Bio/Tools/Infernal.pm, Bio/Tools/Lucy.pm, Bio/Tools/MZEF.pm, Bio/Tools/Match.pm, Bio/Tools/OddCodes.pm, Bio/Tools/Phylo/Gerp.pm, Bio/Tools/Phylo/Gumby.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/Protparam.pm, Bio/Tools/Pseudowise.pm, Bio/Tools/QRNA.pm, Bio/Tools/RNAMotif.pm, Bio/Tools/RandomDistFunctions.pm, Bio/Tools/RepeatMasker.pm, Bio/Tools/Run/GenericParameters.pm, Bio/Tools/Run/ParametersI.pm, Bio/Tools/Run/RemoteBlast.pm, Bio/Tools/Run/StandAloneBlast.pm, Bio/Tools/Run/StandAloneNCBIBlast.pm, Bio/Tools/Run/StandAloneWUBlast.pm, Bio/Tools/Run/WrapperBase.pm, Bio/Tools/Seg.pm, Bio/Tools/SeqPattern.pm, Bio/Tools/SeqStats.pm, Bio/Tools/SeqWords.pm, Bio/Tools/SiRNA.pm, Bio/Tools/SiRNA/Ruleset/saigo.pm, Bio/Tools/SiRNA/Ruleset/tuschl.pm, Bio/Tools/Sigcleave.pm, Bio/Tools/Signalp.pm, Bio/Tools/Signalp/ExtendedSignalp.pm, Bio/Tools/Sim4/Exon.pm, Bio/Tools/Sim4/Results.pm, Bio/Tools/Spidey/Exon.pm, Bio/Tools/Spidey/Results.pm, Bio/Tools/TandemRepeatsFinder.pm, Bio/Tools/TargetP.pm, Bio/Tools/Tmhmm.pm, Bio/Tools/dpAlign.pm, Bio/Tools/ipcress.pm, Bio/Tools/isPcr.pm, Bio/Tools/pICalculator.pm, Bio/Tools/pSW.pm, Bio/Tools/tRNAscanSE.pm, Bio/Tree/AlleleNode.pm, Bio/Tree/AnnotatableNode.pm, Bio/Tree/Compatible.pm, Bio/Tree/DistanceFactory.pm, Bio/Tree/Draw/Cladogram.pm, Bio/Tree/Node.pm, Bio/Tree/NodeI.pm, Bio/Tree/NodeNHX.pm, Bio/Tree/RandomFactory.pm, Bio/Tree/Statistics.pm, Bio/Tree/Tree.pm, Bio/Tree/TreeFunctionsI.pm, Bio/Tree/TreeI.pm, Bio/TreeIO.pm, Bio/TreeIO/TreeEventBuilder.pm, Bio/TreeIO/cluster.pm, Bio/TreeIO/lintree.pm, Bio/TreeIO/newick.pm, Bio/TreeIO/nexus.pm, Bio/TreeIO/nhx.pm, Bio/TreeIO/pag.pm, Bio/TreeIO/phyloxml.pm, Bio/TreeIO/svggraph.pm, Bio/TreeIO/tabtree.pm, Bio/UpdateableSeqI.pm, Bio/Variation/AAChange.pm, Bio/Variation/AAReverseMutate.pm, Bio/Variation/Allele.pm, Bio/Variation/DNAMutation.pm, Bio/Variation/IO.pm, Bio/Variation/IO/flat.pm, Bio/Variation/IO/xml.pm, Bio/Variation/RNAChange.pm, Bio/Variation/SNP.pm, Bio/Variation/SeqDiff.pm, Bio/Variation/VariantI.pm, Bio/WebAgent.pm, Bio/DB/GFF/Adaptor/berkeleydb.pm, Bio/DB/HIV/HIVQueryHelper.pm, Bio/DB/HIV/HIVQueryHelper.pm, Bio/DB/HIV/HIVQueryHelper.pm, Bio/DB/HIV/HIVQueryHelper.pm
- 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::ProteinStatistics, Bio::Align::StatisticsI, Bio::Align::Utilities, Bio::AlignIO, Bio::AlignIO::arp, Bio::AlignIO::bl2seq, Bio::AlignIO::clustalw, Bio::AlignIO::emboss, Bio::AlignIO::fasta, Bio::AlignIO::largemultifasta, Bio::AlignIO::maf, Bio::AlignIO::mase, Bio::AlignIO::mega, Bio::AlignIO::meme, Bio::AlignIO::metafasta, Bio::AlignIO::msf, Bio::AlignIO::nexus, Bio::AlignIO::pfam, Bio::AlignIO::phylip, Bio::AlignIO::po, Bio::AlignIO::proda, Bio::AlignIO::prodom, Bio::AlignIO::psi, Bio::AlignIO::selex, Bio::AlignIO::stockholm, Bio::AlignIO::xmfa, 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::Relation, Bio::Annotation::SimpleValue, Bio::Annotation::StructuredValue, Bio::Annotation::TagTree, Bio::Annotation::Target, Bio::Annotation::Tree, 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::IO::tigr, Bio::Assembly::Scaffold, Bio::Assembly::ScaffoldI, Bio::Assembly::Singlet, Bio::Assembly::Tools::ContigSpectrum, Bio::Biblio, Bio::Biblio::Article, Bio::Biblio::BiblioBase, Bio::Biblio::Book, Bio::Biblio::BookArticle, Bio::Biblio::IO, Bio::Biblio::IO::medline2ref, Bio::Biblio::IO::medlinexml, Bio::Biblio::IO::pubmed2ref, Bio::Biblio::IO::pubmedxml, Bio::Biblio::Journal, Bio::Biblio::JournalArticle, Bio::Biblio::MedlineArticle, Bio::Biblio::MedlineBook, Bio::Biblio::MedlineBookArticle, Bio::Biblio::MedlineJournal, Bio::Biblio::MedlineJournalArticle, Bio::Biblio::Organisation, Bio::Biblio::Patent, Bio::Biblio::Person, Bio::Biblio::Proceeding, Bio::Biblio::Provider, Bio::Biblio::PubmedArticle, Bio::Biblio::PubmedBookArticle, Bio::Biblio::PubmedJournalArticle, Bio::Biblio::Ref, Bio::Biblio::Service, Bio::Biblio::TechReport, Bio::Biblio::Thesis, Bio::Biblio::WebResource, Bio::Cluster::ClusterFactory, Bio::Cluster::FamilyI, Bio::Cluster::SequenceFamily, Bio::Cluster::UniGene, Bio::Cluster::UniGeneI, Bio::ClusterI, Bio::ClusterIO, Bio::ClusterIO::dbsnp, Bio::ClusterIO::unigene, Bio::CodonUsage::IO, Bio::CodonUsage::Table, Bio::Coordinate::Chain, Bio::Coordinate::Collection, Bio::Coordinate::ExtrapolatingPair, Bio::Coordinate::GeneMapper, Bio::Coordinate::Graph, Bio::Coordinate::MapperI, Bio::Coordinate::Pair, Bio::Coordinate::Result, Bio::Coordinate::Result::Gap, Bio::Coordinate::Result::Match, Bio::Coordinate::ResultI, Bio::Coordinate::Utils, Bio::DB::Ace, Bio::DB::Biblio::biofetch, Bio::DB::Biblio::eutils, Bio::DB::Biblio::soap, Bio::DB::BiblioI, Bio::DB::BioFetch, Bio::DB::CUTG, Bio::DB::DBFetch, Bio::DB::EMBL, Bio::DB::EUtilities, Bio::DB::EntrezGene, Bio::DB::Expression, Bio::DB::Expression::geo, Bio::DB::Failover, Bio::DB::Fasta, Bio::DB::FileCache, Bio::DB::Flat, Bio::DB::Flat::BDB, Bio::DB::Flat::BDB::embl, Bio::DB::Flat::BDB::fasta, Bio::DB::Flat::BDB::genbank, Bio::DB::Flat::BDB::swiss, Bio::DB::Flat::BinarySearch, Bio::DB::GFF, Bio::DB::GFF::Adaptor::ace, Bio::DB::GFF::Adaptor::berkeleydb, Bio::DB::GFF::Adaptor::berkeleydb::iterator, Bio::DB::GFF::Adaptor::biofetch, Bio::DB::GFF::Adaptor::biofetch_oracle, Bio::DB::GFF::Adaptor::dbi, Bio::DB::GFF::Adaptor::dbi::caching_handle, Bio::DB::GFF::Adaptor::dbi::iterator, Bio::DB::GFF::Adaptor::dbi::mysql, Bio::DB::GFF::Adaptor::dbi::mysqlace, Bio::DB::GFF::Adaptor::dbi::mysqlcmap, Bio::DB::GFF::Adaptor::dbi::mysqlopt, Bio::DB::GFF::Adaptor::dbi::oracle, Bio::DB::GFF::Adaptor::dbi::oracleace, Bio::DB::GFF::Adaptor::dbi::pg, Bio::DB::GFF::Adaptor::dbi::pg_fts, Bio::DB::GFF::Adaptor::memory, Bio::DB::GFF::Adaptor::memory::feature_serializer, Bio::DB::GFF::Adaptor::memory::iterator, Bio::DB::GFF::Aggregator, Bio::DB::GFF::Aggregator::alignment, Bio::DB::GFF::Aggregator::clone, Bio::DB::GFF::Aggregator::coding, Bio::DB::GFF::Aggregator::gene, Bio::DB::GFF::Aggregator::match, Bio::DB::GFF::Aggregator::none, Bio::DB::GFF::Aggregator::orf, Bio::DB::GFF::Aggregator::processed_transcript, Bio::DB::GFF::Aggregator::so_transcript, Bio::DB::GFF::Aggregator::transcript, Bio::DB::GFF::Aggregator::ucsc_acembly, Bio::DB::GFF::Aggregator::ucsc_ensgene, Bio::DB::GFF::Aggregator::ucsc_genscan, Bio::DB::GFF::Aggregator::ucsc_refgene, Bio::DB::GFF::Aggregator::ucsc_sanger22, Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo, Bio::DB::GFF::Aggregator::ucsc_softberry, Bio::DB::GFF::Aggregator::ucsc_twinscan, Bio::DB::GFF::Aggregator::ucsc_unigene, Bio::DB::GFF::Featname, Bio::DB::GFF::Feature, Bio::DB::GFF::Homol, Bio::DB::GFF::RelSegment, Bio::DB::GFF::Segment, Bio::DB::GFF::Typename, Bio::DB::GFF::Util::Binning, Bio::DB::GFF::Util::Rearrange, Bio::DB::GenBank, Bio::DB::GenPept, Bio::DB::HIV, Bio::DB::HIV::HIVAnnotProcessor, Bio::DB::HIV::HIVQueryHelper, Bio::DB::InMemoryCache, Bio::DB::LocationI, Bio::DB::MeSH, Bio::DB::NCBIHelper, Bio::DB::Qual, Bio::DB::Query::GenBank, Bio::DB::Query::HIVQuery, Bio::DB::Query::WebQuery, Bio::DB::QueryI, Bio::DB::RandomAccessI, Bio::DB::RefSeq, Bio::DB::ReferenceI, Bio::DB::Registry, Bio::DB::SeqFeature, Bio::DB::SeqFeature::NormalizedFeature, Bio::DB::SeqFeature::NormalizedFeatureI, Bio::DB::SeqFeature::NormalizedTableFeatureI, Bio::DB::SeqFeature::Segment, Bio::DB::SeqFeature::Store::DBI::Iterator, Bio::DB::SeqFeature::Store::DBI::mysql, Bio::DB::SeqFeature::Store::FeatureFileLoader, Bio::DB::SeqFeature::Store::GFF2Loader, Bio::DB::SeqFeature::Store::GFF3Loader, Bio::DB::SeqFeature::Store::LoadHelper, Bio::DB::SeqFeature::Store::Loader, Bio::DB::SeqFeature::Store::bdb, Bio::DB::SeqFeature::Store::berkeleydb, Bio::DB::SeqFeature::Store::memory, Bio::DB::SeqHound, Bio::DB::SeqI, Bio::DB::SeqVersion, Bio::DB::SeqVersion::gi, Bio::DB::SwissProt, Bio::DB::TFBS, Bio::DB::TFBS::transfac_pro, Bio::DB::Taxonomy, Bio::DB::Taxonomy::entrez, Bio::DB::Taxonomy::flatfile, Bio::DB::Taxonomy::list, Bio::DB::Universal, Bio::DB::UpdateableSeqI, Bio::DB::WebDBSeqI, Bio::DBLinkContainerI, Bio::Das::FeatureTypeI, Bio::Das::SegmentI, Bio::DasI, Bio::DescribableI, Bio::Event::EventGeneratorI, Bio::Event::EventHandlerI, Bio::Expression::Contact, Bio::Expression::DataSet, Bio::Expression::FeatureGroup, Bio::Expression::FeatureGroup::FeatureGroupMas50, Bio::Expression::FeatureI, Bio::Expression::FeatureSet::FeatureSetMas50, Bio::Expression::Platform, Bio::Expression::ProbeI, Bio::Expression::Sample, Bio::Factory::AnalysisI, Bio::Factory::ApplicationFactoryI, Bio::Factory::DriverFactory, Bio::Factory::FTLocationFactory, Bio::Factory::LocationFactoryI, Bio::Factory::MapFactoryI, Bio::Factory::ObjectBuilderI, Bio::Factory::ObjectFactory, Bio::Factory::ObjectFactoryI, Bio::Factory::SeqAnalysisParserFactory, Bio::Factory::SeqAnalysisParserFactoryI, Bio::Factory::SequenceFactoryI, Bio::Factory::SequenceProcessorI, Bio::Factory::SequenceStreamI, Bio::Factory::TreeFactoryI, Bio::FeatureHolderI, Bio::FeatureIO, Bio::FeatureIO::bed, Bio::FeatureIO::gff, Bio::FeatureIO::gtf, Bio::FeatureIO::interpro, Bio::FeatureIO::ptt, Bio::FeatureIO::vecscreen_simple, Bio::IdCollectionI, Bio::IdentifiableI, Bio::Index::Abstract, Bio::Index::AbstractSeq, Bio::Index::Blast, Bio::Index::BlastTable, Bio::Index::EMBL, Bio::Index::Fasta, Bio::Index::Fastq, Bio::Index::GenBank, Bio::Index::Hmmer, Bio::Index::Qual, Bio::Index::Stockholm, Bio::Index::SwissPfam, Bio::Index::Swissprot, Bio::LiveSeq::AARange, Bio::LiveSeq::Chain, Bio::LiveSeq::ChainI, Bio::LiveSeq::DNA, Bio::LiveSeq::Exon, Bio::LiveSeq::Gene, Bio::LiveSeq::IO::BioPerl, Bio::LiveSeq::IO::Loader, Bio::LiveSeq::Intron, Bio::LiveSeq::Mutation, Bio::LiveSeq::Mutator, Bio::LiveSeq::Prim_Transcript, Bio::LiveSeq::Range, Bio::LiveSeq::Repeat_Region, Bio::LiveSeq::Repeat_Unit, Bio::LiveSeq::SeqI, Bio::LiveSeq::Transcript, Bio::LiveSeq::Translation, Bio::LocatableSeq, Bio::Location::Atomic, Bio::Location::AvWithinCoordPolicy, Bio::Location::CoordinatePolicyI, Bio::Location::Fuzzy, Bio::Location::FuzzyLocationI, Bio::Location::NarrowestCoordPolicy, Bio::Location::Simple, Bio::Location::Split, Bio::Location::SplitLocationI, Bio::Location::WidestCoordPolicy, Bio::LocationI, Bio::Map::Clone, Bio::Map::Contig, Bio::Map::CytoMap, Bio::Map::CytoMarker, Bio::Map::CytoPosition, Bio::Map::EntityI, Bio::Map::FPCMarker, Bio::Map::Gene, Bio::Map::GeneMap, Bio::Map::GenePosition, Bio::Map::GeneRelative, Bio::Map::LinkageMap, Bio::Map::LinkagePosition, Bio::Map::MapI, Bio::Map::Mappable, Bio::Map::MappableI, Bio::Map::Marker, Bio::Map::MarkerI, Bio::Map::Microsatellite, Bio::Map::OrderedPosition, Bio::Map::OrderedPositionWithDistance, Bio::Map::Physical, Bio::Map::Position, Bio::Map::PositionHandler, Bio::Map::PositionHandlerI, Bio::Map::PositionI, Bio::Map::PositionWithSequence, Bio::Map::Prediction, Bio::Map::Relative, Bio::Map::RelativeI, Bio::Map::SimpleMap, Bio::Map::TranscriptionFactor, Bio::MapIO, Bio::MapIO::fpc, Bio::MapIO::mapmaker, Bio::Matrix::Generic, Bio::Matrix::IO, Bio::Matrix::IO::mlagan, Bio::Matrix::IO::phylip, Bio::Matrix::IO::scoring, Bio::Matrix::MatrixI, Bio::Matrix::Mlagan, Bio::Matrix::PSM::IO, Bio::Matrix::PSM::IO::mast, Bio::Matrix::PSM::IO::masta, Bio::Matrix::PSM::IO::meme, Bio::Matrix::PSM::IO::psiblast, Bio::Matrix::PSM::IO::transfac, Bio::Matrix::PSM::InstanceSite, Bio::Matrix::PSM::InstanceSiteI, Bio::Matrix::PSM::ProtMatrix, Bio::Matrix::PSM::ProtPsm, Bio::Matrix::PSM::Psm, Bio::Matrix::PSM::PsmHeader, Bio::Matrix::PSM::PsmHeaderI, Bio::Matrix::PSM::PsmI, Bio::Matrix::PSM::SiteMatrix, Bio::Matrix::PSM::SiteMatrixI, Bio::Matrix::PhylipDist, Bio::Matrix::Scoring, Bio::MolEvol::CodonModel, Bio::Ontology::DocumentRegistry, Bio::Ontology::GOterm, Bio::Ontology::InterProTerm, Bio::Ontology::OBOEngine, Bio::Ontology::OBOterm, Bio::Ontology::Ontology, Bio::Ontology::OntologyEngineI, Bio::Ontology::OntologyI, Bio::Ontology::OntologyStore, Bio::Ontology::Path, Bio::Ontology::PathI, Bio::Ontology::Relationship, Bio::Ontology::RelationshipFactory, Bio::Ontology::RelationshipI, Bio::Ontology::RelationshipType, Bio::Ontology::SimpleGOEngine::GraphAdaptor, Bio::Ontology::SimpleGOEngine::GraphAdaptor02, Bio::Ontology::SimpleOntologyEngine, Bio::Ontology::Term, Bio::Ontology::TermFactory, Bio::Ontology::TermI, Bio::OntologyIO, Bio::OntologyIO::Handlers::BaseSAXHandler, Bio::OntologyIO::Handlers::InterProHandler, Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler, Bio::OntologyIO::InterProParser, Bio::OntologyIO::dagflat, Bio::OntologyIO::goflat, Bio::OntologyIO::obo, Bio::OntologyIO::simplehierarchy, Bio::OntologyIO::soflat, Bio::Perl, Bio::Phenotype::Correlate, Bio::Phenotype::MeSH::Term, Bio::Phenotype::MeSH::Twig, Bio::Phenotype::Measure, Bio::Phenotype::OMIM::MiniMIMentry, Bio::Phenotype::OMIM::OMIMentry, Bio::Phenotype::OMIM::OMIMentryAllelicVariant, Bio::Phenotype::OMIM::OMIMparser, Bio::Phenotype::Phenotype, Bio::Phenotype::PhenotypeI, Bio::PopGen::Genotype, Bio::PopGen::GenotypeI, Bio::PopGen::HtSNP, Bio::PopGen::IO, Bio::PopGen::IO::csv, Bio::PopGen::IO::hapmap, Bio::PopGen::IO::phase, Bio::PopGen::IO::prettybase, Bio::PopGen::Individual, Bio::PopGen::IndividualI, Bio::PopGen::Marker, Bio::PopGen::MarkerI, Bio::PopGen::PopStats, Bio::PopGen::Population, Bio::PopGen::PopulationI, Bio::PopGen::Simulation::Coalescent, Bio::PopGen::Simulation::GeneticDrift, Bio::PopGen::Statistics, Bio::PopGen::TagHaplotype, Bio::PopGen::Utilities, Bio::PrimarySeq, Bio::PrimarySeqI, Bio::PullParserI, Bio::Range, Bio::RangeI, Bio::Restriction::Analysis, Bio::Restriction::Enzyme, Bio::Restriction::Enzyme::MultiCut, Bio::Restriction::Enzyme::MultiSite, Bio::Restriction::EnzymeCollection, Bio::Restriction::EnzymeI, Bio::Restriction::IO, Bio::Restriction::IO::bairoch, Bio::Restriction::IO::base, Bio::Restriction::IO::itype2, Bio::Restriction::IO::prototype, Bio::Restriction::IO::withrefm, Bio::Root::Exception, Bio::Root::HTTPget, Bio::Root::IO, Bio::Root::Root, Bio::Root::RootI, Bio::Root::Storable, Bio::Root::Utilities, Bio::Root::Version, Bio::Search::BlastStatistics, Bio::Search::BlastUtils, Bio::Search::DatabaseI, Bio::Search::GenericDatabase, Bio::Search::GenericStatistics, Bio::Search::HSP::BlastHSP, Bio::Search::HSP::BlastPullHSP, Bio::Search::HSP::FastaHSP, Bio::Search::HSP::GenericHSP, Bio::Search::HSP::HMMERHSP, Bio::Search::HSP::HSPFactory, Bio::Search::HSP::HSPI, Bio::Search::HSP::HmmpfamHSP, Bio::Search::HSP::ModelHSP, Bio::Search::HSP::PSLHSP, Bio::Search::HSP::PsiBlastHSP, Bio::Search::HSP::PullHSPI, Bio::Search::HSP::WABAHSP, Bio::Search::Hit::BlastHit, Bio::Search::Hit::BlastPullHit, Bio::Search::Hit::Fasta, Bio::Search::Hit::GenericHit, Bio::Search::Hit::HMMERHit, Bio::Search::Hit::HitFactory, Bio::Search::Hit::HitI, Bio::Search::Hit::HmmpfamHit, Bio::Search::Hit::ModelHit, Bio::Search::Hit::PsiBlastHit, Bio::Search::Hit::PullHitI, Bio::Search::Iteration::GenericIteration, Bio::Search::Iteration::IterationI, Bio::Search::Processor, Bio::Search::Result::BlastPullResult, Bio::Search::Result::BlastResult, Bio::Search::Result::CrossMatchResult, Bio::Search::Result::GenericResult, Bio::Search::Result::HMMERResult, Bio::Search::Result::HmmpfamResult, Bio::Search::Result::PullResultI, Bio::Search::Result::ResultFactory, Bio::Search::Result::ResultI, Bio::Search::Result::WABAResult, Bio::Search::SearchUtils, Bio::Search::StatisticsI, Bio::SearchDist, Bio::SearchIO, Bio::SearchIO::EventHandlerI, Bio::SearchIO::FastHitEventBuilder, Bio::SearchIO::IteratedSearchResultEventBuilder, Bio::SearchIO::SearchResultEventBuilder, Bio::SearchIO::SearchWriterI, Bio::SearchIO::Writer::BSMLResultWriter, Bio::SearchIO::Writer::GbrowseGFF, Bio::SearchIO::Writer::HSPTableWriter, Bio::SearchIO::Writer::HTMLResultWriter, Bio::SearchIO::Writer::HitTableWriter, Bio::SearchIO::Writer::ResultTableWriter, Bio::SearchIO::Writer::TextResultWriter, Bio::SearchIO::XML::BlastHandler, Bio::SearchIO::XML::PsiBlastHandler, Bio::SearchIO::axt, Bio::SearchIO::blast, Bio::SearchIO::blast_pull, Bio::SearchIO::blasttable, Bio::SearchIO::blastxml, Bio::SearchIO::cross_match, Bio::SearchIO::erpin, Bio::SearchIO::exonerate, Bio::SearchIO::fasta, Bio::SearchIO::hmmer, Bio::SearchIO::hmmer_pull, Bio::SearchIO::infernal, Bio::SearchIO::megablast, Bio::SearchIO::psl, Bio::SearchIO::rnamotif, Bio::SearchIO::sim4, Bio::SearchIO::waba, Bio::SearchIO::wise, Bio::Seq, Bio::Seq::BaseSeqProcessor, Bio::Seq::EncodedSeq, Bio::Seq::LargeLocatableSeq, Bio::Seq::LargePrimarySeq, Bio::Seq::LargeSeq, Bio::Seq::LargeSeqI, Bio::Seq::Meta, Bio::Seq::Meta::Array, Bio::Seq::MetaI, Bio::Seq::PrimaryQual, Bio::Seq::PrimedSeq, Bio::Seq::QualI, Bio::Seq::Quality, Bio::Seq::RichSeq, Bio::Seq::RichSeqI, Bio::Seq::SeqBuilder, Bio::Seq::SeqFactory, Bio::Seq::SeqFastaSpeedFactory, Bio::Seq::SeqWithQuality, Bio::Seq::SequenceTrace, Bio::Seq::TraceI, Bio::SeqAnalysisParserI, Bio::SeqEvolution::DNAPoint, Bio::SeqEvolution::EvolutionI, Bio::SeqEvolution::Factory, Bio::SeqFeature::Annotated, Bio::SeqFeature::AnnotationAdaptor, Bio::SeqFeature::Collection, Bio::SeqFeature::CollectionI, Bio::SeqFeature::Computation, Bio::SeqFeature::FeaturePair, Bio::SeqFeature::Gene::Exon, Bio::SeqFeature::Gene::ExonI, Bio::SeqFeature::Gene::GeneStructure, Bio::SeqFeature::Gene::GeneStructureI, Bio::SeqFeature::Gene::Intron, Bio::SeqFeature::Gene::NC_Feature, Bio::SeqFeature::Gene::Poly_A_site, Bio::SeqFeature::Gene::Promoter, Bio::SeqFeature::Gene::Transcript, Bio::SeqFeature::Gene::TranscriptI, Bio::SeqFeature::Gene::UTR, Bio::SeqFeature::Generic, Bio::SeqFeature::Lite, Bio::SeqFeature::PositionProxy, Bio::SeqFeature::Primer, Bio::SeqFeature::Similarity, Bio::SeqFeature::SimilarityPair, Bio::SeqFeature::Tools::FeatureNamer, Bio::SeqFeature::Tools::IDHandler, Bio::SeqFeature::Tools::TypeMapper, Bio::SeqFeature::Tools::Unflattener, Bio::SeqFeature::TypedSeqFeatureI, Bio::SeqFeatureI, Bio::SeqI, Bio::SeqIO, Bio::SeqIO::FTHelper, Bio::SeqIO::MultiFile, Bio::SeqIO::abi, Bio::SeqIO::ace, Bio::SeqIO::agave, Bio::SeqIO::alf, Bio::SeqIO::asciitree, Bio::SeqIO::bsml, Bio::SeqIO::bsml_sax, Bio::SeqIO::chadoxml, Bio::SeqIO::chaos, Bio::SeqIO::chaosxml, Bio::SeqIO::ctf, Bio::SeqIO::embl, Bio::SeqIO::embldriver, Bio::SeqIO::entrezgene, Bio::SeqIO::excel, Bio::SeqIO::exp, Bio::SeqIO::fasta, Bio::SeqIO::fastq, Bio::SeqIO::flybase_chadoxml, Bio::SeqIO::game, Bio::SeqIO::game::featHandler, Bio::SeqIO::game::gameHandler, Bio::SeqIO::game::gameSubs, Bio::SeqIO::game::gameWriter, Bio::SeqIO::game::seqHandler, Bio::SeqIO::gcg, Bio::SeqIO::genbank, Bio::SeqIO::interpro, Bio::SeqIO::kegg, Bio::SeqIO::largefasta, Bio::SeqIO::lasergene, Bio::SeqIO::locuslink, Bio::SeqIO::metafasta, Bio::SeqIO::phd, Bio::SeqIO::pir, Bio::SeqIO::pln, Bio::SeqIO::qual, Bio::SeqIO::raw, Bio::SeqIO::scf, Bio::SeqIO::swiss, Bio::SeqIO::swissdriver, Bio::SeqIO::tab, Bio::SeqIO::table, Bio::SeqIO::tigr, Bio::SeqIO::tigrxml, Bio::SeqIO::tinyseq, Bio::SeqIO::ztr, Bio::SeqUtils, Bio::SimpleAlign, Bio::SimpleAnalysisI, Bio::Species, Bio::Structure::Atom, Bio::Structure::Chain, Bio::Structure::Entry, Bio::Structure::IO, Bio::Structure::IO::pdb, Bio::Structure::Model, Bio::Structure::Residue, Bio::Structure::SecStr::DSSP::Res, Bio::Structure::SecStr::STRIDE::Res, Bio::Structure::StructureI, Bio::Symbol::Alphabet, Bio::Symbol::AlphabetI, Bio::Symbol::DNAAlphabet, Bio::Symbol::ProteinAlphabet, Bio::Symbol::Symbol, Bio::Symbol::SymbolI, Bio::Taxon, Bio::Taxonomy, Bio::Taxonomy::FactoryI, Bio::Taxonomy::Node, Bio::Taxonomy::Taxon, Bio::Taxonomy::Tree, Bio::Tools::AlignFactory, Bio::Tools::Alignment::Consed, Bio::Tools::Alignment::Trim, Bio::Tools::Analysis::DNA::ESEfinder, Bio::Tools::Analysis::Protein::Domcut, Bio::Tools::Analysis::Protein::ELM, Bio::Tools::Analysis::Protein::GOR4, Bio::Tools::Analysis::Protein::HNN, Bio::Tools::Analysis::Protein::Mitoprot, Bio::Tools::Analysis::Protein::NetPhos, Bio::Tools::Analysis::Protein::Scansite, Bio::Tools::Analysis::Protein::Sopma, Bio::Tools::Analysis::SimpleAnalysisBase, Bio::Tools::AnalysisResult, Bio::Tools::Blat, Bio::Tools::CodonTable, Bio::Tools::Coil, Bio::Tools::ECnumber, Bio::Tools::EMBOSS::Palindrome, Bio::Tools::EPCR, Bio::Tools::ERPIN, Bio::Tools::ESTScan, Bio::Tools::EUtilities::Link::UrlLink, Bio::Tools::Eponine, Bio::Tools::Est2Genome, Bio::Tools::Fgenesh, Bio::Tools::FootPrinter, Bio::Tools::GFF, Bio::Tools::Gel, Bio::Tools::Geneid, Bio::Tools::Genemark, Bio::Tools::Genewise, Bio::Tools::Genomewise, Bio::Tools::Genscan, Bio::Tools::Glimmer, Bio::Tools::Grail, Bio::Tools::HMM, Bio::Tools::HMMER::Domain, Bio::Tools::HMMER::Results, Bio::Tools::HMMER::Set, Bio::Tools::Hmmpfam, Bio::Tools::IUPAC, Bio::Tools::Infernal, Bio::Tools::Lucy, Bio::Tools::MZEF, Bio::Tools::Match, Bio::Tools::OddCodes, Bio::Tools::Phylo::Gerp, Bio::Tools::Phylo::Gumby, Bio::Tools::Phylo::Molphy, Bio::Tools::Phylo::Molphy::Result, Bio::Tools::Phylo::PAML, Bio::Tools::Phylo::PAML::ModelResult, Bio::Tools::Phylo::PAML::Result, Bio::Tools::Phylo::Phylip::ProtDist, Bio::Tools::Prediction::Exon, Bio::Tools::Prediction::Gene, Bio::Tools::Primer3, Bio::Tools::Primer::Assessor::Base, Bio::Tools::Primer::AssessorI, Bio::Tools::Primer::Feature, Bio::Tools::Primer::Pair, Bio::Tools::Prints, Bio::Tools::Profile, Bio::Tools::Promoterwise, Bio::Tools::PrositeScan, Bio::Tools::Protparam, Bio::Tools::Pseudowise, Bio::Tools::QRNA, Bio::Tools::RNAMotif, Bio::Tools::RandomDistFunctions, Bio::Tools::RepeatMasker, Bio::Tools::Run::GenericParameters, Bio::Tools::Run::ParametersI, Bio::Tools::Run::RemoteBlast, Bio::Tools::Run::StandAloneBlast, Bio::Tools::Run::StandAloneNCBIBlast, Bio::Tools::Run::StandAloneWUBlast, Bio::Tools::Run::WrapperBase, Bio::Tools::Seg, Bio::Tools::SeqPattern, Bio::Tools::SeqStats, Bio::Tools::SeqWords, Bio::Tools::Sigcleave, Bio::Tools::Signalp, Bio::Tools::Signalp::ExtendedSignalp, Bio::Tools::Sim4::Exon, Bio::Tools::Sim4::Results, Bio::Tools::Spidey::Exon, Bio::Tools::Spidey::Results, Bio::Tools::TandemRepeatsFinder, Bio::Tools::TargetP, Bio::Tools::Tmhmm, Bio::Tools::dpAlign, Bio::Tools::ipcress, Bio::Tools::isPcr, Bio::Tools::pICalculator, Bio::Tools::pSW, Bio::Tools::tRNAscanSE, Bio::Tree::AlleleNode, Bio::Tree::AnnotatableNode, Bio::Tree::Compatible, Bio::Tree::DistanceFactory, Bio::Tree::Draw::Cladogram, Bio::Tree::Node, Bio::Tree::NodeI, Bio::Tree::NodeNHX, Bio::Tree::RandomFactory, Bio::Tree::Statistics, Bio::Tree::Tree, Bio::Tree::TreeFunctionsI, Bio::Tree::TreeI, Bio::TreeIO, Bio::TreeIO::TreeEventBuilder, Bio::TreeIO::cluster, Bio::TreeIO::lintree, Bio::TreeIO::newick, Bio::TreeIO::nexus, Bio::TreeIO::nhx, Bio::TreeIO::pag, Bio::TreeIO::phyloxml, 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
- meta_yml_has_repository_resource
-
Add a 'repository' resource to the META.yml via 'meta_add' accessor (for Module::Build) or META_ADD parameter (for ExtUtils::MakeMaker).
Modules
| Name | Abstract | Version | View |
|---|---|---|---|
| Bio::Align::AlignI | An interface for describing sequence alignments. | 1.005009_004 | metacpan |
| Bio::Align::DNAStatistics | Calculate some statistics for a DNA alignment | 1.005009_004 | metacpan |
| Bio::Align::PairwiseStatistics | Base statistic object for Pairwise Alignments | 1.005009_004 | metacpan |
| Bio::Align::ProteinStatistics | Calculate Protein Alignment statistics (mostly distances) | 1.005009_004 | metacpan |
| Bio::Align::StatisticsI | Calculate some statistics for an alignment | 1.005009_004 | metacpan |
| Bio::Align::Utilities | A collection of utilities regarding converting and manipulating alignment objects | 1.005009_004 | metacpan |
| Bio::AlignIO | Handler for AlignIO Formats | 1.005009_004 | metacpan |
| Bio::AlignIO::Handler::GenericAlignHandler | Bio::HandlerI-based generic data handler class for alignment-based data | 1.005009_004 | metacpan |
| Bio::AlignIO::arp | ARP MSA Sequence input/output stream | 1.005009_004 | metacpan |
| Bio::AlignIO::bl2seq | bl2seq sequence input/output stream | 1.005009_004 | metacpan |
| Bio::AlignIO::clustalw | clustalw sequence input/output stream | 1.005009_004 | metacpan |
| Bio::AlignIO::emboss | Parse EMBOSS alignment output (from applications water and needle) | 1.005009_004 | metacpan |
| Bio::AlignIO::fasta | fasta MSA Sequence input/output stream | 1.005009_004 | metacpan |
| Bio::AlignIO::largemultifasta | Largemultifasta MSA Sequence input/output stream | 1.005009_004 | metacpan |
| Bio::AlignIO::maf | Multiple Alignment Format sequence input stream | 1.005009_004 | metacpan |
| Bio::AlignIO::mase | mase sequence input/output stream | 1.005009_004 | metacpan |
| Bio::AlignIO::mega | Parse and Create MEGA format data files | 1.005009_004 | metacpan |
| Bio::AlignIO::meme | meme sequence input/output stream | 1.005009_004 | metacpan |
| Bio::AlignIO::metafasta | Metafasta MSA Sequence input/output stream | 1.005009_004 | metacpan |
| Bio::AlignIO::msf | msf sequence input/output stream | 1.005009_004 | metacpan |
| Bio::AlignIO::nexus | NEXUS format sequence input/output stream | 1.005009_004 | metacpan |
| Bio::AlignIO::pfam | pfam sequence input/output stream | 1.005009_004 | metacpan |
| Bio::AlignIO::phylip | PHYLIP format sequence input/output stream | 1.005009_004 | metacpan |
| Bio::AlignIO::po | po MSA Sequence input/output stream | 1.005009_004 | metacpan |
| Bio::AlignIO::proda | proda sequence input/output stream | 1.005009_004 | metacpan |
| Bio::AlignIO::prodom | prodom sequence input/output stream | 1.005009_004 | metacpan |
| Bio::AlignIO::psi | Read/Write PSI-BLAST profile alignment files | 1.005009_004 | metacpan |
| Bio::AlignIO::selex | selex sequence input/output stream | 1.005009_004 | metacpan |
| Bio::AlignIO::stockholm | stockholm sequence input/output stream | 1.005009_004 | metacpan |
| Bio::AlignIO::xmfa | XMFA MSA Sequence input/output stream | 1.005009_004 | metacpan |
| Bio::AnalysisI | An interface to any (local or remote) analysis tool | 1.005009_004 | metacpan |
| Bio::AnalysisI::JobI | 1.005009_004 | metacpan | |
| Bio::AnalysisParserI | Generic analysis output parser interface | 1.005009_004 | metacpan |
| Bio::AnalysisResultI | Interface for analysis result objects | 1.005009_004 | metacpan |
| Bio::AnnotatableI | the base interface an annotatable object must implement | 1.005009_004 | metacpan |
| Bio::Annotation::AnnotationFactory | Instantiates a new Bio::AnnotationI (or derived class) through a factory | 1.005009_004 | metacpan |
| Bio::Annotation::Collection | Default Perl implementation of AnnotationCollectionI | 1.005009_004 | metacpan |
| Bio::Annotation::Comment | A comment object, holding text | 1.005009_004 | metacpan |
| Bio::Annotation::DBLink | untyped links between databases | 1.005009_004 | metacpan |
| Bio::Annotation::OntologyTerm | An ontology term adapted to AnnotationI | 1.005009_004 | metacpan |
| Bio::Annotation::Reference | Specialised DBLink object for Literature References | 1.005009_004 | metacpan |
| Bio::Annotation::Relation | Relationship (pairwise) with other objects SeqI and NodeI; | 1.005009_004 | metacpan |
| Bio::Annotation::SimpleValue | A simple scalar | 1.005009_004 | metacpan |
| Bio::Annotation::StructuredValue | A scalar with embedded structured information | 1.005009_004 | metacpan |
| Bio::Annotation::TagTree | AnnotationI with tree-like hierarchal key-value relationships ('structured tags') that can be represented as simple text. | 1.005009_004 | metacpan |
| Bio::Annotation::Target | Provides an object which represents a target (ie, a similarity hit) from one object to something in another database | 1.005009_004 | metacpan |
| Bio::Annotation::Tree | Provide a tree as an annotation to a Bio::AnnotatableI object | 1.005009_004 | metacpan |
| Bio::Annotation::TypeManager | Manages types for annotation collections | 1.005009_004 | metacpan |
| Bio::AnnotationCollectionI | Interface for annotation collections | 1.005009_004 | metacpan |
| Bio::AnnotationI | Annotation interface | 1.005009_004 | metacpan |
| Bio::Assembly::Contig | Perl module to hold and manipulate sequence assembly contigs. | 1.005009_004 | metacpan |
| Bio::Assembly::ContigAnalysis | 1.005009_004 | metacpan | |
| Bio::Assembly::IO | Handler for Assembly::IO Formats | 1.005009_004 | metacpan |
| Bio::Assembly::IO::ace | module to load ACE files from various assembly programs | 1.005009_004 | metacpan |
| Bio::Assembly::IO::phrap | driver to load phrap.out files. | 1.005009_004 | metacpan |
| Bio::Assembly::IO::tigr | Driver to read and write assembly files in the TIGR Assembler v2 default format. | 1.005009_004 | metacpan |
| Bio::Assembly::Scaffold | Perl module to hold and manipulate sequence assembly data. | 1.005009_004 | metacpan |
| Bio::Assembly::ScaffoldI | Abstract Inteface of Sequence Assemblies | 1.005009_004 | metacpan |
| Bio::Assembly::Singlet | Perl module to hold and manipulate singlets from sequence assembly contigs. | 1.005009_004 | metacpan |
| Bio::Assembly::Tools::ContigSpectrum | 1.005009_004 | metacpan | |
| Bio::Biblio | A Bibliographic Query Service module | 1.005009_004 | metacpan |
| Bio::Biblio::Article | Representation of a general article | 1.005009_004 | metacpan |
| Bio::Biblio::BiblioBase | An abstract base for other biblio classes | 1.005009_004 | metacpan |
| Bio::Biblio::Book | Representation of a book | 1.005009_004 | metacpan |
| Bio::Biblio::BookArticle | Representation of a book article | 1.005009_004 | metacpan |
| Bio::Biblio::IO | Handling the bibliographic references | 1.005009_004 | metacpan |
| Bio::Biblio::IO::medline2ref | A converter of a raw hash to MEDLINE citations | 1.005009_004 | metacpan |
| Bio::Biblio::IO::medlinexml | A converter of XML files with MEDLINE citations | 1.005009_004 | metacpan |
| Bio::Biblio::IO::pubmed2ref | A converter of a raw hash to PUBMED citations | 1.005009_004 | metacpan |
| Bio::Biblio::IO::pubmedxml | A converter of XML files with PUBMED citations | 1.005009_004 | metacpan |
| Bio::Biblio::Journal | Representation of a journal | 1.005009_004 | metacpan |
| Bio::Biblio::JournalArticle | Representation of a journal article | 1.005009_004 | metacpan |
| Bio::Biblio::MedlineArticle | Representation of a MEDLINE article | 1.005009_004 | metacpan |
| Bio::Biblio::MedlineBook | Representation of a MEDLINE book | 1.005009_004 | metacpan |
| Bio::Biblio::MedlineBookArticle | Representation of a MEDLINE book article | 1.005009_004 | metacpan |
| Bio::Biblio::MedlineJournal | Representation of a MEDLINE journal | 1.005009_004 | metacpan |
| Bio::Biblio::MedlineJournalArticle | Representation of a MEDLINE journal article | 1.005009_004 | metacpan |
| Bio::Biblio::Organisation | Representation of an organisation | 1.005009_004 | metacpan |
| Bio::Biblio::Patent | Representation of a patent | 1.005009_004 | metacpan |
| Bio::Biblio::Person | Representation of a person | 1.005009_004 | metacpan |
| Bio::Biblio::Proceeding | Representation of a conference proceeding | 1.005009_004 | metacpan |
| Bio::Biblio::Provider | Representation of a general provider | 1.005009_004 | metacpan |
| Bio::Biblio::PubmedArticle | Representation of a PUBMED article | 1.005009_004 | metacpan |
| Bio::Biblio::PubmedBookArticle | Representation of a PUBMED book article | 1.005009_004 | metacpan |
| Bio::Biblio::PubmedJournalArticle | Representation of a PUBMED journal article | 1.005009_004 | metacpan |
| Bio::Biblio::Ref | Representation of a bibliographic reference | 1.005009_004 | metacpan |
| Bio::Biblio::Service | Representation of a provider of type service | 1.005009_004 | metacpan |
| Bio::Biblio::TechReport | Representation of a technical report | 1.005009_004 | metacpan |
| Bio::Biblio::Thesis | Representation of thesis | 1.005009_004 | metacpan |
| Bio::Biblio::WebResource | Representation of a web resource | 1.005009_004 | metacpan |
| Bio::Cluster::ClusterFactory | Instantiates a new Bio::ClusterI (or derived class) through a factory | 1.005009_004 | metacpan |
| Bio::Cluster::FamilyI | Family Interface | 1.005009_004 | metacpan |
| Bio::Cluster::SequenceFamily | Sequence Family object | 1.005009_004 | metacpan |
| Bio::Cluster::UniGene | UniGene object | 1.005009_004 | metacpan |
| Bio::Cluster::UniGeneI | abstract interface of UniGene object | 1.005009_004 | metacpan |
| Bio::ClusterI | Cluster Interface | 1.005009_004 | metacpan |
| Bio::ClusterIO | Handler for Cluster Formats | 1.005009_004 | metacpan |
| Bio::ClusterIO::dbsnp | dbSNP input stream | 1.005009_004 | metacpan |
| Bio::ClusterIO::unigene | UniGene input stream | 1.005009_004 | metacpan |
| Bio::CodonUsage::IO | for reading and writing codon usage tables to file | 1.005009_004 | metacpan |
| Bio::CodonUsage::Table | for access to the Codon usage Database at http://www.kazusa.or.jp/codon. | 1.005009_004 | metacpan |
| Bio::Coordinate::Chain | Mapping locations through a chain of coordinate mappers | 1.005009_004 | metacpan |
| Bio::Coordinate::Collection | Noncontinuous match between two coordinate sets | 1.005009_004 | metacpan |
| Bio::Coordinate::ExtrapolatingPair | Continuous match between two coordinate sets | 1.005009_004 | metacpan |
| Bio::Coordinate::GeneMapper | transformations between gene related coordinate systems | 1.005009_004 | metacpan |
| Bio::Coordinate::Graph | Finds shortest path between nodes in a graph | 1.005009_004 | metacpan |
| Bio::Coordinate::MapperI | Interface describing coordinate mappers | 1.005009_004 | metacpan |
| Bio::Coordinate::Pair | Continuous match between two coordinate sets | 1.005009_004 | metacpan |
| Bio::Coordinate::Result | Results from coordinate transformation | 1.005009_004 | metacpan |
| Bio::Coordinate::Result::Gap | Another name for Bio::Location::Simple | 1.005009_004 | metacpan |
| Bio::Coordinate::Result::Match | Another name for Bio::Location::Simple | 1.005009_004 | metacpan |
| Bio::Coordinate::ResultI | Interface to identify coordinate mapper results | 1.005009_004 | metacpan |
| Bio::Coordinate::Utils | Additional methods to create Bio::Coordinate objects | 1.005009_004 | metacpan |
| Bio::DB::Ace | Database object interface to ACeDB servers | 1.005009_004 | metacpan |
| Bio::DB::Biblio::biofetch | A BioFetch-based access to a bibliographic citation retrieval | 1.005009_004 | metacpan |
| Bio::DB::Biblio::eutils | Access to PubMed's bibliographic query service | 1.005009_004 | metacpan |
| Bio::DB::Biblio::soap | A SOAP-based access to a bibliographic query service | 1.005009_004 | metacpan |
| Bio::DB::BiblioI | An interface to a Bibliographic Query Service | 1.005009_004 | metacpan |
| Bio::DB::BioFetch | Database object interface to BioFetch retrieval | 1.005009_004 | metacpan |
| Bio::DB::CUTG | for access to the Codon usage Database at http://www.kazusa.or.jp/codon. | 1.005009_004 | metacpan |
| Bio::DB::DBFetch | Database object for retrieving using the dbfetch script | 1.005009_004 | metacpan |
| Bio::DB::EMBL | Database object interface for EMBL entry retrieval | 1.005009_004 | metacpan |
| Bio::DB::EUtilities | webagent which interacts with and retrieves data from NCBI's eUtils | 1.005009_004 | metacpan |
| Bio::DB::EntrezGene | Database object interface to Entrez Gene | 1.005009_004 | metacpan |
| Bio::DB::Expression | DESCRIPTION of Object | 1.005009_004 | metacpan |
| Bio::DB::Expression::geo | *** DESCRIPTION of Class | 1.005009_004 | metacpan |
| Bio::DB::Failover | A Bio::DB::RandomAccessI compliant class which wraps a prioritized list of DBs | 1.005009_004 | metacpan |
| Bio::DB::Fasta | Fast indexed access to a directory of fasta files | 1.005009_004 | metacpan |
| Bio::DB::Fasta::Stream | 1.005009_004 | metacpan | |
| Bio::DB::FileCache | In file cache for BioSeq objects | 1.005009_004 | metacpan |
| Bio::DB::Flat | Interface for indexed flat files | 1.005009_004 | metacpan |
| Bio::DB::Flat::BDB | Interface for BioHackathon standard BDB-indexed flat file | 1.005009_004 | metacpan |
| Bio::DB::Flat::BDB::embl | embl adaptor for Open-bio standard BDB-indexed flat file | 1.005009_004 | metacpan |
| Bio::DB::Flat::BDB::fasta | fasta adaptor for Open-bio standard BDB-indexed flat file | 1.005009_004 | metacpan |
| Bio::DB::Flat::BDB::genbank | genbank adaptor for Open-bio standard BDB-indexed flat file | 1.005009_004 | metacpan |
| Bio::DB::Flat::BDB::swiss | swissprot adaptor for Open-bio standard BDB-indexed flat file | 1.005009_004 | metacpan |
| Bio::DB::Flat::BinarySearch | BinarySearch search indexing system for sequence files | 1.005009_004 | metacpan |
| Bio::DB::GFF | Storage and retrieval of sequence annotation data | 1.005009_004 | metacpan |
| Bio::DB::GFF::Adaptor::ace | ace interface (for multiple inheritance) | 1.005009_004 | metacpan |
| Bio::DB::GFF::Adaptor::berkeleydb | Bio::DB::GFF database adaptor for in-memory databases | 1.005009_004 | metacpan |
| Bio::DB::GFF::Adaptor::berkeleydb::iterator | iterator for Bio::DB::GFF::Adaptor::berkeleydb | 1.005009_004 | metacpan |
| Bio::DB::GFF::Adaptor::biofetch | Cache BioFetch objects in a Bio::DB::GFF database | 1.005009_004 | metacpan |
| Bio::DB::GFF::Adaptor::biofetch_oracle | Cache BioFetch objects in a Bio::DB::GFF database | 1.005009_004 | metacpan |
| Bio::DB::GFF::Adaptor::dbi | Database adaptor for DBI (SQL) databases | 1.005009_004 | metacpan |
| Bio::DB::GFF::Adaptor::dbi::caching_handle | Cache for database handles | 1.005009_004 | metacpan |
| Bio::DB::GFF::Adaptor::dbi::faux_dbh | 1.005009_004 | metacpan | |
| Bio::DB::GFF::Adaptor::dbi::iterator | iterator for Bio::DB::GFF::Adaptor::dbi | 1.005009_004 | metacpan |
| Bio::DB::GFF::Adaptor::dbi::mysql | Database adaptor for a specific mysql schema | 1.005009_004 | metacpan |
| Bio::DB::GFF::Adaptor::dbi::mysqlace | Unholy union between mysql GFF database and acedb database | 1.005009_004 | metacpan |
| Bio::DB::GFF::Adaptor::dbi::mysqlcmap | Database adaptor for an integraded CMap/GBrowse mysql schema | 1.005009_004 | metacpan |
| Bio::DB::GFF::Adaptor::dbi::mysqlopt | Deprecated database adaptor | 1.005009_004 | metacpan |
| Bio::DB::GFF::Adaptor::dbi::oracle | Database adaptor for a specific oracle schema | 1.005009_004 | metacpan |
| Bio::DB::GFF::Adaptor::dbi::oracleace | Unholy union between oracle GFF database and acedb database | 1.005009_004 | metacpan |
| Bio::DB::GFF::Adaptor::dbi::pg | Database adaptor for a specific postgres schema | 1.005009_004 | metacpan |
| Bio::DB::GFF::Adaptor::dbi::pg_fts | Database adaptor for a specific postgres schema with a TSearch2 implementation | 1.005009_004 | metacpan |
| Bio::DB::GFF::Adaptor::memory | Bio::DB::GFF database adaptor for in-memory databases | 1.005009_004 | metacpan |
| Bio::DB::GFF::Adaptor::memory::feature_serializer | 1.005009_004 | metacpan | |
| Bio::DB::GFF::Adaptor::memory::iterator | iterator for Bio::DB::GFF::Adaptor::memory | 1.005009_004 | metacpan |
| Bio::DB::GFF::Aggregator | Aggregate GFF groups into composite features | 1.005009_004 | metacpan |
| Bio::DB::GFF::Aggregator::alignment | Alignment aggregator | 1.005009_004 | metacpan |
| Bio::DB::GFF::Aggregator::clone | Clone aggregator | 1.005009_004 | metacpan |
| Bio::DB::GFF::Aggregator::coding | The Coding Region Aggregator | 1.005009_004 | metacpan |
| Bio::DB::GFF::Aggregator::gene | Sequence Ontology Geene | 1.005009_004 | metacpan |
| Bio::DB::GFF::Aggregator::match | Match aggregator | 1.005009_004 | metacpan |
| Bio::DB::GFF::Aggregator::none | No aggregation | 1.005009_004 | metacpan |
| Bio::DB::GFF::Aggregator::orf | An aggregator for orf regions | 1.005009_004 | metacpan |
| Bio::DB::GFF::Aggregator::processed_transcript | Sequence Ontology Transcript | 1.005009_004 | metacpan |
| Bio::DB::GFF::Aggregator::so_transcript | Sequence Ontology Transcript | 1.005009_004 | metacpan |
| Bio::DB::GFF::Aggregator::transcript | Transcript aggregator | 1.005009_004 | metacpan |
| Bio::DB::GFF::Aggregator::ucsc_acembly | UCSC acembly aggregator | 1.005009_004 | metacpan |
| Bio::DB::GFF::Aggregator::ucsc_ensgene | UCSC ensGene aggregator | 1.005009_004 | metacpan |
| Bio::DB::GFF::Aggregator::ucsc_genscan | UCSC genscan aggregator | 1.005009_004 | metacpan |
| Bio::DB::GFF::Aggregator::ucsc_refgene | UCSC refGene aggregator | 1.005009_004 | metacpan |
| Bio::DB::GFF::Aggregator::ucsc_sanger22 | UCSC sanger22 aggregator | 1.005009_004 | metacpan |
| Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo | UCSC sanger22pseudo aggregator | 1.005009_004 | metacpan |
| Bio::DB::GFF::Aggregator::ucsc_softberry | UCSC softberry aggregator | 1.005009_004 | metacpan |
| Bio::DB::GFF::Aggregator::ucsc_twinscan | UCSC twinscan aggregator | 1.005009_004 | metacpan |
| Bio::DB::GFF::Aggregator::ucsc_unigene | UCSC UniGene aggregator | 1.005009_004 | metacpan |
| Bio::DB::GFF::Featname | The name of a feature | 1.005009_004 | metacpan |
| Bio::DB::GFF::Feature | A relative segment identified by a feature type | 1.005009_004 | metacpan |
| Bio::DB::GFF::Homol | A segment of DNA that is homologous to another | 1.005009_004 | metacpan |
| Bio::DB::GFF::ID_Iterator | 1.005009_004 | metacpan | |
| Bio::DB::GFF::RelSegment | Sequence segment with relative coordinate support | 1.005009_004 | metacpan |
| Bio::DB::GFF::Segment | Simple DNA segment object | 1.005009_004 | metacpan |
| Bio::DB::GFF::Typename | The name of a feature type | 1.005009_004 | metacpan |
| Bio::DB::GFF::Util::Binning | binning utility for Bio::DB::GFF index | 1.005009_004 | metacpan |
| Bio::DB::GFF::Util::Rearrange | rearrange utility | 1.005009_004 | metacpan |
| Bio::DB::GenBank | Database object interface to GenBank | 1.005009_004 | metacpan |
| Bio::DB::GenPept | Database object interface to GenPept | 1.005009_004 | metacpan |
| Bio::DB::GenericWebAgent | helper base class for parameter-based remote server access and response retrieval. | 1.005009_004 | metacpan |
| Bio::DB::HIV | Database object interface to the Los Alamos HIV Sequence Database | 1.005009_004 | metacpan |
| Bio::DB::HIV::HIVAnnotProcessor | 1.005009_004 | metacpan | |
| Bio::DB::HIV::HIVQueryHelper | Routines and packages used by Bio::DB::HIV and Bio::DB::Query::HIVQuery | 1.005009_004 | metacpan |
| Bio::DB::InMemoryCache | Abstract interface for a sequence database | 1.005009_004 | metacpan |
| Bio::DB::LocationI | A RandomAccessI-like abstract interface for retrieving location data from a sequence database and returning Bio::LocationI objects | 1.005009_004 | metacpan |
| Bio::DB::MeSH | Term retrieval from a Web MeSH database | 1.005009_004 | metacpan |
| Bio::DB::NCBIHelper | A collection of routines useful for queries to NCBI databases. | 1.005009_004 | metacpan |
| Bio::DB::Qual | Fast indexed access to a directory of quality files | 1.005009_004 | metacpan |
| Bio::DB::Qual::Stream | 1.005009_004 | metacpan | |
| Bio::DB::Query::GenBank | Build a GenBank Entrez Query | 1.005009_004 | metacpan |
| Bio::DB::Query::HIVQuery | Query interface to the Los Alamos HIV Sequence Database | 1.005009_004 | metacpan |
| Bio::DB::Query::WebQuery | Helper class for web-based sequence queryies | 1.005009_004 | metacpan |
| Bio::DB::QueryI | Object Interface to queryable sequence databases | 1.005009_004 | metacpan |
| Bio::DB::RandomAccessI | Abstract interface for a sequence database | 1.005009_004 | metacpan |
| Bio::DB::RefSeq | Database object interface for RefSeq retrieval | 1.005009_004 | metacpan |
| Bio::DB::ReferenceI | A RandomAccessI-like abstract interface for retrieving Reference data from a sequence database and returning Bio::Annotation::Reference objects | 1.005009_004 | metacpan |
| Bio::DB::Registry | Access to the Open Bio Database Access registry scheme | 1.005009_004 | metacpan |
| Bio::DB::SeqFeature | Normalized feature for use with Bio::DB::SeqFeature::Store | 1.005009_004 | metacpan |
| Bio::DB::SeqFeature::NormalizedFeature | Normalized feature for use with Bio::DB::SeqFeature::Store | 1.005009_004 | metacpan |
| Bio::DB::SeqFeature::NormalizedFeatureI | Interface for normalized features | 1.005009_004 | metacpan |
| Bio::DB::SeqFeature::NormalizedTableFeatureI | Interface for normalized features whose hierarchy is stored in a table | 1.005009_004 | metacpan |
| Bio::DB::SeqFeature::Segment | Location-based access to genome annotation data | 1.005009_004 | metacpan |
| Bio::DB::SeqFeature::Store | Storage and retrieval of sequence annotation data | 1.005009_004 | metacpan |
| Bio::DB::SeqFeature::Store::DBI::Iterator | 1.005009_004 | metacpan | |
| Bio::DB::SeqFeature::Store::DBI::mysql | Mysql implementation of Bio::DB::SeqFeature::Store | 1.005009_004 | metacpan |
| Bio::DB::SeqFeature::Store::FeatureFileLoader | feature file loader for Bio::DB::SeqFeature::Store | 1.005009_004 | metacpan |
| Bio::DB::SeqFeature::Store::GFF2Loader | GFF2 file loader for Bio::DB::SeqFeature::Store | 1.005009_004 | metacpan |
| Bio::DB::SeqFeature::Store::GFF3Loader | GFF3 file loader for Bio::DB::SeqFeature::Store | 1.005009_004 | metacpan |
| Bio::DB::SeqFeature::Store::LoadHelper | Internal utility for Bio::DB::SeqFeature::Store | 1.005009_004 | metacpan |
| Bio::DB::SeqFeature::Store::Loader | Loader | 1.005009_004 | metacpan |
| Bio::DB::SeqFeature::Store::bdb | fetch and store objects from a BerkeleyDB | 1.005009_004 | metacpan |
| Bio::DB::SeqFeature::Store::berkeleydb | Storage and retrieval of sequence annotation data in Berkeleydb files | 1.005009_004 | metacpan |
| Bio::DB::SeqFeature::Store::berkeleydb::Iterator | 1.005009_004 | metacpan | |
| Bio::DB::SeqFeature::Store::memory | In-memory implementation of Bio::DB::SeqFeature::Store | 1.005009_004 | metacpan |
| Bio::DB::SeqFeature::Store::memory::Iterator | 1.005009_004 | metacpan | |
| Bio::DB::SeqHound | Database object interface to SeqHound | 1.005009_004 | metacpan |
| Bio::DB::SeqI | Abstract Interface for Sequence databases | 1.005009_004 | metacpan |
| Bio::DB::SeqVersion | front end to querying databases for identifier versions | 1.005009_004 | metacpan |
| Bio::DB::SeqVersion::gi | interface to NCBI Sequence Revision History page | 1.005009_004 | metacpan |
| Bio::DB::SwissProt | Database object interface to SwissProt retrieval | 1.005009_004 | metacpan |
| Bio::DB::TFBS | Access to a Transcription Factor Binding Site database | 1.005009_004 | metacpan |
| Bio::DB::TFBS::transfac_pro | An implementation of Bio::DB::TFBS which uses local flat files for transfac pro | 1.005009_004 | metacpan |
| Bio::DB::Taxonomy | Access to a taxonomy database | 1.005009_004 | metacpan |
| Bio::DB::Taxonomy::entrez | Taxonomy Entrez driver | 1.005009_004 | metacpan |
| Bio::DB::Taxonomy::flatfile | An implementation of Bio::DB::Taxonomy which uses local flat files | 1.005009_004 | metacpan |
| Bio::DB::Taxonomy::list | An implementation of Bio::DB::Taxonomy that accepts lists of words to build a database | 1.005009_004 | metacpan |
| Bio::DB::Universal | Artificial database that delegates to specific databases | 1.005009_004 | metacpan |
| Bio::DB::UpdateableSeqI | An interface for writing to a database of sequences. | 1.005009_004 | metacpan |
| Bio::DB::WebDBSeqI | Object Interface to generalize Web Databases for retrieving sequences | 1.005009_004 | metacpan |
| Bio::DBLinkContainerI | Abstract interface for any object wanting to use database cross references | 1.005009_004 | metacpan |
| Bio::Das::FeatureTypeI | Simple interface to Sequence Ontology feature types | 1.005009_004 | metacpan |
| Bio::Das::SegmentI | DAS-style access to a feature database | 1.005009_004 | metacpan |
| Bio::DasI | DAS-style access to a feature database | 1.005009_004 | metacpan |
| Bio::DescribableI | interface for objects with human readable names and descriptions | 1.005009_004 | metacpan |
| Bio::Event::EventGeneratorI | This interface describes the basic event generator class. | 1.005009_004 | metacpan |
| Bio::Event::EventHandlerI | An Event Handler Interface | 1.005009_004 | metacpan |
| Bio::Expression::Contact | DESCRIPTION of Object | 1.005009_004 | metacpan |
| Bio::Expression::DataSet | DESCRIPTION of Object | 1.005009_004 | metacpan |
| Bio::Expression::FeatureGroup | a set of DNA/RNA features. ISA Bio::Expression::FeatureI | 1.005009_004 | metacpan |
| Bio::Expression::FeatureGroup::FeatureGroupMas50 | 1.005009_004 | metacpan | |
| Bio::Expression::FeatureI | an interface class for DNA/RNA features | 1.005009_004 | metacpan |
| Bio::Expression::FeatureSet::FeatureSetMas50 | 1.005009_004 | metacpan | |
| Bio::Expression::Platform | DESCRIPTION of Object | 1.005009_004 | metacpan |
| Bio::Expression::ProbeI | an interface class for DNA/RNA probes | 1.005009_004 | metacpan |
| Bio::Expression::Sample | DESCRIPTION of Object | 1.005009_004 | metacpan |
| Bio::Factory::AnalysisI | An interface to analysis tool factory | 1.005009_004 | metacpan |
| Bio::Factory::ApplicationFactoryI | Interface class for Application Factories | 1.005009_004 | metacpan |
| Bio::Factory::DriverFactory | Base class for factory classes loading drivers | 1.005009_004 | metacpan |
| Bio::Factory::FTLocationFactory | A FeatureTable Location Parser | 1.005009_004 | metacpan |
| Bio::Factory::LocationFactoryI | A factory interface for generating locations from a string | 1.005009_004 | metacpan |
| Bio::Factory::MapFactoryI | A Factory for getting markers | 1.005009_004 | metacpan |
| Bio::Factory::ObjectBuilderI | Interface for an object builder | 1.005009_004 | metacpan |
| Bio::Factory::ObjectFactory | Instantiates a new Bio::Root::RootI (or derived class) through a factory | 1.005009_004 | metacpan |
| Bio::Factory::ObjectFactoryI | A General object creator factory | 1.005009_004 | metacpan |
| Bio::Factory::SeqAnalysisParserFactory | class capable of creating SeqAnalysisParserI compliant parsers | 1.005009_004 | metacpan |
| Bio::Factory::SeqAnalysisParserFactoryI | interface describing objects capable of creating SeqAnalysisParserI compliant parsers | 1.005009_004 | metacpan |
| Bio::Factory::SequenceFactoryI | This interface allows for generic building of sequences in factories which create sequences (like SeqIO) | 1.005009_004 | metacpan |
| Bio::Factory::SequenceProcessorI | Interface for chained sequence processing algorithms | 1.005009_004 | metacpan |
| Bio::Factory::SequenceStreamI | Interface describing the basics of a Sequence Stream. | 1.005009_004 | metacpan |
| Bio::Factory::TreeFactoryI | Factory Interface for getting and writing trees from/to a data stream | 1.005009_004 | metacpan |
| Bio::FeatureHolderI | the base interface an object with features must implement | 1.005009_004 | metacpan |
| Bio::FeatureIO | Handler for FeatureIO | 1.005009_004 | metacpan |
| Bio::FeatureIO::bed | read/write features from UCSC BED format | 1.005009_004 | metacpan |
| Bio::FeatureIO::gff | read/write GFF feature files | 1.005009_004 | metacpan |
| Bio::FeatureIO::gtf | read write features in GTF format | 1.005009_004 | metacpan |
| Bio::FeatureIO::interpro | read features from InterPro XML | 1.005009_004 | metacpan |
| Bio::FeatureIO::ptt | read/write features in PTT format | 1.005009_004 | metacpan |
| Bio::FeatureIO::vecscreen_simple | read/write features from NCBI vecscreen -f 3 output | 1.005009_004 | metacpan |
| Bio::HandlerBaseI | Interface class for handler methods which interact with any event-driven parsers (drivers). | 1.005009_004 | metacpan |
| Bio::IdCollectionI | interface for objects with multiple identifiers | 1.005009_004 | metacpan |
| Bio::IdentifiableI | interface for objects with identifiers | 1.005009_004 | metacpan |
| Bio::Index::Abstract | Abstract interface for indexing a flat file | 1.005009_004 | metacpan |
| Bio::Index::AbstractSeq | base class for AbstractSeq | 1.005009_004 | metacpan |
| Bio::Index::Blast | Indexes Blast reports and supports retrieval based on query accession(s) | 1.005009_004 | metacpan |
| Bio::Index::BlastTable | Indexes tabular Blast reports (-m 9 format) and supports retrieval based on query accession(s) | 1.005009_004 | metacpan |
| Bio::Index::EMBL | Interface for indexing (multiple) EMBL/Swissprot .dat files (i.e. flat file EMBL/Swissprot format). | 1.005009_004 | metacpan |
| Bio::Index::Fasta | Interface for indexing (multiple) fasta files | 1.005009_004 | metacpan |
| Bio::Index::Fastq | Interface for indexing (multiple) fastq files | 1.005009_004 | metacpan |
| Bio::Index::GenBank | Interface for indexing one or more GenBank files (i.e. flat file GenBank format). | 1.005009_004 | metacpan |
| Bio::Index::Hmmer | 1.005009_004 | metacpan | |
| Bio::Index::Qual | Interface for indexing (multiple) fasta qual files | 1.005009_004 | metacpan |
| Bio::Index::Stockholm | Indexes Stockholm format alignments (such as those from Pfam and Rfam. Retrieves raw stream data using the ID or a Bio::SimpleAlign (via Bio::AlignIO) | 1.005009_004 | metacpan |
| Bio::Index::SwissPfam | Interface for indexing swisspfam files | 1.005009_004 | metacpan |
| Bio::Index::Swissprot | Interface for indexing one or more Swissprot files. | 1.005009_004 | metacpan |
| Bio::LiveSeq::AARange | AARange abstract class for LiveSeq | 1.005009_004 | metacpan |
| Bio::LiveSeq::Chain | DoubleChain DataStructure for Perl | 1.005009_004 | metacpan |
| Bio::LiveSeq::ChainI | Double linked chain data structure | 1.005009_004 | metacpan |
| Bio::LiveSeq::DNA | DNA object for LiveSeq | 1.005009_004 | metacpan |
| Bio::LiveSeq::Exon | Range abstract class for LiveSeq | 1.005009_004 | metacpan |
| Bio::LiveSeq::Gene | Range abstract class for LiveSeq | 1.005009_004 | metacpan |
| Bio::LiveSeq::IO::BioPerl | Loader for LiveSeq from EMBL entries with BioPerl | 1.005009_004 | metacpan |
| Bio::LiveSeq::IO::Loader | Parent Loader for LiveSeq | 1.005009_004 | metacpan |
| Bio::LiveSeq::Intron | Range abstract class for LiveSeq | 1.005009_004 | metacpan |
| Bio::LiveSeq::Mutation | Mutation event descriptor class | 1.005009_004 | metacpan |
| Bio::LiveSeq::Mutator | Package mutating LiveSequences | 1.005009_004 | metacpan |
| Bio::LiveSeq::Prim_Transcript | Prim_Transcript class for LiveSeq | 1.005009_004 | metacpan |
| Bio::LiveSeq::Range | Range abstract class for LiveSeq | 1.005009_004 | metacpan |
| Bio::LiveSeq::Repeat_Region | Repeat_Region class for LiveSeq | 1.005009_004 | metacpan |
| Bio::LiveSeq::Repeat_Unit | Repeat_Unit class for LiveSeq | 1.005009_004 | metacpan |
| Bio::LiveSeq::SeqI | Abstract sequence interface class for LiveSeq | 1.005009_004 | metacpan |
| Bio::LiveSeq::Transcript | Transcript class for LiveSeq | 1.005009_004 | metacpan |
| Bio::LiveSeq::Translation | Translation class for LiveSeq | 1.005009_004 | metacpan |
| Bio::LocatableSeq | A Bio::PrimarySeq object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq. | 1.005009_004 | metacpan |
| Bio::Location::Atomic | Implementation of a Atomic Location on a Sequence | 1.005009_004 | metacpan |
| Bio::Location::AvWithinCoordPolicy | class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise | 1.005009_004 | metacpan |
| Bio::Location::CoordinatePolicyI | Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location | 1.005009_004 | metacpan |
| Bio::Location::Fuzzy | Implementation of a Location on a Sequence which has unclear start and/or end locations | 1.005009_004 | metacpan |
| Bio::Location::FuzzyLocationI | Abstract interface of a Location on a Sequence which has unclear start/end location | 1.005009_004 | metacpan |
| Bio::Location::NarrowestCoordPolicy | class implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range | 1.005009_004 | metacpan |
| Bio::Location::Simple | Implementation of a Simple Location on a Sequence | 1.005009_004 | metacpan |
| Bio::Location::Split | Implementation of a Location on a Sequence which has multiple locations (start/end points) | 1.005009_004 | metacpan |
| Bio::Location::SplitLocationI | Abstract interface of a Location on a Sequence which has multiple locations (start/end points) | 1.005009_004 | metacpan |
| Bio::Location::WidestCoordPolicy | class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable range | 1.005009_004 | metacpan |
| Bio::LocationI | Abstract interface of a Location on a Sequence | 1.005009_004 | metacpan |
| Bio::Map::Clone | An central map object representing a clone | 1.005009_004 | metacpan |
| Bio::Map::Contig | A MapI implementation handling the contigs of a Physical Map (such as FPC) | 1.005009_004 | metacpan |
| Bio::Map::CytoMap | A Bio::MapI compliant map implementation handling cytogenic bands | 1.005009_004 | metacpan |
| Bio::Map::CytoMarker | An object representing a marker. | 1.005009_004 | metacpan |
| Bio::Map::CytoPosition | Marker class with cytogenetic band storing attributes | 1.005009_004 | metacpan |
| Bio::Map::EntityI | An Entity Interface | 1.005009_004 | metacpan |
| Bio::Map::FPCMarker | An central map object representing a marker | 1.005009_004 | metacpan |
| Bio::Map::Gene | An gene modelled as a mappable element. | 1.005009_004 | metacpan |
| Bio::Map::GeneMap | A MapI implementation to represent the area around a gene | 1.005009_004 | metacpan |
| Bio::Map::GenePosition | A typed position, suitable for modelling the various regions of a gene. | 1.005009_004 | metacpan |
| Bio::Map::GeneRelative | Represents being relative to named sub-regions of a gene. | 1.005009_004 | metacpan |
| Bio::Map::LinkageMap | A representation of a genetic linkage map. | 1.005009_004 | metacpan |
| Bio::Map::LinkagePosition | Create a Position for a Marker that will be placed on a Bio::Map::LinkageMap | 1.005009_004 | metacpan |
| Bio::Map::MapI | Interface for describing Map objects in bioperl | 1.005009_004 | metacpan |
| Bio::Map::Mappable | An object representing a generic map element that can have multiple locations in several maps. | 1.005009_004 | metacpan |
| Bio::Map::MappableI | An object that can be placed in a map | 1.005009_004 | metacpan |
| Bio::Map::Marker | An central map object representing a generic marker that can have multiple location in several maps. | 1.005009_004 | metacpan |
| Bio::Map::MarkerI | Interface for basic marker functionality | 1.005009_004 | metacpan |
| Bio::Map::Microsatellite | An object representing a Microsatellite marker. | 1.005009_004 | 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. | 1.005009_004 | 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. | 1.005009_004 | metacpan |
| Bio::Map::Physical | A class for handling a Physical Map (such as FPC) | 1.005009_004 | metacpan |
| Bio::Map::Position | A single position of a Marker, or the range over which that marker lies, in a Map | 1.005009_004 | metacpan |
| Bio::Map::PositionHandler | A Position Handler Implementation | 1.005009_004 | metacpan |
| Bio::Map::PositionHandlerI | A Position Handler Interface | 1.005009_004 | metacpan |
| Bio::Map::PositionI | Abstracts the notion of a position having a value in the context of a marker and a Map | 1.005009_004 | metacpan |
| Bio::Map::PositionWithSequence | A position with a sequence. | 1.005009_004 | metacpan |
| Bio::Map::Prediction | An object representing the predictions of something that can have multiple locations in several maps. | 1.005009_004 | metacpan |
| Bio::Map::Relative | Represents what a Position's coordiantes are relative to. | 1.005009_004 | metacpan |
| Bio::Map::RelativeI | Interface for describing what a Position's coordiantes are relative to. | 1.005009_004 | metacpan |
| Bio::Map::SimpleMap | A MapI implementation handling the basics of a Map | 1.005009_004 | metacpan |
| Bio::Map::TranscriptionFactor | A transcription factor modelled as a mappable element | 1.005009_004 | metacpan |
| Bio::MapIO | A Map Factory object | 1.005009_004 | metacpan |
| Bio::MapIO::fpc | A FPC Map reader | 1.005009_004 | metacpan |
| Bio::MapIO::mapmaker | A Mapmaker Map reader | 1.005009_004 | metacpan |
| Bio::Matrix::Generic | A generic matrix implementation | 1.005009_004 | metacpan |
| Bio::Matrix::IO | A factory for Matrix parsing | 1.005009_004 | metacpan |
| Bio::Matrix::IO::mlagan | A parser for the mlagan substitution matrix | 1.005009_004 | metacpan |
| Bio::Matrix::IO::phylip | A parser for PHYLIP distance matricies | 1.005009_004 | metacpan |
| Bio::Matrix::IO::scoring | A parser for PAM/BLOSUM matricies | 1.005009_004 | metacpan |
| Bio::Matrix::MatrixI | An interface for describing a Matrix | 1.005009_004 | metacpan |
| Bio::Matrix::Mlagan | A generic matrix with mlagan fields | 1.005009_004 | metacpan |
| Bio::Matrix::PSM::IO | PSM parser | 1.005009_004 | metacpan |
| Bio::Matrix::PSM::IO::mast | PSM mast parser implementation | 1.005009_004 | metacpan |
| Bio::Matrix::PSM::IO::masta | motif fasta format parser | 1.005009_004 | metacpan |
| Bio::Matrix::PSM::IO::meme | PSM meme parser implementation | 1.005009_004 | metacpan |
| Bio::Matrix::PSM::IO::psiblast | PSM psiblast parser | 1.005009_004 | metacpan |
| Bio::Matrix::PSM::IO::transfac | PSM transfac parser | 1.005009_004 | metacpan |
| Bio::Matrix::PSM::InstanceSite | A PSM site occurance | 1.005009_004 | metacpan |
| Bio::Matrix::PSM::InstanceSiteI | InstanceSite interface, holds an instance of a PSM | 1.005009_004 | metacpan |
| Bio::Matrix::PSM::ProtMatrix | SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) with log-odds scoring information. | 1.005009_004 | metacpan |
| Bio::Matrix::PSM::ProtPsm | handle combination of site matricies | 1.005009_004 | metacpan |
| Bio::Matrix::PSM::Psm | handle combination of site matricies | 1.005009_004 | metacpan |
| Bio::Matrix::PSM::PsmHeader | PSM mast parser implementation | 1.005009_004 | metacpan |
| Bio::Matrix::PSM::PsmHeaderI | 1.005009_004 | metacpan | |
| Bio::Matrix::PSM::PsmI | abstract interface to handler of site matricies | 1.005009_004 | metacpan |
| Bio::Matrix::PSM::SiteMatrix | SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds | 1.005009_004 | metacpan |
| Bio::Matrix::PSM::SiteMatrixI | SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds | 1.005009_004 | metacpan |
| Bio::Matrix::PhylipDist | A Phylip Distance Matrix object | 1.005009_004 | metacpan |
| Bio::Matrix::Scoring | Object which can hold scoring matrix information | 1.005009_004 | metacpan |
| Bio::MolEvol::CodonModel | Codon Evolution Models | 1.005009_004 | metacpan |
| Bio::Ontology::DocumentRegistry | Keep track of where to find ontologies. Allows lookups by name. | 1.005009_004 | metacpan |
| Bio::Ontology::GOterm | representation of GO terms | 1.005009_004 | metacpan |
| Bio::Ontology::InterProTerm | Implementation of InterProI term interface | 1.005009_004 | metacpan |
| Bio::Ontology::OBOEngine | An Ontology Engine for OBO style flat file format from the Gene Ontology Consortium | 1.005009_004 | metacpan |
| Bio::Ontology::OBOterm | representation of OBO terms | 1.005009_004 | metacpan |
| Bio::Ontology::Ontology | standard implementation of an Ontology | 1.005009_004 | metacpan |
| Bio::Ontology::OntologyEngineI | Interface a minimal Ontology implementation should satisfy | 1.005009_004 | metacpan |
| Bio::Ontology::OntologyI | Interface for an ontology implementation | 1.005009_004 | metacpan |
| Bio::Ontology::OntologyStore | A repository of ontologies | 1.005009_004 | metacpan |
| Bio::Ontology::Path | a path for an ontology term graph | 1.005009_004 | metacpan |
| Bio::Ontology::PathI | Interface for a path between ontology terms | 1.005009_004 | metacpan |
| Bio::Ontology::Relationship | a relationship for an ontology | 1.005009_004 | metacpan |
| Bio::Ontology::RelationshipFactory | Instantiates a new Bio::Ontology::RelationshipI (or derived class) through a factory | 1.005009_004 | metacpan |
| Bio::Ontology::RelationshipI | Interface for a relationship between ontology terms | 1.005009_004 | metacpan |
| Bio::Ontology::RelationshipType | a relationship type for an ontology | 1.005009_004 | metacpan |
| Bio::Ontology::SimpleGOEngine::GraphAdaptor | Graph adaptor for Bio::Ontology::SimpleGOEngine | 1.005009_004 | metacpan |
| Bio::Ontology::SimpleGOEngine::GraphAdaptor02 | Graph adaptor (v02.x) for Bio::Ontology::SimpleGOEngine | 1.005009_004 | metacpan |
| Bio::Ontology::SimpleOntologyEngine | Implementation of OntologyEngineI interface | 1.005009_004 | metacpan |
| Bio::Ontology::Term | implementation of the interface for ontology terms | 1.005009_004 | metacpan |
| Bio::Ontology::TermFactory | Instantiates a new Bio::Ontology::TermI (or derived class) through a factory | 1.005009_004 | metacpan |
| Bio::Ontology::TermI | interface for ontology terms | 1.005009_004 | metacpan |
| Bio::OntologyIO | Parser factory for Ontology formats | 1.005009_004 | metacpan |
| Bio::OntologyIO::Handlers::BaseSAXHandler | 1.005009_004 | metacpan | |
| Bio::OntologyIO::Handlers::InterProHandler | XML handler class for InterProParser | 1.005009_004 | metacpan |
| Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler | parse an InterPro XML file and persist the resulting terms to a Biosql database | 1.005009_004 | metacpan |
| Bio::OntologyIO::InterProParser | Parser for InterPro xml files. | 1.005009_004 | metacpan |
| Bio::OntologyIO::dagflat | a base class parser for GO flat-file type formats | 1.005009_004 | metacpan |
| Bio::OntologyIO::goflat | a parser for the Gene Ontology flat-file format | 1.005009_004 | metacpan |
| Bio::OntologyIO::obo | a parser for OBO flat-file format from Gene Ontology Consortium | 1.005009_004 | metacpan |
| Bio::OntologyIO::simplehierarchy | a base class parser for simple hierarchy-by-indentation type formats | 1.005009_004 | metacpan |
| Bio::OntologyIO::soflat | a parser for the Sequence Ontology flat-file format | 1.005009_004 | metacpan |
| Bio::ParameterBaseI | Simple interface class for any parameter-related data such as IDs, database name, program arguments, and other odds and ends. | 1.005009_004 | metacpan |
| Bio::Perl | Functional access to BioPerl for people who don't know objects | 1.005009_004 | metacpan |
| Bio::Phenotype::Correlate | Representation of a correlating phenotype in a given species | 1.005009_004 | metacpan |
| Bio::Phenotype::MeSH::Term | A MeSH term | 1.005009_004 | metacpan |
| Bio::Phenotype::MeSH::Twig | Context for a MeSH term | 1.005009_004 | metacpan |
| Bio::Phenotype::Measure | Representation of context/value(-range)/unit triplets | 1.005009_004 | metacpan |
| Bio::Phenotype::OMIM::MiniMIMentry | Representation of a Mini MIM entry | 1.005009_004 | metacpan |
| Bio::Phenotype::OMIM::OMIMentry | represents OMIM (Online Mendelian Inheritance in Man) database entries | 1.005009_004 | metacpan |
| Bio::Phenotype::OMIM::OMIMentryAllelicVariant | Representation of a allelic variant of the OMIM database | 1.005009_004 | metacpan |
| Bio::Phenotype::OMIM::OMIMparser | parser for the OMIM database | 1.005009_004 | metacpan |
| Bio::Phenotype::Phenotype | A class for modeling phenotypes | 1.005009_004 | metacpan |
| Bio::Phenotype::PhenotypeI | An interface for classes modeling phenotypes | 1.005009_004 | metacpan |
| Bio::PhyloNetwork | Module to compute with Phylogenetic Networks | 1.005009_004 | metacpan |
| Bio::PhyloNetwork::Factory | Module to sequentially generate Phylogenetic Networks | 1.005009_004 | metacpan |
| Bio::PhyloNetwork::FactoryX | Module to sequentially generate Phylogenetic Networks | 1.005009_004 | metacpan |
| Bio::PhyloNetwork::GraphViz | Interface between PhyloNetwork and GraphViz | 1.005009_004 | metacpan |
| Bio::PhyloNetwork::RandomFactory | Module to generate random Phylogenetic Networks | 1.005009_004 | metacpan |
| Bio::PhyloNetwork::TreeFactory | Module to sequentially generate Phylogenetic Trees | 1.005009_004 | metacpan |
| Bio::PhyloNetwork::TreeFactoryMulti | Module to sequentially generate Phylogenetic Trees | 1.005009_004 | metacpan |
| Bio::PhyloNetwork::TreeFactoryX | Module to sequentially generate Phylogenetic Trees | 1.005009_004 | metacpan |
| Bio::PhyloNetwork::muVector | Module to compute with vectors of arbitrary dimension | 1.005009_004 | metacpan |
| Bio::PopGen::Genotype | An implementation of GenotypeI which is just an allele container | 1.005009_004 | metacpan |
| Bio::PopGen::GenotypeI | A marker and alleles for a specific individual | 1.005009_004 | metacpan |
| Bio::PopGen::HtSNP | 1.005009_004 | metacpan | |
| Bio::PopGen::IO | Input individual,marker,allele information | 1.005009_004 | metacpan |
| Bio::PopGen::IO::csv | 1.005009_004 | metacpan | |
| Bio::PopGen::IO::hapmap | A parser for HapMap output data | 1.005009_004 | metacpan |
| Bio::PopGen::IO::phase | A parser for Phase format data | 1.005009_004 | metacpan |
| Bio::PopGen::IO::prettybase | Extract individual allele data from PrettyBase format | 1.005009_004 | metacpan |
| Bio::PopGen::Individual | An implementation of an Individual who has Genotype or Sequence Results | 1.005009_004 | metacpan |
| Bio::PopGen::IndividualI | An individual who has Genotype or Sequence Results | 1.005009_004 | metacpan |
| Bio::PopGen::Marker | A genetic marker which one uses to generate genotypes | 1.005009_004 | metacpan |
| Bio::PopGen::MarkerI | A Population Genetic conceptual marker | 1.005009_004 | metacpan |
| Bio::PopGen::PopStats | A collection of methods for calculating statistics about a population or sets of populations | 1.005009_004 | metacpan |
| Bio::PopGen::Population | A population of individuals | 1.005009_004 | metacpan |
| Bio::PopGen::PopulationI | Interface for Populations | 1.005009_004 | metacpan |
| Bio::PopGen::Simulation::Coalescent | A Coalescent simulation factory | 1.005009_004 | metacpan |
| Bio::PopGen::Simulation::GeneticDrift | A simple genetic drift simulation | 1.005009_004 | metacpan |
| Bio::PopGen::Statistics | Population Genetics statistical tests | 1.005009_004 | metacpan |
| Bio::PopGen::TagHaplotype | 1.005009_004 | metacpan | |
| Bio::PopGen::Utilities | Utilities for working with PopGen data and objects | 1.005009_004 | metacpan |
| Bio::PrimarySeq | Bioperl lightweight Sequence Object | 1.005009_004 | metacpan |
| Bio::PrimarySeq::Fasta | 1.005009_004 | metacpan | |
| Bio::PrimarySeqI | Interface definition for a Bio::PrimarySeq | 1.005009_004 | metacpan |
| Bio::PullParserI | A base module for fast 'pull' parsing | 1.005009_004 | metacpan |
| Bio::Range | Pure perl RangeI implementation | 1.005009_004 | metacpan |
| Bio::RangeI | Range interface | 1.005009_004 | metacpan |
| Bio::Restriction::Analysis | cutting sequences with restriction enzymes | 1.005009_004 | metacpan |
| Bio::Restriction::Enzyme | A single restriction endonuclease (cuts DNA at specific locations) | 1.005009_004 | metacpan |
| Bio::Restriction::Enzyme::MultiCut | A single restriction endonuclease | 1.005009_004 | metacpan |
| Bio::Restriction::Enzyme::MultiSite | A single restriction endonuclease | 1.005009_004 | metacpan |
| Bio::Restriction::EnzymeCollection | Set of restriction endonucleases | 1.005009_004 | metacpan |
| Bio::Restriction::EnzymeI | Interface class for restriction endonuclease | 1.005009_004 | metacpan |
| Bio::Restriction::IO | Handler for sequence variation IO Formats | 1.005009_004 | metacpan |
| Bio::Restriction::IO::bairoch | bairoch enzyme set | 1.005009_004 | metacpan |
| Bio::Restriction::IO::base | base enzyme set | 1.005009_004 | metacpan |
| Bio::Restriction::IO::itype2 | itype2 enzyme set | 1.005009_004 | metacpan |
| Bio::Restriction::IO::prototype | prototype enzyme set | 1.005009_004 | metacpan |
| Bio::Restriction::IO::withrefm | withrefm enzyme set | 1.005009_004 | metacpan |
| Bio::Root::Build | A common Module::Build subclass base for Bioperl distributions | 1.005009_004 | metacpan |
| Bio::Root::Exception | Generic exception objects for Bioperl | 1.005009_004 | metacpan |
| Bio::Root::HTTPget | module for fallback HTTP get operations when LWP:: is unavailable | 1.005009_004 | metacpan |
| Bio::Root::IO | module providing several methods often needed when dealing with file IO | 1.005009_004 | metacpan |
| Bio::Root::Root | Hash-based implementation of Bio::Root::RootI | 1.005009_004 | metacpan |
| Bio::Root::RootI | Abstract interface to root object code | 1.005009_004 | metacpan |
| Bio::Root::Storable | object serialisation methods | 1.005009_004 | metacpan |
| Bio::Root::Test | A common base for all Bioperl test scripts. | 1.005009_004 | metacpan |
| Bio::Root::Test::Warn | Perl extension to test Bioperl methods for warnings | 1.005009_004 | metacpan |
| Bio::Root::Utilities | General-purpose utility module | 1.005009_004 | metacpan |
| Bio::Root::Version | provide global, distribution-level versioning | 1.005009_004 | metacpan |
| Bio::Search::BlastStatistics | An object for Blast statistics | 1.005009_004 | metacpan |
| Bio::Search::BlastUtils | Utility functions for Bio::Search:: BLAST objects | 1.005009_004 | metacpan |
| Bio::Search::DatabaseI | Interface for a database used in a sequence search | 1.005009_004 | metacpan |
| Bio::Search::GenericDatabase | Generic implementation of Bio::Search::DatabaseI | 1.005009_004 | metacpan |
| Bio::Search::GenericStatistics | An object for statistics | 1.005009_004 | metacpan |
| Bio::Search::HSP::BlastHSP | Bioperl BLAST High-Scoring Pair object | 1.005009_004 | metacpan |
| Bio::Search::HSP::BlastPullHSP | A parser and HSP object for BlastN hsps | 1.005009_004 | metacpan |
| Bio::Search::HSP::FastaHSP | HSP object for FASTA specific data | 1.005009_004 | metacpan |
| Bio::Search::HSP::GenericHSP | A "Generic" implementation of a High Scoring Pair | 1.005009_004 | metacpan |
| Bio::Search::HSP::HMMERHSP | A HSP object for HMMER results | 1.005009_004 | metacpan |
| Bio::Search::HSP::HSPFactory | A factory to create Bio::Search::HSP::HSPI objects | 1.005009_004 | metacpan |
| Bio::Search::HSP::HSPI | Interface for a High Scoring Pair in a similarity search result | 1.005009_004 | metacpan |
| Bio::Search::HSP::HmmpfamHSP | A parser and HSP object for hmmpfam hsps | 1.005009_004 | metacpan |
| Bio::Search::HSP::ModelHSP | A HSP object for model-based searches | 1.005009_004 | metacpan |
| Bio::Search::HSP::PSLHSP | A HSP for PSL output | 1.005009_004 | metacpan |
| Bio::Search::HSP::PsiBlastHSP | Bioperl BLAST High-Scoring Pair object | 1.005009_004 | metacpan |
| Bio::Search::HSP::PullHSPI | Bio::Search::HSP::HSPI interface for pull parsers. | 1.005009_004 | metacpan |
| Bio::Search::HSP::WABAHSP | HSP object suitable for describing WABA alignments | 1.005009_004 | metacpan |
| Bio::Search::Hit::BlastHit | Blast-specific subclass of Bio::Search::Hit::GenericHit | 1.005009_004 | metacpan |
| Bio::Search::Hit::BlastPullHit | A parser and hit object for BLASTN hits | 1.005009_004 | metacpan |
| Bio::Search::Hit::Fasta | Hit object specific for Fasta-generated hits | 1.005009_004 | metacpan |
| Bio::Search::Hit::GenericHit | A generic implementation of the Bio::Search::Hit::HitI interface | 1.005009_004 | metacpan |
| Bio::Search::Hit::HMMERHit | A Hit module for HMMER hits | 1.005009_004 | metacpan |
| Bio::Search::Hit::HitFactory | A factory to create Bio::Search::Hit::HitI objects | 1.005009_004 | metacpan |
| Bio::Search::Hit::HitI | Interface for a hit in a similarity search result | 1.005009_004 | metacpan |
| Bio::Search::Hit::HmmpfamHit | A parser and hit object for hmmpfam hits | 1.005009_004 | metacpan |
| Bio::Search::Hit::ModelHit | A model-based implementation of the Bio::Search::Hit::HitI interface | 1.005009_004 | metacpan |
| Bio::Search::Hit::PsiBlastHit | Bioperl BLAST Hit object | 1.005009_004 | metacpan |
| Bio::Search::Hit::PullHitI | Bio::Search::Hit::HitI interface for pull parsers. | 1.005009_004 | metacpan |
| Bio::Search::Iteration::GenericIteration | A generic implementation of the Bio::Search::Iteration::IterationI interface. | 1.005009_004 | metacpan |
| Bio::Search::Iteration::IterationI | Abstract interface to an iteration from an iterated search result, such as PSI-BLAST. | 1.005009_004 | metacpan |
| Bio::Search::Processor | DESCRIPTION of Object | 1.005009_004 | metacpan |
| Bio::Search::Result::BlastPullResult | A parser and result object for BLASTN results | 1.005009_004 | metacpan |
| Bio::Search::Result::BlastResult | Blast-specific subclass of Bio::Search::Result::GenericResult | 1.005009_004 | metacpan |
| Bio::Search::Result::CrossMatchResult | CrossMatch-specific subclass of Bio::Search::Result::GenericResult | 1.005009_004 | metacpan |
| Bio::Search::Result::GenericResult | Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results. | 1.005009_004 | metacpan |
| Bio::Search::Result::HMMERResult | A Result object for HMMER results | 1.005009_004 | metacpan |
| Bio::Search::Result::HmmpfamResult | A parser and result object for hmmpfam results | 1.005009_004 | metacpan |
| Bio::Search::Result::PullResultI | Bio::Search::Result::ResultI interface for 'pull' parsers | 1.005009_004 | metacpan |
| Bio::Search::Result::ResultFactory | A factory to create Bio::Search::Result::ResultI objects | 1.005009_004 | metacpan |
| Bio::Search::Result::ResultI | Abstract interface to Search Result objects | 1.005009_004 | metacpan |
| Bio::Search::Result::WABAResult | Result object for WABA alignment output | 1.005009_004 | metacpan |
| Bio::Search::SearchUtils | Utility functions for Bio::Search:: objects | 1.005009_004 | metacpan |
| Bio::Search::StatisticsI | A Base object for statistics | 1.005009_004 | metacpan |
| Bio::SearchDist | A perl wrapper around Sean Eddy's histogram object | 1.005009_004 | metacpan |
| Bio::SearchIO | Driver for parsing Sequence Database Searches (BLAST, FASTA, ...) | 1.005009_004 | metacpan |
| Bio::SearchIO::EventHandlerI | An abstract Event Handler for Search Result parsing | 1.005009_004 | metacpan |
| Bio::SearchIO::FastHitEventBuilder | Event Handler for SearchIO events. | 1.005009_004 | metacpan |
| Bio::SearchIO::IteratedSearchResultEventBuilder | Event Handler for SearchIO events. | 1.005009_004 | metacpan |
| Bio::SearchIO::SearchResultEventBuilder | Event Handler for SearchIO events. | 1.005009_004 | metacpan |
| Bio::SearchIO::SearchWriterI | Interface for outputting parsed Search results | 1.005009_004 | metacpan |
| Bio::SearchIO::Writer::BSMLResultWriter | BSML output writer | 1.005009_004 | metacpan |
| Bio::SearchIO::Writer::GbrowseGFF | Interface for outputting parsed search results in Gbrowse GFF format | 1.005009_004 | metacpan |
| Bio::SearchIO::Writer::HSPTableWriter | Tab-delimited data for Bio::Search::HSP::HSPI objects | 1.005009_004 | metacpan |
| Bio::SearchIO::Writer::HTMLResultWriter | write a Bio::Search::ResultI in HTML | 1.005009_004 | metacpan |
| Bio::SearchIO::Writer::HitTableWriter | Tab-delimited data for Bio::Search::Hit::HitI objects | 1.005009_004 | metacpan |
| Bio::SearchIO::Writer::ResultTableWriter | Outputs tab-delimited data for each Bio::Search::Result::ResultI object. | 1.005009_004 | metacpan |
| Bio::SearchIO::Writer::TextResultWriter | Object to implement writing a Bio::Search::ResultI in Text. | 1.005009_004 | metacpan |
| Bio::SearchIO::XML::BlastHandler | XML Handler for NCBI Blast XML parsing. | 1.005009_004 | metacpan |
| Bio::SearchIO::XML::PsiBlastHandler | XML Handler for NCBI Blast PSIBLAST XML parsing. | 1.005009_004 | metacpan |
| Bio::SearchIO::axt | a parser for axt format reports | 1.005009_004 | metacpan |
| Bio::SearchIO::blast | Event generator for event based parsing of blast reports | 1.005009_004 | metacpan |
| Bio::SearchIO::blast_pull | A parser for BLAST output | 1.005009_004 | metacpan |
| Bio::SearchIO::blasttable | Driver module for SearchIO for parsing NCBI -m 8/9 format | 1.005009_004 | metacpan |
| Bio::SearchIO::blastxml | A SearchIO implementation of NCBI Blast XML parsing. | 1.005009_004 | metacpan |
| Bio::SearchIO::cross_match | CrossMatch-specific subclass of Bio::SearchIO | 1.005009_004 | metacpan |
| Bio::SearchIO::erpin | SearchIO-based ERPIN parser | 1.005009_004 | metacpan |
| Bio::SearchIO::exonerate | parser for Exonerate | 1.005009_004 | metacpan |
| Bio::SearchIO::fasta | A SearchIO parser for FASTA results | 1.005009_004 | metacpan |
| Bio::SearchIO::hmmer | A parser for HMMER output (hmmpfam, hmmsearch) | 1.005009_004 | metacpan |
| Bio::SearchIO::hmmer_pull | A parser for HMMER output | 1.005009_004 | metacpan |
| Bio::SearchIO::infernal | SearchIO-based Infernal parser | 1.005009_004 | metacpan |
| Bio::SearchIO::megablast | a driver module for Bio::SearchIO to parse megablast reports (format 0) | 1.005009_004 | metacpan |
| Bio::SearchIO::psl | A parser for PSL output (UCSC) | 1.005009_004 | metacpan |
| Bio::SearchIO::rnamotif | SearchIO-based RNAMotif parser | 1.005009_004 | metacpan |
| Bio::SearchIO::sim4 | parser for Sim4 alignments | 1.005009_004 | metacpan |
| Bio::SearchIO::waba | SearchIO parser for Jim Kent WABA program alignment output | 1.005009_004 | metacpan |
| Bio::SearchIO::wise | Parsing of wise output as alignments | 1.005009_004 | metacpan |
| Bio::Seq | Sequence object, with features | 1.005009_004 | metacpan |
| Bio::Seq::BaseSeqProcessor | Base implementation for a SequenceProcessor | 1.005009_004 | metacpan |
| Bio::Seq::EncodedSeq | subtype of L<Bio::LocatableSeq|Bio::LocatableSeq> to store DNA that encodes a protein | 1.005009_004 | metacpan |
| Bio::Seq::LargeLocatableSeq | LocatableSeq object that stores sequence as files in the tempdir | 1.005009_004 | 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 | 1.005009_004 | metacpan |
| Bio::Seq::LargeSeq | SeqI compliant object that stores sequence as files in /tmp | 1.005009_004 | metacpan |
| Bio::Seq::LargeSeqI | Interface class for sequences that cache their residues in a temporary file | 1.005009_004 | metacpan |
| Bio::Seq::Meta | Generic superclass for sequence objects with residue-based meta information | 1.005009_004 | metacpan |
| Bio::Seq::Meta::Array | array-based generic implementation of a sequence class with residue-based meta information | 1.005009_004 | metacpan |
| Bio::Seq::MetaI | Interface for sequence objects with residue-based meta information | 1.005009_004 | metacpan |
| Bio::Seq::PrimaryQual | Bioperl lightweight Quality Object | 1.005009_004 | metacpan |
| Bio::Seq::PrimaryQual::Qual | 1.005009_004 | metacpan | |
| Bio::Seq::PrimedSeq | A representation of a sequence and two primers flanking a target region | 1.005009_004 | metacpan |
| Bio::Seq::QualI | Interface definition for a Bio::Seq::Qual | 1.005009_004 | metacpan |
| Bio::Seq::Quality | Implementation of sequence with residue quality and trace values | 1.005009_004 | metacpan |
| Bio::Seq::RichSeq | Module implementing a sequence created from a rich sequence database entry | 1.005009_004 | metacpan |
| Bio::Seq::RichSeqI | interface for sequences from rich data sources, mostly databases | 1.005009_004 | metacpan |
| Bio::Seq::SeqBuilder | Configurable object builder for sequence stream parsers | 1.005009_004 | metacpan |
| Bio::Seq::SeqFactory | Instantiates a new Bio::PrimarySeqI (or derived class) through a factory | 1.005009_004 | metacpan |
| Bio::Seq::SeqFastaSpeedFactory | Instantiates a new Bio::PrimarySeqI (or derived class) through a factory | 1.005009_004 | metacpan |
| Bio::Seq::SeqWithQuality | Bioperl object packaging a sequence with its quality. Deprecated class, use Bio::Seq::Quality instead! | 1.005009_004 | metacpan |
| Bio::Seq::SequenceTrace | Bioperl object packaging a sequence with its trace | 1.005009_004 | metacpan |
| Bio::Seq::TraceI | Interface definition for a Bio::Seq::Trace | 1.005009_004 | metacpan |
| Bio::SeqAnalysisParserI | Sequence analysis output parser interface | 1.005009_004 | metacpan |
| Bio::SeqEvolution::DNAPoint | evolve a sequence by point mutations | 1.005009_004 | metacpan |
| Bio::SeqEvolution::EvolutionI | the interface for evolving sequences | 1.005009_004 | metacpan |
| Bio::SeqEvolution::Factory | Factory object to instantiate sequence evolving classes | 1.005009_004 | metacpan |
| Bio::SeqFeature::Annotated | PLEASE PUT SOMETHING HERE | 1.005009_004 | metacpan |
| Bio::SeqFeature::AnnotationAdaptor | integrates SeqFeatureIs annotation | 1.005009_004 | 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. | 1.005009_004 | metacpan |
| Bio::SeqFeature::CollectionI | An interface for a collection of SeqFeatureI objects. | 1.005009_004 | metacpan |
| Bio::SeqFeature::Computation | Computation SeqFeature | 1.005009_004 | metacpan |
| Bio::SeqFeature::FeaturePair | hold pair feature information e.g. blast hits | 1.005009_004 | metacpan |
| Bio::SeqFeature::Gene::Exon | a feature representing an exon | 1.005009_004 | metacpan |
| Bio::SeqFeature::Gene::ExonI | Interface for a feature representing an exon | 1.005009_004 | metacpan |
| Bio::SeqFeature::Gene::GeneStructure | A feature representing an arbitrarily complex structure of a gene | 1.005009_004 | metacpan |
| Bio::SeqFeature::Gene::GeneStructureI | A feature representing an arbitrarily complex structure of a gene | 1.005009_004 | metacpan |
| Bio::SeqFeature::Gene::Intron | An intron feature | 1.005009_004 | metacpan |
| Bio::SeqFeature::Gene::NC_Feature | 1.005009_004 | metacpan | |
| Bio::SeqFeature::Gene::Poly_A_site | poly A feature | 1.005009_004 | metacpan |
| Bio::SeqFeature::Gene::Promoter | Describes a promoter | 1.005009_004 | metacpan |
| Bio::SeqFeature::Gene::Transcript | A feature representing a transcript | 1.005009_004 | metacpan |
| Bio::SeqFeature::Gene::TranscriptI | Interface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site. | 1.005009_004 | metacpan |
| Bio::SeqFeature::Gene::UTR | A feature representing an untranslated region that is part of a transcriptional unit | 1.005009_004 | metacpan |
| Bio::SeqFeature::Generic | Generic SeqFeature | 1.005009_004 | metacpan |
| Bio::SeqFeature::Lite | Lightweight Bio::SeqFeatureI class | 1.005009_004 | metacpan |
| Bio::SeqFeature::PositionProxy | handle features when truncation/revcom sequences span a feature | 1.005009_004 | metacpan |
| Bio::SeqFeature::Primer | Primer Generic SeqFeature | 1.005009_004 | metacpan |
| Bio::SeqFeature::SiRNA::Oligo | Perl object for small inhibitory RNAs. | 1.005009_004 | metacpan |
| Bio::SeqFeature::SiRNA::Pair | Perl object for small inhibitory RNA (SiRNA) oligo pairs | 1.005009_004 | metacpan |
| Bio::SeqFeature::Similarity | A sequence feature based on similarity | 1.005009_004 | metacpan |
| Bio::SeqFeature::SimilarityPair | Sequence feature based on the similarity of two sequences. | 1.005009_004 | metacpan |
| Bio::SeqFeature::Tools::FeatureNamer | generates unique persistent names for features | 1.005009_004 | metacpan |
| Bio::SeqFeature::Tools::IDHandler | maps $seq_feature->primary_tag | 1.005009_004 | metacpan |
| Bio::SeqFeature::Tools::TypeMapper | maps $seq_feature->primary_tag | 1.005009_004 | metacpan |
| Bio::SeqFeature::Tools::Unflattener | turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy | 1.005009_004 | metacpan |
| Bio::SeqFeature::TypedSeqFeatureI | a strongly typed SeqFeature | 1.005009_004 | metacpan |
| Bio::SeqFeatureI | Abstract interface of a Sequence Feature | 1.005009_004 | metacpan |
| Bio::SeqI | 1.005009_004 | metacpan | |
| Bio::SeqIO | Handler for SeqIO Formats | 1.005009_004 | metacpan |
| Bio::SeqIO::FTHelper | Helper class for Embl/Genbank feature tables | 1.005009_004 | metacpan |
| Bio::SeqIO::Handler::GenericRichSeqHandler | Bio::HandlerI-based data handler for GenBank/EMBL/UniProt (and other) sequence data | 1.005009_004 | metacpan |
| Bio::SeqIO::MultiFile | Treating a set of files as a single input stream | 1.005009_004 | metacpan |
| Bio::SeqIO::abi | abi trace sequence input/output stream | 1.005009_004 | metacpan |
| Bio::SeqIO::ace | ace sequence input/output stream | 1.005009_004 | metacpan |
| Bio::SeqIO::agave | AGAVE sequence output stream. | 1.005009_004 | metacpan |
| Bio::SeqIO::alf | alf trace sequence input/output stream | 1.005009_004 | metacpan |
| Bio::SeqIO::asciitree | asciitree sequence input/output stream | 1.005009_004 | metacpan |
| Bio::SeqIO::bsml | BSML sequence input/output stream | 1.005009_004 | metacpan |
| Bio::SeqIO::bsml_sax | BSML sequence input/output stream using SAX | 1.005009_004 | metacpan |
| Bio::SeqIO::chadoxml | chadoxml sequence output stream | 1.005009_004 | metacpan |
| Bio::SeqIO::chaos | chaos sequence input/output stream | 1.005009_004 | metacpan |
| Bio::SeqIO::chaosxml | chaosxml sequence input/output stream | 1.005009_004 | metacpan |
| Bio::SeqIO::ctf | ctf trace sequence input/output stream | 1.005009_004 | metacpan |
| Bio::SeqIO::embl | EMBL sequence input/output stream | 1.005009_004 | metacpan |
| Bio::SeqIO::embldriver | EMBL sequence input/output stream | 1.005009_004 | metacpan |
| Bio::SeqIO::entrezgene | Entrez Gene ASN1 parser | 1.005009_004 | metacpan |
| Bio::SeqIO::excel | sequence input/output stream from a MSExcel-formatted table | 1.005009_004 | metacpan |
| Bio::SeqIO::exp | exp trace sequence input/output stream | 1.005009_004 | metacpan |
| Bio::SeqIO::fasta | fasta sequence input/output stream | 1.005009_004 | metacpan |
| Bio::SeqIO::fastq | fastq sequence input/output stream | 1.005009_004 | metacpan |
| Bio::SeqIO::flybase_chadoxml | FlyBase variant of chadoxml with sequence output stream | 1.005009_004 | metacpan |
| Bio::SeqIO::game | a class for parsing and writing game-XML | 1.005009_004 | metacpan |
| Bio::SeqIO::game::featHandler | a class for handling feature elements | 1.005009_004 | metacpan |
| Bio::SeqIO::game::gameHandler | PerlSAX handler for game-XML | 1.005009_004 | metacpan |
| Bio::SeqIO::game::gameSubs | a base class for game-XML parsing | 1.005009_004 | metacpan |
| Bio::SeqIO::game::gameWriter | a class for writing game-XML | 1.005009_004 | metacpan |
| Bio::SeqIO::game::seqHandler | a class for handling game-XML sequences | 1.005009_004 | metacpan |
| Bio::SeqIO::gbdriver | GenBank handler-based push parser | 1.005009_004 | metacpan |
| Bio::SeqIO::gcg | GCG sequence input/output stream | 1.005009_004 | metacpan |
| Bio::SeqIO::genbank | GenBank sequence input/output stream | 1.005009_004 | metacpan |
| Bio::SeqIO::interpro | InterProScan XML input/output stream | 1.005009_004 | metacpan |
| Bio::SeqIO::kegg | KEGG sequence input/output stream | 1.005009_004 | metacpan |
| Bio::SeqIO::largefasta | method i/o on very large fasta sequence files | 1.005009_004 | metacpan |
| Bio::SeqIO::lasergene | Lasergene sequence file input/output stream | 1.005009_004 | metacpan |
| Bio::SeqIO::locuslink | LocusLink input/output stream | 1.005009_004 | metacpan |
| Bio::SeqIO::metafasta | metafasta sequence input/output stream | 1.005009_004 | metacpan |
| Bio::SeqIO::phd | .phd file input/output stream | 1.005009_004 | metacpan |
| Bio::SeqIO::pir | PIR sequence input/output stream | 1.005009_004 | metacpan |
| Bio::SeqIO::pln | pln trace sequence input/output stream | 1.005009_004 | metacpan |
| Bio::SeqIO::qual | .qual file input/output stream | 1.005009_004 | metacpan |
| Bio::SeqIO::raw | raw sequence file input/output stream | 1.005009_004 | metacpan |
| Bio::SeqIO::scf | .scf file input/output stream | 1.005009_004 | metacpan |
| Bio::SeqIO::strider | DNA strider sequence input/output stream | 1.005009_004 | metacpan |
| Bio::SeqIO::swiss | Swissprot sequence input/output stream | 1.005009_004 | metacpan |
| Bio::SeqIO::swissdriver | SwissProt/UniProt handler-based push parser | 1.005009_004 | metacpan |
| Bio::SeqIO::tab | nearly raw sequence file input/output stream. Reads/writes id"\t"sequence"\n" | 1.005009_004 | metacpan |
| Bio::SeqIO::table | sequence input/output stream from a delimited table | 1.005009_004 | metacpan |
| Bio::SeqIO::tigr | TIGR XML sequence input/output stream | 1.005009_004 | metacpan |
| Bio::SeqIO::tigrxml | Parse TIGR (new) XML | 1.005009_004 | metacpan |
| Bio::SeqIO::tinyseq | reading/writing sequences in NCBI TinySeq format | 1.005009_004 | metacpan |
| Bio::SeqIO::tinyseq::tinyseqHandler | XML event handlers to support NCBI TinySeq XML parsing | 1.005009_004 | metacpan |
| Bio::SeqIO::ztr | ztr trace sequence input/output stream | 1.005009_004 | metacpan |
| Bio::SeqUtils | Additional methods for PrimarySeq objects | 1.005009_004 | metacpan |
| Bio::SimpleAlign | Multiple alignments held as a set of sequences | 1.005009_004 | metacpan |
| Bio::SimpleAnalysisI | A simple interface to any (local or remote) analysis tool | 1.005009_004 | metacpan |
| Bio::Species | Generic species object | 1.005009_004 | metacpan |
| Bio::Structure::Atom | Bioperl structure Object, describes an Atom | 1.005009_004 | metacpan |
| Bio::Structure::Chain | Bioperl structure Object, describes a chain | 1.005009_004 | metacpan |
| Bio::Structure::Entry | Bioperl structure Object, describes the whole entry | 1.005009_004 | metacpan |
| Bio::Structure::IO | Handler for Structure Formats | 1.005009_004 | metacpan |
| Bio::Structure::IO::pdb | PDB input/output stream | 1.005009_004 | metacpan |
| Bio::Structure::Model | Bioperl structure Object, describes a Model | 1.005009_004 | metacpan |
| Bio::Structure::Residue | Bioperl structure Object, describes a Residue | 1.005009_004 | metacpan |
| Bio::Structure::SecStr::DSSP::Res | Module for parsing/accessing dssp output | 1.005009_004 | metacpan |
| Bio::Structure::SecStr::STRIDE::Res | Module for parsing/accessing stride output | 1.005009_004 | metacpan |
| Bio::Structure::StructureI | Abstract Interface for a Structure objects | 1.005009_004 | metacpan |
| Bio::Symbol::Alphabet | BSANE/BioCORBA compliant symbol list alphabet | 1.005009_004 | metacpan |
| Bio::Symbol::AlphabetI | A Symbol Alphabet | 1.005009_004 | metacpan |
| Bio::Symbol::DNAAlphabet | A ready made DNA alphabet | 1.005009_004 | metacpan |
| Bio::Symbol::ProteinAlphabet | A ready made Protein alphabet | 1.005009_004 | metacpan |
| Bio::Symbol::Symbol | A biological symbol | 1.005009_004 | metacpan |
| Bio::Symbol::SymbolI | Interface for a Symbol | 1.005009_004 | metacpan |
| Bio::Taxon | A node in a represented taxonomy | 1.005009_004 | metacpan |
| Bio::Taxonomy | representing Taxonomy. | 1.005009_004 | metacpan |
| Bio::Taxonomy::FactoryI | interface to define how to access NCBI Taxonoy | 1.005009_004 | metacpan |
| Bio::Taxonomy::Node | A node in a represented taxonomy | 1.005009_004 | metacpan |
| Bio::Taxonomy::Taxon | Generic Taxonomic Entity object | 1.005009_004 | metacpan |
| Bio::Taxonomy::Tree | An Organism Level Implementation of TreeI interface. | 1.005009_004 | metacpan |
| Bio::Tools::AlignFactory | Base object for alignment factories | 1.005009_004 | metacpan |
| Bio::Tools::Alignment::Consed | A module to work with objects from consed .ace files | 1.005009_004 | metacpan |
| Bio::Tools::Alignment::Trim | A kludge to do specialized trimming of sequence based on quality. | 1.005009_004 | metacpan |
| Bio::Tools::Analysis::DNA::ESEfinder | a wrapper around ESEfinder server | 1.005009_004 | metacpan |
| Bio::Tools::Analysis::Protein::Domcut | a wrapper around Domcut server | 1.005009_004 | metacpan |
| Bio::Tools::Analysis::Protein::ELM | a wrapper around the ELM server which predicts short functional motifs on amino acid sequences | 1.005009_004 | metacpan |
| Bio::Tools::Analysis::Protein::GOR4 | a wrapper around GOR4 protein secondary structure prediction server | 1.005009_004 | metacpan |
| Bio::Tools::Analysis::Protein::HNN | a wrapper around the HNN protein secondary structure prediction server | 1.005009_004 | metacpan |
| Bio::Tools::Analysis::Protein::Mitoprot | a wrapper around Mitoprot server | 1.005009_004 | metacpan |
| Bio::Tools::Analysis::Protein::NetPhos | a wrapper around NetPhos server | 1.005009_004 | metacpan |
| Bio::Tools::Analysis::Protein::Scansite | a wrapper around the Scansite server | 1.005009_004 | metacpan |
| Bio::Tools::Analysis::Protein::Sopma | a wrapper around the Sopma protein secondary structure prediction server | 1.005009_004 | metacpan |
| Bio::Tools::Analysis::SimpleAnalysisBase | abstract superclass for SimpleAnalysis implementations | 1.005009_004 | metacpan |
| Bio::Tools::AnalysisResult | Base class for analysis result objects and parsers | 1.005009_004 | metacpan |
| Bio::Tools::Blat | parser for Blat program | 1.005009_004 | metacpan |
| Bio::Tools::CodonTable | Codon table object | 1.005009_004 | metacpan |
| Bio::Tools::Coil | parser for Coil output | 1.005009_004 | metacpan |
| Bio::Tools::ECnumber | representation of EC numbers (Enzyme Classification) | 1.005009_004 | metacpan |
| Bio::Tools::EMBOSS::Palindrome | parse EMBOSS palindrome output | 1.005009_004 | metacpan |
| Bio::Tools::EPCR | Parse ePCR output and make features | 1.005009_004 | metacpan |
| Bio::Tools::ERPIN | a parser for ERPIN output | 1.005009_004 | metacpan |
| Bio::Tools::ESTScan | Results of one ESTScan run | 1.005009_004 | metacpan |
| Bio::Tools::EUtilities | NCBI eutil XML parsers | 1.005009_004 | metacpan |
| Bio::Tools::EUtilities::EUtilDataI | eutil data object interface | 1.005009_004 | metacpan |
| Bio::Tools::EUtilities::EUtilParameters | Manipulation of NCBI eutil-based parameters for remote database requests. | 1.005009_004 | metacpan |
| Bio::Tools::EUtilities::History | 1.005009_004 | metacpan | |
| Bio::Tools::EUtilities::HistoryI | simple extension of EUtilDataI interface class for classes which hold NCBI server history data | 1.005009_004 | metacpan |
| Bio::Tools::EUtilities::Info | interface class for storing einfo data | 1.005009_004 | metacpan |
| Bio::Tools::EUtilities::Info::FieldInfo | class for storing einfo field data | 1.005009_004 | metacpan |
| Bio::Tools::EUtilities::Info::LinkInfo | class for storing einfo link data | 1.005009_004 | metacpan |
| Bio::Tools::EUtilities::Link | general API for accessing data retrieved from elink queries | 1.005009_004 | metacpan |
| Bio::Tools::EUtilities::Link::LinkSet | 1.005009_004 | metacpan | |
| Bio::Tools::EUtilities::Link::UrlLink | 1.005009_004 | metacpan | |
| Bio::Tools::EUtilities::Query | parse and collect esearch, epost, espell, egquery information | 1.005009_004 | metacpan |
| Bio::Tools::EUtilities::Query::GlobalQuery | 1.005009_004 | metacpan | |
| Bio::Tools::EUtilities::Summary | 1.005009_004 | metacpan | |
| Bio::Tools::EUtilities::Summary::DocSum | data object for document summary data from esummary | 1.005009_004 | metacpan |
| Bio::Tools::EUtilities::Summary::Item | simple layered object for DocSum item data | 1.005009_004 | metacpan |
| Bio::Tools::Eponine | Results of one Eponine run | 1.005009_004 | metacpan |
| Bio::Tools::Est2Genome | Parse est2genome output, makes simple Bio::SeqFeature::Generic objects | 1.005009_004 | metacpan |
| Bio::Tools::Fgenesh | parse results of one Fgenesh run | 1.005009_004 | metacpan |
| Bio::Tools::FootPrinter | write sequence features in FootPrinter format | 1.005009_004 | metacpan |
| Bio::Tools::GFF | A Bio::SeqAnalysisParserI compliant GFF format parser | 1.005009_004 | metacpan |
| Bio::Tools::Gel | Calculates relative electrophoretic migration distances | 1.005009_004 | metacpan |
| Bio::Tools::Geneid | Results of one geneid run | 1.005009_004 | metacpan |
| Bio::Tools::Genemark | Results of one Genemark run | 1.005009_004 | metacpan |
| Bio::Tools::Genewise | Results of one Genewise run | 1.005009_004 | metacpan |
| Bio::Tools::Genomewise | Results of one Genomewise run | 1.005009_004 | metacpan |
| Bio::Tools::Genscan | Results of one Genscan run | 1.005009_004 | metacpan |
| Bio::Tools::Glimmer | parser for Glimmer 2.X/3.X prokaryotic and GlimmerM/GlimmerHMM eukaryotic gene predictions | 1.005009_004 | metacpan |
| Bio::Tools::Grail | Results of one Grail run | 1.005009_004 | metacpan |
| Bio::Tools::GuessSeqFormat | Module for determining the sequence format of the contents of a file, a string, or through a filehandle. | 1.005009_004 | metacpan |
| Bio::Tools::HMM | Perl extension to perform Hidden Markov Model calculations | 1.005009_004 | metacpan |
| Bio::Tools::HMMER::Domain | One particular domain hit from HMMER | 1.005009_004 | metacpan |
| Bio::Tools::HMMER::Results | Object representing HMMER output results | 1.005009_004 | metacpan |
| Bio::Tools::HMMER::Set | Set of identical domains from HMMER matches | 1.005009_004 | metacpan |
| Bio::Tools::Hmmpfam | Parser for Hmmpfam program | 1.005009_004 | metacpan |
| Bio::Tools::IUPAC | Generates unique Seq objects from an ambiguous Seq object | 1.005009_004 | metacpan |
| Bio::Tools::Infernal | A parser for Infernal output | 1.005009_004 | metacpan |
| Bio::Tools::Lucy | Object for analyzing the output from Lucy, a vector and quality trimming program from TIGR | 1.005009_004 | metacpan |
| Bio::Tools::MZEF | Results of one MZEF run | 1.005009_004 | metacpan |
| Bio::Tools::Match | Parses output from Transfac's match(TM) | 1.005009_004 | metacpan |
| Bio::Tools::OddCodes | Object holding alternative alphabet coding for one protein sequence | 1.005009_004 | metacpan |
| Bio::Tools::Phylo::Gerp | Parses output from GERP | 1.005009_004 | metacpan |
| Bio::Tools::Phylo::Gumby | Parses output from gumby | 1.005009_004 | metacpan |
| Bio::Tools::Phylo::Molphy | parser for Molphy output | 1.005009_004 | metacpan |
| Bio::Tools::Phylo::Molphy::Result | container for data parsed from a ProtML run | 1.005009_004 | metacpan |
| Bio::Tools::Phylo::PAML | Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00 | 1.005009_004 | metacpan |
| Bio::Tools::Phylo::PAML::ModelResult | A container for NSSite Model Result from PAML | 1.005009_004 | metacpan |
| Bio::Tools::Phylo::PAML::Result | A PAML result set object | 1.005009_004 | metacpan |
| Bio::Tools::Phylo::Phylip::ProtDist | parser for ProtDist output | 1.005009_004 | metacpan |
| Bio::Tools::Prediction::Exon | A predicted exon feature | 1.005009_004 | metacpan |
| Bio::Tools::Prediction::Gene | a predicted gene structure feature | 1.005009_004 | metacpan |
| Bio::Tools::Primer3 | Create input for and work with the output from the program primer3 | 1.005009_004 | metacpan |
| Bio::Tools::Primer::Assessor::Base | base class for common assessor things | 1.005009_004 | metacpan |
| Bio::Tools::Primer::AssessorI | interface for assessing primer pairs | 1.005009_004 | metacpan |
| Bio::Tools::Primer::Feature | position of a single primer | 1.005009_004 | metacpan |
| Bio::Tools::Primer::Pair | two primers on left and right side | 1.005009_004 | metacpan |
| Bio::Tools::Prints | Parser for FingerPRINTScanII program | 1.005009_004 | metacpan |
| Bio::Tools::Profile | parse Profile output | 1.005009_004 | metacpan |
| Bio::Tools::Promoterwise | parser for Promoterwise tab format output | 1.005009_004 | metacpan |
| Bio::Tools::PrositeScan | Parser for ps_scan result | 1.005009_004 | metacpan |
| Bio::Tools::Protparam | submit to and parse output from protparam ; | 1.005009_004 | metacpan |
| Bio::Tools::Pseudowise | Results of one Pseudowise run | 1.005009_004 | metacpan |
| Bio::Tools::QRNA | A Parser for qrna output | 1.005009_004 | metacpan |
| Bio::Tools::RNAMotif | A parser for RNAMotif output | 1.005009_004 | metacpan |
| Bio::Tools::RandomDistFunctions | A set of routines useful for generating random data in different distributions | 1.005009_004 | metacpan |
| Bio::Tools::RepeatMasker | a parser for RepeatMasker output | 1.005009_004 | metacpan |
| Bio::Tools::Run::GenericParameters | An object for the parameters used to run programs | 1.005009_004 | metacpan |
| Bio::Tools::Run::ParametersI | A Base object for the parameters used to run programs | 1.005009_004 | metacpan |
| Bio::Tools::Run::RemoteBlast | Object for remote execution of the NCBI Blast via HTTP | 1.005009_004 | 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 and NCBI rpsblast. | 1.005009_004 | metacpan |
| Bio::Tools::Run::StandAloneNCBIBlast | Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). With experimental support for NCBI rpsblast. | 1.005009_004 | metacpan |
| Bio::Tools::Run::StandAloneWUBlast | Object for the local execution of WU-Blast. | 1.005009_004 | metacpan |
| Bio::Tools::Run::WrapperBase | A Base object for wrappers around executables | 1.005009_004 | metacpan |
| Bio::Tools::Seg | parse C<seg> output | 1.005009_004 | metacpan |
| Bio::Tools::SeqPattern | represent a sequence pattern or motif | 1.005009_004 | metacpan |
| Bio::Tools::SeqStats | Object holding statistics for one particular sequence | 1.005009_004 | metacpan |
| Bio::Tools::SeqWords | Object holding n-mer statistics for a sequence | 1.005009_004 | metacpan |
| Bio::Tools::SiRNA | 1.005009_004 | metacpan | |
| Bio::Tools::SiRNA::Ruleset::saigo | Perl object implementing the Saigo group's rules for designing small inhibitory RNAs | 1.005009_004 | metacpan |
| Bio::Tools::SiRNA::Ruleset::tuschl | Perl object implementing the tuschl group's rules for designing small inhibitory RNAs | 1.005009_004 | metacpan |
| Bio::Tools::Sigcleave | Bioperl object for sigcleave analysis | 1.005009_004 | metacpan |
| Bio::Tools::Signalp | parser for Signalp output | 1.005009_004 | metacpan |
| Bio::Tools::Signalp::ExtendedSignalp | enhanced parser for Signalp output | 1.005009_004 | metacpan |
| Bio::Tools::Sim4::Exon | A single exon determined by an alignment | 1.005009_004 | metacpan |
| Bio::Tools::Sim4::Results | Results of one Sim4 run | 1.005009_004 | metacpan |
| Bio::Tools::Spidey::Exon | A single exon determined by an alignment | 1.005009_004 | metacpan |
| Bio::Tools::Spidey::Results | Results of a Spidey run | 1.005009_004 | metacpan |
| Bio::Tools::TandemRepeatsFinder | a parser for Tandem Repeats Finder output | 1.005009_004 | metacpan |
| Bio::Tools::TargetP | Results of one TargetP run | 1.005009_004 | metacpan |
| Bio::Tools::Tmhmm | parse TMHMM output (TransMembrane HMM) | 1.005009_004 | metacpan |
| Bio::Tools::dpAlign | Perl extension to do pairwise dynamic programming sequence alignment | 1.005009_004 | metacpan |
| Bio::Tools::ipcress | Parse ipcress output and make features | 1.005009_004 | metacpan |
| Bio::Tools::isPcr | Parse isPcr output and make features | 1.005009_004 | metacpan |
| Bio::Tools::pICalculator | calculate the isoelectric point of a protein | 1.005009_004 | metacpan |
| Bio::Tools::pSW | pairwise Smith Waterman object | 1.005009_004 | metacpan |
| Bio::Tools::tRNAscanSE | A parser for tRNAscan-SE output | 1.005009_004 | metacpan |
| Bio::Tree::AlleleNode | A Node with Alleles attached | 1.005009_004 | metacpan |
| Bio::Tree::AnnotatableNode | A Tree Node with support for annotation | 1.005009_004 | metacpan |
| Bio::Tree::Compatible | Testing compatibility of phylogenetic trees with nested taxa. | 1.005009_004 | metacpan |
| Bio::Tree::DistanceFactory | Construct a tree using distance based methods | 1.005009_004 | metacpan |
| Bio::Tree::Draw::Cladogram | Drawing phylogenetic trees in Encapsulated PostScript (EPS) format. | 1.005009_004 | metacpan |
| Bio::Tree::Node | A Simple Tree Node | 1.005009_004 | metacpan |
| Bio::Tree::NodeI | Interface describing a Tree Node | 1.005009_004 | metacpan |
| Bio::Tree::NodeNHX | A Simple Tree Node with support for NHX tags | 1.005009_004 | metacpan |
| Bio::Tree::RandomFactory | TreeFactory for generating Random Trees | 1.005009_004 | metacpan |
| Bio::Tree::Statistics | Calculate certain statistics for a Tree | 1.005009_004 | metacpan |
| Bio::Tree::Tree | An Implementation of TreeI interface. | 1.005009_004 | metacpan |
| Bio::Tree::TreeFunctionsI | Decorated Interface implementing basic Tree exploration methods | 1.005009_004 | metacpan |
| Bio::Tree::TreeI | A Tree object suitable for lots of things, designed originally for Phylogenetic Trees. | 1.005009_004 | metacpan |
| Bio::TreeIO | Parser for Tree files | 1.005009_004 | metacpan |
| Bio::TreeIO::TreeEventBuilder | Build Bio::Tree::Tree's and Bio::Tree::Node's from Events | 1.005009_004 | metacpan |
| Bio::TreeIO::cluster | A TreeIO driver module for parsing Algorithm::Cluster::treecluster() output | 1.005009_004 | metacpan |
| Bio::TreeIO::lintree | Parser for lintree output trees | 1.005009_004 | metacpan |
| Bio::TreeIO::newick | TreeIO implementation for parsing Newick/New Hampshire/PHYLIP format. | 1.005009_004 | metacpan |
| Bio::TreeIO::nexus | A TreeIO driver module for parsing Nexus tree output from PAUP | 1.005009_004 | metacpan |
| Bio::TreeIO::nhx | TreeIO implementation for parsing Newick/New Hampshire eXtendend (NHX) format. | 1.005009_004 | metacpan |
| Bio::TreeIO::pag | Bio::TreeIO driver for Pagel format | 1.005009_004 | metacpan |
| Bio::TreeIO::phyloxml | TreeIO implementation for parsing PhyloXML format. | 1.005009_004 | metacpan |
| Bio::TreeIO::svggraph | A simple output format that converts a Tree object to an SVG output | 1.005009_004 | metacpan |
| Bio::TreeIO::tabtree | A simple output format which displays a tree as an ASCII drawing | 1.005009_004 | metacpan |
| Bio::UpdateableSeqI | Descendant of Bio::SeqI that allows updates | 1.005009_004 | metacpan |
| Bio::Variation::AAChange | Sequence change class for polypeptides | 1.005009_004 | metacpan |
| Bio::Variation::AAReverseMutate | point mutation and codon information from single amino acid changes | 1.005009_004 | metacpan |
| Bio::Variation::Allele | Sequence object with allele-specific attributes | 1.005009_004 | metacpan |
| Bio::Variation::DNAMutation | DNA level mutation class | 1.005009_004 | metacpan |
| Bio::Variation::IO | Handler for sequence variation IO Formats | 1.005009_004 | metacpan |
| Bio::Variation::IO::flat | flat file sequence variation input/output stream | 1.005009_004 | metacpan |
| Bio::Variation::IO::xml | XML sequence variation input/output stream | 1.005009_004 | metacpan |
| Bio::Variation::RNAChange | Sequence change class for RNA level | 1.005009_004 | metacpan |
| Bio::Variation::SNP | submitted SNP | 1.005009_004 | metacpan |
| Bio::Variation::SeqDiff | Container class for mutation/variant descriptions | 1.005009_004 | metacpan |
| Bio::Variation::VariantI | Sequence Change SeqFeature abstract class | 1.005009_004 | metacpan |
| Bio::WebAgent | A base class for Web (any protocol) access | 1.005009_004 | metacpan |
| FeatureStore | 1.005009_004 | metacpan | |
| HIVSchema | 1.005009_004 | metacpan | |
| Q | 1.005009_004 | metacpan | |
| QRY | 1.005009_004 | metacpan | |
| R | 1.005009_004 | metacpan |