Kwalitee Issues

no_pod_errors

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

Error: bioperl-1.5.2_102/Bio/FeatureIO/ptt.pm -- Around line 31: '=item' outside of any '=over'Around line 68: You forgot a '=back' before '=head1' bioperl-1.5.2_102/Bio/Root/Exception.pm -- Around line 213: L<> starts or ends with whitespace bioperl-1.5.2_102/Bio/Tools/Geneid.pm -- Around line 36: Non-ASCII character seen before =encoding in 'Guigó'. Assuming CP1252 bioperl-1.5.2_102/Bio/Tools/GuessSeqFormat.pm -- Around line 213: Non-ASCII character seen before =encoding in 'Kähäri,'. Assuming CP1252

package_version_matches_dist_version

Fix the version(s).

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::DB::SeqFeature::Store::DBI::mysql, Bio::DB::SeqFeature::Store::GFF3Loader, Bio::DB::XEMBLService, Bio::Graph::ProteinGraph, Bio::Graphics::Feature, Bio::Graphics::FeatureFile::Iterator, Bio::Graphics::Glyph::three_letters, Bio::Location::Split, Bio::Matrix::PSM::SiteMatrixI, Bio::Phenotype::PhenotypeI, Bio::Search::BlastUtils, Bio::SearchIO::SearchWriterI, Bio::SeqIO::game, Bio::Tools::Analysis::Protein::ELM, Bio::Tools::HMM, Bio::Tools::Primer::Assessor::Base, Bio::Tools::Primer::AssessorI, Bio::Tools::Primer::Feature, Bio::Tools::Primer::Pair, Bio::Tools::dpAlign

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

use_warnings

Add 'use warnings' (or its equivalents) to all modules (this will require perl > 5.6), or convince us that your favorite module is well-known enough and people can easily see the modules warn when something bad happens.

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

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. 1.005002102 metacpan
Bio::Align::DNAStatistics Calculate some statistics for a DNA alignment 1.005002102 metacpan
Bio::Align::PairwiseStatistics Base statistic object for Pairwise Alignments 1.005002102 metacpan
Bio::Align::ProteinStatistics Calculate Protein Alignment statistics (mostly distances) 1.005002102 metacpan
Bio::Align::StatisticsI Calculate some statistics for an alignment 1.005002102 metacpan
Bio::Align::Utilities A collection of utilities regarding converting and manipulating alignment objects 1.005002102 metacpan
Bio::AlignIO Handler for AlignIO Formats 1.005002102 metacpan
Bio::AlignIO::bl2seq bl2seq sequence input/output stream 1.005002102 metacpan
Bio::AlignIO::clustalw clustalw sequence input/output stream 1.005002102 metacpan
Bio::AlignIO::emboss Parse EMBOSS alignment output (from applications water and needle) 1.005002102 metacpan
Bio::AlignIO::fasta fasta MSA Sequence input/output stream 1.005002102 metacpan
Bio::AlignIO::largemultifasta Largemultifasta MSA Sequence input/output stream 1.005002102 metacpan
Bio::AlignIO::maf Multipla Alignment Format sequence input stream 1.005002102 metacpan
Bio::AlignIO::mase mase sequence input/output stream 1.005002102 metacpan
Bio::AlignIO::mega Parse and Create MEGA format data files 1.005002102 metacpan
Bio::AlignIO::meme meme sequence input/output stream 1.005002102 metacpan
Bio::AlignIO::metafasta Metafasta MSA Sequence input/output stream 1.005002102 metacpan
Bio::AlignIO::msf msf sequence input/output stream 1.005002102 metacpan
Bio::AlignIO::nexus NEXUS format sequence input/output stream 1.005002102 metacpan
Bio::AlignIO::pfam pfam sequence input/output stream 1.005002102 metacpan
Bio::AlignIO::phylip PHYLIP format sequence input/output stream 1.005002102 metacpan
Bio::AlignIO::po po MSA Sequence input/output stream 1.005002102 metacpan
Bio::AlignIO::prodom prodom sequence input/output stream 1.005002102 metacpan
Bio::AlignIO::psi Read/Write PSI-BLAST profile alignment files 1.005002102 metacpan
Bio::AlignIO::selex selex sequence input/output stream 1.005002102 metacpan
Bio::AlignIO::stockholm stockholm sequence input/output stream 1.005002102 metacpan
Bio::AnalysisI An interface to any (local or remote) analysis tool 1.005002102 metacpan
Bio::AnalysisI::JobI 1.005002102 metacpan
Bio::AnalysisParserI Generic analysis output parser interface 1.005002102 metacpan
Bio::AnalysisResultI Interface for analysis result objects 1.005002102 metacpan
Bio::AnnotatableI the base interface an annotatable object must implement 1.005002102 metacpan
Bio::Annotation::AnnotationFactory Instantiates a new Bio::AnnotationI (or derived class) through a factory 1.005002102 metacpan
Bio::Annotation::Collection Default Perl implementation of AnnotationCollectionI 1.005002102 metacpan
Bio::Annotation::Comment A comment object, holding text 1.005002102 metacpan
Bio::Annotation::DBLink untyped links between databases 1.005002102 metacpan
Bio::Annotation::OntologyTerm An ontology term adapted to AnnotationI 1.005002102 metacpan
Bio::Annotation::Reference Specialised DBLink object for Literature References 1.005002102 metacpan
Bio::Annotation::SimpleValue A simple scalar 1.005002102 metacpan
Bio::Annotation::StructuredValue A scalar with embedded structured information 1.005002102 metacpan
Bio::Annotation::Target Provides an object which represents a target (ie, a similarity hit) from one object to something in another database 1.005002102 metacpan
Bio::Annotation::TypeManager Manages types for annotation collections 1.005002102 metacpan
Bio::AnnotationCollectionI Interface for annotation collections 1.005002102 metacpan
Bio::AnnotationI Annotation interface 1.005002102 metacpan
Bio::Assembly::Contig Perl module to hold and manipulate sequence assembly contigs. 1.005002102 metacpan
Bio::Assembly::ContigAnalysis 1.005002102 metacpan
Bio::Assembly::IO Handler for Assembly::IO Formats 1.005002102 metacpan
Bio::Assembly::IO::ace module to load phrap ACE files. 1.005002102 metacpan
Bio::Assembly::IO::phrap driver to load phrap.out files. 1.005002102 metacpan
Bio::Assembly::Scaffold Perl module to hold and manipulate sequence assembly data. 1.005002102 metacpan
Bio::Assembly::ScaffoldI Abstract Inteface of Sequence Assemblies 1.005002102 metacpan
Bio::Assembly::Singlet Perl module to hold and manipulate singlets from sequence assembly contigs. 1.005002102 metacpan
Bio::Biblio A Bibliographic Query Service module 1.005002102 metacpan
Bio::Biblio::Article Representation of a general article 1.005002102 metacpan
Bio::Biblio::BiblioBase An abstract base for other biblio classes 1.005002102 metacpan
Bio::Biblio::Book Representation of a book 1.005002102 metacpan
Bio::Biblio::BookArticle Representation of a book article 1.005002102 metacpan
Bio::Biblio::IO Handling the bibliographic references 1.005002102 metacpan
Bio::Biblio::IO::medline2ref A converter of a raw hash to MEDLINE citations 1.005002102 metacpan
Bio::Biblio::IO::medlinexml A converter of XML files with MEDLINE citations 1.005002102 metacpan
Bio::Biblio::IO::pubmed2ref A converter of a raw hash to PUBMED citations 1.005002102 metacpan
Bio::Biblio::IO::pubmedxml A converter of XML files with PUBMED citations 1.005002102 metacpan
Bio::Biblio::Journal Representation of a journal 1.005002102 metacpan
Bio::Biblio::JournalArticle Representation of a journal article 1.005002102 metacpan
Bio::Biblio::MedlineArticle Representation of a MEDLINE article 1.005002102 metacpan
Bio::Biblio::MedlineBook Representation of a MEDLINE book 1.005002102 metacpan
Bio::Biblio::MedlineBookArticle Representation of a MEDLINE book article 1.005002102 metacpan
Bio::Biblio::MedlineJournal Representation of a MEDLINE journal 1.005002102 metacpan
Bio::Biblio::MedlineJournalArticle Representation of a MEDLINE journal article 1.005002102 metacpan
Bio::Biblio::Organisation Representation of an organisation 1.005002102 metacpan
Bio::Biblio::Patent Representation of a patent 1.005002102 metacpan
Bio::Biblio::Person Representation of a person 1.005002102 metacpan
Bio::Biblio::Proceeding Representation of a conference proceeding 1.005002102 metacpan
Bio::Biblio::Provider Representation of a general provider 1.005002102 metacpan
Bio::Biblio::PubmedArticle Representation of a PUBMED article 1.005002102 metacpan
Bio::Biblio::PubmedBookArticle Representation of a PUBMED book article 1.005002102 metacpan
Bio::Biblio::PubmedJournalArticle Representation of a PUBMED journal article 1.005002102 metacpan
Bio::Biblio::Ref Representation of a bibliographic reference 1.005002102 metacpan
Bio::Biblio::Service Representation of a provider of type service 1.005002102 metacpan
Bio::Biblio::TechReport Representation of a technical report 1.005002102 metacpan
Bio::Biblio::Thesis Representation of thesis 1.005002102 metacpan
Bio::Biblio::WebResource Representation of a web resource 1.005002102 metacpan
Bio::Cluster::ClusterFactory Instantiates a new Bio::ClusterI (or derived class) through a factory 1.005002102 metacpan
Bio::Cluster::FamilyI Family Interface 1.005002102 metacpan
Bio::Cluster::SequenceFamily Sequence Family object 1.005002102 metacpan
Bio::Cluster::UniGene UniGene object 1.005002102 metacpan
Bio::Cluster::UniGeneI abstract interface of UniGene object 1.005002102 metacpan
Bio::ClusterI Cluster Interface 1.005002102 metacpan
Bio::ClusterIO Handler for Cluster Formats 1.005002102 metacpan
Bio::ClusterIO::dbsnp dbSNP input stream 1.005002102 metacpan
Bio::ClusterIO::unigene UniGene input stream 1.005002102 metacpan
Bio::CodonUsage::IO for reading and writing codon usage tables to file 1.005002102 metacpan
Bio::CodonUsage::Table for access to the Codon usage Database at http://www.kazusa.or.jp/codon. 1.005002102 metacpan
Bio::Coordinate::Chain Mapping locations through a chain of coordinate mappers 1.005002102 metacpan
Bio::Coordinate::Collection Noncontinuous match between two coordinate sets 1.005002102 metacpan
Bio::Coordinate::ExtrapolatingPair Continuous match between two coordinate sets 1.005002102 metacpan
Bio::Coordinate::GeneMapper transformations between gene related coordinate systems 1.005002102 metacpan
Bio::Coordinate::Graph Finds shortest path between nodes in a graph 1.005002102 metacpan
Bio::Coordinate::MapperI Interface describing coordinate mappers 1.005002102 metacpan
Bio::Coordinate::Pair Continuous match between two coordinate sets 1.005002102 metacpan
Bio::Coordinate::Result Results from coordinate transformation 1.005002102 metacpan
Bio::Coordinate::Result::Gap Another name for Bio::Location::Simple 1.005002102 metacpan
Bio::Coordinate::Result::Match Another name for Bio::Location::Simple 1.005002102 metacpan
Bio::Coordinate::ResultI Interface to identify coordinate mapper results 1.005002102 metacpan
Bio::Coordinate::Utils Additional methods to create Bio::Coordinate objects 1.005002102 metacpan
Bio::DB::Ace Database object interface to ACeDB servers 1.005002102 metacpan
Bio::DB::Biblio::biofetch A BioFetch-based access to a bibliographic citation retrieval 1.005002102 metacpan
Bio::DB::Biblio::eutils Access to PubMed's bibliographic query service 1.005002102 metacpan
Bio::DB::Biblio::pdf Fetch PDF for a PubMed ID 1.005002102 metacpan
Bio::DB::Biblio::soap A SOAP-based access to a bibliographic query service 1.005002102 metacpan
Bio::DB::BiblioI An interface to a Bibliographic Query Service 1.005002102 metacpan
Bio::DB::BioFetch Database object interface to BioFetch retrieval 1.005002102 metacpan
Bio::DB::CUTG for access to the Codon usage Database at http://www.kazusa.or.jp/codon. 1.005002102 metacpan
Bio::DB::DBFetch Database object for retrieving using the dbfetch script 1.005002102 metacpan
Bio::DB::EMBL Database object interface for EMBL entry retrieval 1.005002102 metacpan
Bio::DB::EUtilities interface for handling web queries and data retrieval from Entrez Utilities at NCBI. 1.005002102 metacpan
Bio::DB::EUtilities::Cookie simple object to hold NCBI cookie information and descriptions 1.005002102 metacpan
Bio::DB::EUtilities::ElinkData 1.005002102 metacpan
Bio::DB::EUtilities::efetch retrieval of records from a list of IDs or the user's environment. 1.005002102 metacpan
Bio::DB::EUtilities::egquery counts for a global query of Entrez databases 1.005002102 metacpan
Bio::DB::EUtilities::einfo NCBI database information 1.005002102 metacpan
Bio::DB::EUtilities::elink check for and retrieve external or related ID's from a list of one or more primary ID's, including relevancy scores. 1.005002102 metacpan
Bio::DB::EUtilities::epost posting IDs on the remote NCBI server for batch retrieval and chained queries 1.005002102 metacpan
Bio::DB::EUtilities::esearch Base interface class for handling web queries and data retrieval from Entrez Utilities from NCBI. You shouldn't use this class directly. 1.005002102 metacpan
Bio::DB::EUtilities::esummary retrieval of NCBI DocSum data from a list of primary IDs or a Cookie 1.005002102 metacpan
Bio::DB::EntrezGene Database object interface to Entrez Gene 1.005002102 metacpan
Bio::DB::Expression DESCRIPTION of Object 1.005002102 metacpan
Bio::DB::Expression::geo *** DESCRIPTION of Class 1.005002102 metacpan
Bio::DB::Failover A Bio::DB::RandomAccessI compliant class which wraps a prioritized list of DBs 1.005002102 metacpan
Bio::DB::Fasta Fast indexed access to a directory of fasta files 1.005002102 metacpan
Bio::DB::Fasta::Stream 1.005002102 metacpan
Bio::DB::FileCache In file cache for BioSeq objects 1.005002102 metacpan
Bio::DB::Flat Interface for indexed flat files 1.005002102 metacpan
Bio::DB::Flat::BDB Interface for BioHackathon standard BDB-indexed flat file 1.005002102 metacpan
Bio::DB::Flat::BDB::embl embl adaptor for Open-bio standard BDB-indexed flat file 1.005002102 metacpan
Bio::DB::Flat::BDB::fasta fasta adaptor for Open-bio standard BDB-indexed flat file 1.005002102 metacpan
Bio::DB::Flat::BDB::genbank genbank adaptor for Open-bio standard BDB-indexed flat file 1.005002102 metacpan
Bio::DB::Flat::BDB::swiss swissprot adaptor for Open-bio standard BDB-indexed flat file 1.005002102 metacpan
Bio::DB::Flat::BDB::swissprot swissprot adaptor for Open-bio standard BDB-indexed flat file 1.005002102 metacpan
Bio::DB::Flat::BinarySearch BinarySearch search indexing system for sequence files 1.005002102 metacpan
Bio::DB::GDB Database object interface to GDB HTTP query 1.005002102 metacpan
Bio::DB::GFF Storage and retrieval of sequence annotation data 1.005002102 metacpan
Bio::DB::GFF::Adaptor::ace ace interface (for multiple inheritance) 1.005002102 metacpan
Bio::DB::GFF::Adaptor::berkeleydb Bio::DB::GFF database adaptor for in-memory databases 1.005002102 metacpan
Bio::DB::GFF::Adaptor::berkeleydb::iterator iterator for Bio::DB::GFF::Adaptor::berkeleydb 1.005002102 metacpan
Bio::DB::GFF::Adaptor::biofetch Cache BioFetch objects in a Bio::DB::GFF database 1.005002102 metacpan
Bio::DB::GFF::Adaptor::biofetch_oracle Cache BioFetch objects in a Bio::DB::GFF database 1.005002102 metacpan
Bio::DB::GFF::Adaptor::dbi Database adaptor for DBI (SQL) databases 1.005002102 metacpan
Bio::DB::GFF::Adaptor::dbi::caching_handle Cache for database handles 1.005002102 metacpan
Bio::DB::GFF::Adaptor::dbi::faux_dbh 1.005002102 metacpan
Bio::DB::GFF::Adaptor::dbi::iterator iterator for Bio::DB::GFF::Adaptor::dbi 1.005002102 metacpan
Bio::DB::GFF::Adaptor::dbi::mysql Database adaptor for a specific mysql schema 1.005002102 metacpan
Bio::DB::GFF::Adaptor::dbi::mysqlace Unholy union between mysql GFF database and acedb database 1.005002102 metacpan
Bio::DB::GFF::Adaptor::dbi::mysqlcmap Database adaptor for an integraded CMap/GBrowse mysql schema 1.005002102 metacpan
Bio::DB::GFF::Adaptor::dbi::mysqlopt Deprecated database adaptor 1.005002102 metacpan
Bio::DB::GFF::Adaptor::dbi::oracle Database adaptor for a specific oracle schema 1.005002102 metacpan
Bio::DB::GFF::Adaptor::dbi::oracleace Unholy union between oracle GFF database and acedb database 1.005002102 metacpan
Bio::DB::GFF::Adaptor::dbi::pg Database adaptor for a specific postgres schema 1.005002102 metacpan
Bio::DB::GFF::Adaptor::dbi::pg_fts Database adaptor for a specific postgres schema with a TSearch2 implementation 1.005002102 metacpan
Bio::DB::GFF::Adaptor::memory Bio::DB::GFF database adaptor for in-memory databases 1.005002102 metacpan
Bio::DB::GFF::Adaptor::memory::feature_serializer 1.005002102 metacpan
Bio::DB::GFF::Adaptor::memory::iterator iterator for Bio::DB::GFF::Adaptor::memory 1.005002102 metacpan
Bio::DB::GFF::Aggregator Aggregate GFF groups into composite features 1.005002102 metacpan
Bio::DB::GFF::Aggregator::alignment Alignment aggregator 1.005002102 metacpan
Bio::DB::GFF::Aggregator::clone Clone aggregator 1.005002102 metacpan
Bio::DB::GFF::Aggregator::coding The Coding Region Aggregator 1.005002102 metacpan
Bio::DB::GFF::Aggregator::match Match aggregator 1.005002102 metacpan
Bio::DB::GFF::Aggregator::none No aggregation 1.005002102 metacpan
Bio::DB::GFF::Aggregator::processed_transcript Sequence Ontology Transcript 1.005002102 metacpan
Bio::DB::GFF::Aggregator::so_transcript Sequence Ontology Transcript 1.005002102 metacpan
Bio::DB::GFF::Aggregator::transcript Transcript aggregator 1.005002102 metacpan
Bio::DB::GFF::Aggregator::ucsc_acembly UCSC acembly aggregator 1.005002102 metacpan
Bio::DB::GFF::Aggregator::ucsc_ensgene UCSC ensGene aggregator 1.005002102 metacpan
Bio::DB::GFF::Aggregator::ucsc_genscan UCSC genscan aggregator 1.005002102 metacpan
Bio::DB::GFF::Aggregator::ucsc_refgene UCSC refGene aggregator 1.005002102 metacpan
Bio::DB::GFF::Aggregator::ucsc_sanger22 UCSC sanger22 aggregator 1.005002102 metacpan
Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo UCSC sanger22pseudo aggregator 1.005002102 metacpan
Bio::DB::GFF::Aggregator::ucsc_softberry UCSC softberry aggregator 1.005002102 metacpan
Bio::DB::GFF::Aggregator::ucsc_twinscan UCSC twinscan aggregator 1.005002102 metacpan
Bio::DB::GFF::Aggregator::ucsc_unigene UCSC UniGene aggregator 1.005002102 metacpan
Bio::DB::GFF::Featname The name of a feature 1.005002102 metacpan
Bio::DB::GFF::Feature A relative segment identified by a feature type 1.005002102 metacpan
Bio::DB::GFF::Homol A segment of DNA that is homologous to another 1.005002102 metacpan
Bio::DB::GFF::ID_Iterator 1.005002102 metacpan
Bio::DB::GFF::RelSegment Sequence segment with relative coordinate support 1.005002102 metacpan
Bio::DB::GFF::Segment Simple DNA segment object 1.005002102 metacpan
Bio::DB::GFF::Typename The name of a feature type 1.005002102 metacpan
Bio::DB::GFF::Util::Binning binning utility for Bio::DB::GFF index 1.005002102 metacpan
Bio::DB::GFF::Util::Rearrange rearrange utility 1.005002102 metacpan
Bio::DB::GenBank Database object interface to GenBank 1.005002102 metacpan
Bio::DB::GenPept Database object interface to GenPept 1.005002102 metacpan
Bio::DB::GenericWebDBI abstract interface for parameter-based remote database access 1.005002102 metacpan
Bio::DB::InMemoryCache Abstract interface for a sequence database 1.005002102 metacpan
Bio::DB::LocationI A RandomAccessI-like abstract interface for retrieving location data from a sequence database and returning Bio::LocationI objects 1.005002102 metacpan
Bio::DB::MeSH Term retrieval from a Web MeSH database 1.005002102 metacpan
Bio::DB::NCBIHelper A collection of routines useful for queries to NCBI databases. 1.005002102 metacpan
Bio::DB::Query::GenBank Build a GenBank Entrez Query 1.005002102 metacpan
Bio::DB::Query::WebQuery Helper class for web-based sequence queryies 1.005002102 metacpan
Bio::DB::QueryI Object Interface to queryable sequence databases 1.005002102 metacpan
Bio::DB::RandomAccessI Abstract interface for a sequence database 1.005002102 metacpan
Bio::DB::RefSeq Database object interface for RefSeq retrieval 1.005002102 metacpan
Bio::DB::ReferenceI A RandomAccessI-like abstract interface for retrieving Reference data from a sequence database and returning Bio::Annotation::Reference objects 1.005002102 metacpan
Bio::DB::Registry Access to the Open Bio Database Access registry scheme 1.005002102 metacpan
Bio::DB::SeqFeature Normalized feature for use with Bio::DB::SeqFeature::Store 1.005002102 metacpan
Bio::DB::SeqFeature::NormalizedFeature Normalized feature for use with Bio::DB::SeqFeature::Store 1.005002102 metacpan
Bio::DB::SeqFeature::NormalizedFeatureI Interface for normalized features 1.005002102 metacpan
Bio::DB::SeqFeature::NormalizedTableFeatureI Interface for normalized features whose hierarchy is stored in a table 1.005002102 metacpan
Bio::DB::SeqFeature::Segment Location-based access to genome annotation data 1.005002102 metacpan
Bio::DB::SeqFeature::Store Storage and retrieval of sequence annotation data 1.005002102 metacpan
Bio::DB::SeqFeature::Store::DBI::Iterator 1.005002102 metacpan
Bio::DB::SeqFeature::Store::DBI::mysql Mysql implementation of Bio::DB::SeqFeature::Store 1.005002102 metacpan
Bio::DB::SeqFeature::Store::GFF3Loader GFF3 file loader for Bio::DB::SeqFeature::Store 1.005002102 metacpan
Bio::DB::SeqFeature::Store::bdb fetch and store objects from a BerkeleyDB 1.005002102 metacpan
Bio::DB::SeqFeature::Store::berkeleydb Storage and retrieval of sequence annotation data in Berkeleydb files 1.005002102 metacpan
Bio::DB::SeqFeature::Store::berkeleydb::Iterator 1.005002102 metacpan
Bio::DB::SeqFeature::Store::memory In-memory implementation of Bio::DB::SeqFeature::Store 1.005002102 metacpan
Bio::DB::SeqFeature::Store::memory::Iterator 1.005002102 metacpan
Bio::DB::SeqHound Database object interface to SeqHound 1.005002102 metacpan
Bio::DB::SeqI Abstract Interface for Sequence databases 1.005002102 metacpan
Bio::DB::SeqVersion front end to querying databases for identifier versions 1.005002102 metacpan
Bio::DB::SeqVersion::gi interface to NCBI Sequence Revision History page 1.005002102 metacpan
Bio::DB::SwissProt Database object interface to SwissProt retrieval 1.005002102 metacpan
Bio::DB::Taxonomy Access to a taxonomy database 1.005002102 metacpan
Bio::DB::Taxonomy::entrez Taxonomy Entrez driver 1.005002102 metacpan
Bio::DB::Taxonomy::flatfile An implementation of Bio::DB::Taxonomy which uses local flat files 1.005002102 metacpan
Bio::DB::Taxonomy::list An implementation of Bio::DB::Taxonomy that accepts lists of words to build a database 1.005002102 metacpan
Bio::DB::Universal Artificial database that delegates to specific databases 1.005002102 metacpan
Bio::DB::UpdateableSeqI An interface for writing to a database of sequences. 1.005002102 metacpan
Bio::DB::WebDBSeqI Object Interface to generalize Web Databases for retrieving sequences 1.005002102 metacpan
Bio::DB::XEMBL Database object interface for XEMBL entry retrieval 1.005002102 metacpan
Bio::DB::XEMBLService SOAP service definition for XEMBL 1.005002102 metacpan
Bio::DBLinkContainerI Abstract interface for any object wanting to use database cross references 1.005002102 metacpan
Bio::Das::FeatureTypeI Simple interface to Sequence Ontology feature types 1.005002102 metacpan
Bio::Das::SegmentI DAS-style access to a feature database 1.005002102 metacpan
Bio::DasI DAS-style access to a feature database 1.005002102 metacpan
Bio::DescribableI interface for objects with human readable names and descriptions 1.005002102 metacpan
Bio::Event::EventGeneratorI This interface describes the basic event generator class. 1.005002102 metacpan
Bio::Event::EventHandlerI An Event Handler Interface 1.005002102 metacpan
Bio::Expression::Contact DESCRIPTION of Object 1.005002102 metacpan
Bio::Expression::DataSet DESCRIPTION of Object 1.005002102 metacpan
Bio::Expression::FeatureGroup a set of DNA/RNA features. ISA Bio::Expression::FeatureI 1.005002102 metacpan
Bio::Expression::FeatureGroup::FeatureGroupMas50 1.005002102 metacpan
Bio::Expression::FeatureI an interface class for DNA/RNA features 1.005002102 metacpan
Bio::Expression::FeatureSet::FeatureSetMas50 1.005002102 metacpan
Bio::Expression::Platform DESCRIPTION of Object 1.005002102 metacpan
Bio::Expression::ProbeI an interface class for DNA/RNA probes 1.005002102 metacpan
Bio::Expression::Sample DESCRIPTION of Object 1.005002102 metacpan
Bio::Factory::AnalysisI An interface to analysis tool factory 1.005002102 metacpan
Bio::Factory::ApplicationFactoryI Interface class for Application Factories 1.005002102 metacpan
Bio::Factory::DriverFactory Base class for factory classes loading drivers 1.005002102 metacpan
Bio::Factory::FTLocationFactory A FeatureTable Location Parser 1.005002102 metacpan
Bio::Factory::HitFactoryI Interface for an object that builds Bio::Search::Hit::HitI objects 1.005002102 metacpan
Bio::Factory::LocationFactoryI A factory interface for generating locations from a string 1.005002102 metacpan
Bio::Factory::MapFactoryI A Factory for getting markers 1.005002102 metacpan
Bio::Factory::ObjectBuilderI Interface for an object builder 1.005002102 metacpan
Bio::Factory::ObjectFactory Instantiates a new Bio::Root::RootI (or derived class) through a factory 1.005002102 metacpan
Bio::Factory::ObjectFactoryI A General object creator factory 1.005002102 metacpan
Bio::Factory::ResultFactoryI Interface for an object that builds Bio::Search::Result::ResultI objects 1.005002102 metacpan
Bio::Factory::SeqAnalysisParserFactory class capable of creating SeqAnalysisParserI compliant parsers 1.005002102 metacpan
Bio::Factory::SeqAnalysisParserFactoryI interface describing objects capable of creating SeqAnalysisParserI compliant parsers 1.005002102 metacpan
Bio::Factory::SequenceFactoryI This interface allows for generic building of sequences in factories which create sequences (like SeqIO) 1.005002102 metacpan
Bio::Factory::SequenceProcessorI Interface for chained sequence processing algorithms 1.005002102 metacpan
Bio::Factory::SequenceStreamI Interface describing the basics of a Sequence Stream. 1.005002102 metacpan
Bio::Factory::TreeFactoryI Factory Interface for getting and writing trees from/to a data stream 1.005002102 metacpan
Bio::FeatureHolderI the base interface an object with features must implement 1.005002102 metacpan
Bio::FeatureIO Handler for FeatureIO 1.005002102 metacpan
Bio::FeatureIO::bed write features from UCSC BED format 1.005002102 metacpan
Bio::FeatureIO::gff read/write GFF feature files 1.005002102 metacpan
Bio::FeatureIO::gtf read write features in GTF format 1.005002102 metacpan
Bio::FeatureIO::interpro read features from InterPro XML 1.005002102 metacpan
Bio::FeatureIO::ptt read/write features in PTT format 1.005002102 metacpan
Bio::Graph::Edge encapsulation of an interaction between 2 Bio::Seq objects 1.005002102 metacpan
Bio::Graph::IO Class for reading /writing biological graph data. 1.005002102 metacpan
Bio::Graph::IO::dip class for parsing interaction data in dip format 1.005002102 metacpan
Bio::Graph::IO::psi_xml access and manipulate PSI XML graphs 1.005002102 metacpan
Bio::Graph::ProteinGraph a representation of a protein interaction graph. 1.005002102 metacpan
Bio::Graph::SimpleGraph create and manipulate undirected graphs 1.005002102 metacpan
Bio::Graph::SimpleGraph::Traversal graph traversal operations for Bio::Graph::SimpleGraph and Bio::Graph::Protein::Graph objects 1.005002102 metacpan
Bio::Graphics Generate GD images of Bio::Seq objects 1.005002102 metacpan
Bio::Graphics::ConfiguratorI A sectioned map of configuration options (a map of maps), with a default section. Intended to augment existing tag-E<gt>value semantics (ie. of Bio::AnnotationCollectionI) for object-representation information (eg. foreground color), and for general interface preferences (eg. image width in gbrowse). 1.005002102 metacpan
Bio::Graphics::Feature A simple feature object for use with Bio::Graphics::Panel 1.005002102 metacpan
Bio::Graphics::FeatureBase Base class for Bio::Graphics::Feature 1.005002102 metacpan
Bio::Graphics::FeatureFile A set of Bio::Graphics features, stored in a file 1.005002102 metacpan
Bio::Graphics::FeatureFile::Iterator Iterator across a Bio::Graphics::FeatureFile 1.005002102 metacpan
Bio::Graphics::Glyph Base class for Bio::Graphics::Glyph objects 1.005002102 metacpan
Bio::Graphics::Glyph::Factory Factory for Bio::Graphics::Glyph objects 1.005002102 metacpan
Bio::Graphics::Glyph::alignment The "alignment" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::anchored_arrow The "anchored_arrow" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::arrow the "arrow" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::box The "box" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::broken_line The "broken line" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::cds The "cds" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::christmas_arrow The "christmas arrow" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::crossbox The "crossbox" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::dashed_line The "dashed line" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::diamond The "diamond" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::dna The "dna" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::dot The "dot" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::dumbbell A glyph that draws a "dumbbell" with the same shapes on both ends. 1.005002102 metacpan
Bio::Graphics::Glyph::ellipse The "ellipse" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::ex the "ex", or "crossed box" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::extending_arrow The "extending arrow" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::flag the "flag" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::gene A GFF3-compatible gene glyph 1.005002102 metacpan
Bio::Graphics::Glyph::generic The "generic" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::graded_segments The "graded_segments" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::group The "group" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::heterogeneous_segments The "heterogeneous_segments" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::image A glyph that draws photographs & other images 1.005002102 metacpan
Bio::Graphics::Glyph::lightning The "lightning" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::line The "line" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::merge_parts a base class which suppors semantic zooming of scored alignment features 1.005002102 metacpan
Bio::Graphics::Glyph::merged_alignment The "merged_alignment" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::minmax The minmax glyph 1.005002102 metacpan
Bio::Graphics::Glyph::oval The "oval" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::pentagram The "pentagram" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::pinsertion The "Drosophila P-element Insertion" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::primers The "STS primers" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::processed_transcript The sequence ontology transcript glyph 1.005002102 metacpan
Bio::Graphics::Glyph::protein The "protein" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::ragged_ends The "ragged ends" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::redgreen_box The "redgreen_box" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::redgreen_segment 1.005002102 metacpan
Bio::Graphics::Glyph::repeating_shape A glyph that draws the same shape repeatedly. 1.005002102 metacpan
Bio::Graphics::Glyph::rndrect The "round rect" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::ruler_arrow glyph for drawing an arrow as ruler (5' and 3' are marked as label) 1.005002102 metacpan
Bio::Graphics::Glyph::saw_teeth The "saw teeth" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::segmented_keyglyph The "segmented_keyglyph" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::segments The "segments" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::so_transcript The sequence ontology transcript glyph 1.005002102 metacpan
Bio::Graphics::Glyph::span The "span" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::splice_site The "splice_site" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::text_in_box The "text in box" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::three_letters DAS-compatible package to use for drawing a line of groups of three letters 1.005002102 metacpan
Bio::Graphics::Glyph::tic_tac_toe The "tic-tac-toe" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::toomany The "too many to show" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::track The "track" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::transcript The "transcript" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::transcript2 The "transcript2" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::translation The "6-frame translation" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::triangle The "triangle" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::two_bolts The "two bolts" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::wave The "wave" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::weighted_arrow The "weighted arrow" glyph 1.005002102 metacpan
Bio::Graphics::Glyph::whiskerplot The whiskerplot glyph 1.005002102 metacpan
Bio::Graphics::Glyph::xyplot The xyplot glyph 1.005002102 metacpan
Bio::Graphics::Panel Generate GD images of Bio::Seq objects 1.005002102 metacpan
Bio::Graphics::Pictogram generate SVG output of Pictogram display for consensus motifs 1.005002102 metacpan
Bio::Graphics::RendererI A renderer for the Bio::Graphics class that renders Bio::SeqFeature::CollectionI objects onto Bio::Graphics::Panels using configuration information provided by a Bio::Graphics::ConfiguratorI. 1.005002102 metacpan
Bio::Graphics::Util non-object-oriented utilities used in Bio::Graphics modules 1.005002102 metacpan
Bio::IdCollectionI interface for objects with multiple identifiers 1.005002102 metacpan
Bio::IdentifiableI interface for objects with identifiers 1.005002102 metacpan
Bio::Index::Abstract Abstract interface for indexing a flat file 1.005002102 metacpan
Bio::Index::AbstractSeq base class for AbstractSeq 1.005002102 metacpan
Bio::Index::Blast Indexes Blast reports and supports retrieval based on query accession(s) 1.005002102 metacpan
Bio::Index::EMBL Interface for indexing (multiple) EMBL/Swissprot .dat files (i.e. flat file EMBL/Swissprot format). 1.005002102 metacpan
Bio::Index::Fasta Interface for indexing (multiple) fasta files 1.005002102 metacpan
Bio::Index::Fastq Interface for indexing (multiple) fastq files 1.005002102 metacpan
Bio::Index::GenBank Interface for indexing one or more GenBank files (i.e. flat file GenBank format). 1.005002102 metacpan
Bio::Index::Hmmer 1.005002102 metacpan
Bio::Index::Qual Interface for indexing (multiple) fasta qual files 1.005002102 metacpan
Bio::Index::SwissPfam Interface for indexing swisspfam files 1.005002102 metacpan
Bio::Index::Swissprot Interface for indexing one or more Swissprot files. 1.005002102 metacpan
Bio::LiveSeq::AARange AARange abstract class for LiveSeq 1.005002102 metacpan
Bio::LiveSeq::Chain DoubleChain DataStructure for Perl 1.005002102 metacpan
Bio::LiveSeq::ChainI Double linked chain data structure 1.005002102 metacpan
Bio::LiveSeq::DNA DNA object for LiveSeq 1.005002102 metacpan
Bio::LiveSeq::Exon Range abstract class for LiveSeq 1.005002102 metacpan
Bio::LiveSeq::Gene Range abstract class for LiveSeq 1.005002102 metacpan
Bio::LiveSeq::IO::BioPerl Loader for LiveSeq from EMBL entries with BioPerl 1.005002102 metacpan
Bio::LiveSeq::IO::Loader Parent Loader for LiveSeq 1.005002102 metacpan
Bio::LiveSeq::Intron Range abstract class for LiveSeq 1.005002102 metacpan
Bio::LiveSeq::Mutation Mutation event descriptor class 1.005002102 metacpan
Bio::LiveSeq::Mutator Package mutating LiveSequences 1.005002102 metacpan
Bio::LiveSeq::Prim_Transcript Prim_Transcript class for LiveSeq 1.005002102 metacpan
Bio::LiveSeq::Range Range abstract class for LiveSeq 1.005002102 metacpan
Bio::LiveSeq::Repeat_Region Repeat_Region class for LiveSeq 1.005002102 metacpan
Bio::LiveSeq::Repeat_Unit Repeat_Unit class for LiveSeq 1.005002102 metacpan
Bio::LiveSeq::SeqI Abstract sequence interface class for LiveSeq 1.005002102 metacpan
Bio::LiveSeq::Transcript Transcript class for LiveSeq 1.005002102 metacpan
Bio::LiveSeq::Translation Translation class for LiveSeq 1.005002102 metacpan
Bio::LocatableSeq A Sequence object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq. 1.005002102 metacpan
Bio::Location::Atomic Implementation of a Atomic Location on a Sequence 1.005002102 metacpan
Bio::Location::AvWithinCoordPolicy class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise 1.005002102 metacpan
Bio::Location::CoordinatePolicyI Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location 1.005002102 metacpan
Bio::Location::Fuzzy Implementation of a Location on a Sequence which has unclear start and/or end locations 1.005002102 metacpan
Bio::Location::FuzzyLocationI Abstract interface of a Location on a Sequence which has unclear start/end location 1.005002102 metacpan
Bio::Location::NarrowestCoordPolicy class implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range 1.005002102 metacpan
Bio::Location::Simple Implementation of a Simple Location on a Sequence 1.005002102 metacpan
Bio::Location::Split Implementation of a Location on a Sequence which has multiple locations (start/end points) 1.005002102 metacpan
Bio::Location::SplitLocationI Abstract interface of a Location on a Sequence which has multiple locations (start/end points) 1.005002102 metacpan
Bio::Location::WidestCoordPolicy class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable range 1.005002102 metacpan
Bio::LocationI Abstract interface of a Location on a Sequence 1.005002102 metacpan
Bio::Map::Clone An central map object representing a clone 1.005002102 metacpan
Bio::Map::Contig A MapI implementation handling the contigs of a Physical Map (such as FPC) 1.005002102 metacpan
Bio::Map::CytoMap A Bio::MapI compliant map implementation handling cytogenic bands 1.005002102 metacpan
Bio::Map::CytoMarker An object representing a marker. 1.005002102 metacpan
Bio::Map::CytoPosition Marker class with cytogenetic band storing attributes 1.005002102 metacpan
Bio::Map::EntityI An Entity Interface 1.005002102 metacpan
Bio::Map::FPCMarker An central map object representing a marker 1.005002102 metacpan
Bio::Map::LinkageMap A representation of a genetic linkage map. 1.005002102 metacpan
Bio::Map::LinkagePosition Create a Position for a Marker that will be placed on a Bio::Map::LinkageMap 1.005002102 metacpan
Bio::Map::MapI Interface for describing Map objects in bioperl 1.005002102 metacpan
Bio::Map::Mappable An object representing a generic map element that can have multiple locations in several maps. 1.005002102 metacpan
Bio::Map::MappableI An object that can be placed in a map 1.005002102 metacpan
Bio::Map::Marker An central map object representing a generic marker that can have multiple location in several maps. 1.005002102 metacpan
Bio::Map::MarkerI Interface for basic marker functionality 1.005002102 metacpan
Bio::Map::Microsatellite An object representing a Microsatellite marker. 1.005002102 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. 1.005002102 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. 1.005002102 metacpan
Bio::Map::Physical A class for handling a Physical Map (such as FPC) 1.005002102 metacpan
Bio::Map::Position A single position of a Marker, or the range over which that marker lies, in a Map 1.005002102 metacpan
Bio::Map::PositionHandler A Position Handler Implementation 1.005002102 metacpan
Bio::Map::PositionHandlerI A Position Handler Interface 1.005002102 metacpan
Bio::Map::PositionI Abstracts the notion of a position having a value in the context of a marker and a Map 1.005002102 metacpan
Bio::Map::Relative Represents what a Position's coordiantes are relative to. 1.005002102 metacpan
Bio::Map::RelativeI Interface for describing what a Position's coordiantes are relative to. 1.005002102 metacpan
Bio::Map::SimpleMap A MapI implementation handling the basics of a Map 1.005002102 metacpan
Bio::MapIO A Map Factory object 1.005002102 metacpan
Bio::MapIO::fpc A FPC Map reader 1.005002102 metacpan
Bio::MapIO::mapmaker A Mapmaker Map reader 1.005002102 metacpan
Bio::Matrix::Generic A generic matrix implementation 1.005002102 metacpan
Bio::Matrix::IO A factory for Matrix parsing 1.005002102 metacpan
Bio::Matrix::IO::phylip A parser for PHYLIP distance matricies 1.005002102 metacpan
Bio::Matrix::IO::scoring A parser for PAM/BLOSUM matricies 1.005002102 metacpan
Bio::Matrix::MatrixI An interface for describing a Matrix 1.005002102 metacpan
Bio::Matrix::PSM::IO PSM parser 1.005002102 metacpan
Bio::Matrix::PSM::IO::mast PSM mast parser implementation 1.005002102 metacpan
Bio::Matrix::PSM::IO::masta motif fasta format parser 1.005002102 metacpan
Bio::Matrix::PSM::IO::meme PSM meme parser implementation 1.005002102 metacpan
Bio::Matrix::PSM::IO::psiblast PSM psiblast parser 1.005002102 metacpan
Bio::Matrix::PSM::IO::transfac PSM transfac parser 1.005002102 metacpan
Bio::Matrix::PSM::InstanceSite A PSM site occurance 1.005002102 metacpan
Bio::Matrix::PSM::InstanceSiteI InstanceSite interface, holds an instance of a PSM 1.005002102 metacpan
Bio::Matrix::PSM::ProtMatrix SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) with log-odds scoring information. 1.005002102 metacpan
Bio::Matrix::PSM::ProtPsm handle combination of site matricies 1.005002102 metacpan
Bio::Matrix::PSM::Psm handle combination of site matricies 1.005002102 metacpan
Bio::Matrix::PSM::PsmHeader PSM mast parser implementation 1.005002102 metacpan
Bio::Matrix::PSM::PsmHeaderI 1.005002102 metacpan
Bio::Matrix::PSM::PsmI abstract interface to handler of site matricies 1.005002102 metacpan
Bio::Matrix::PSM::SiteMatrix SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds 1.005002102 metacpan
Bio::Matrix::PSM::SiteMatrixI SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds 1.005002102 metacpan
Bio::Matrix::PhylipDist A Phylip Distance Matrix object 1.005002102 metacpan
Bio::Matrix::Scoring Object which can hold scoring matrix information 1.005002102 metacpan
Bio::Ontology::DocumentRegistry Keep track of where to find ontologies. Allows lookups by name. 1.005002102 metacpan
Bio::Ontology::GOterm representation of GO terms 1.005002102 metacpan
Bio::Ontology::InterProTerm Implementation of InterProI term interface 1.005002102 metacpan
Bio::Ontology::OBOEngine An Ontology Engine for OBO style flat file format from the Gene Ontology Consortium 1.005002102 metacpan
Bio::Ontology::OBOterm representation of OBO terms 1.005002102 metacpan
Bio::Ontology::Ontology standard implementation of an Ontology 1.005002102 metacpan
Bio::Ontology::OntologyEngineI Interface a minimal Ontology implementation should satisfy 1.005002102 metacpan
Bio::Ontology::OntologyI Interface for an ontology implementation 1.005002102 metacpan
Bio::Ontology::OntologyStore A repository of ontologies 1.005002102 metacpan
Bio::Ontology::Path a path for an ontology term graph 1.005002102 metacpan
Bio::Ontology::PathI Interface for a path between ontology terms 1.005002102 metacpan
Bio::Ontology::Relationship a relationship for an ontology 1.005002102 metacpan
Bio::Ontology::RelationshipFactory Instantiates a new Bio::Ontology::RelationshipI (or derived class) through a factory 1.005002102 metacpan
Bio::Ontology::RelationshipI Interface for a relationship between ontology terms 1.005002102 metacpan
Bio::Ontology::RelationshipType a relationship type for an ontology 1.005002102 metacpan
Bio::Ontology::SimpleGOEngine a Ontology Engine for GO implementing OntologyEngineI 1.005002102 metacpan
Bio::Ontology::SimpleGOEngine::GraphAdaptor Graph adaptor for Bio::Ontology::SimpleGOEngine 1.005002102 metacpan
Bio::Ontology::SimpleGOEngine::GraphAdaptor02 Graph adaptor (v02.x) for Bio::Ontology::SimpleGOEngine 1.005002102 metacpan
Bio::Ontology::SimpleOntologyEngine Implementation of OntologyEngineI interface 1.005002102 metacpan
Bio::Ontology::Term implementation of the interface for ontology terms 1.005002102 metacpan
Bio::Ontology::TermFactory Instantiates a new Bio::Ontology::TermI (or derived class) through a factory 1.005002102 metacpan
Bio::Ontology::TermI interface for ontology terms 1.005002102 metacpan
Bio::OntologyIO Parser factory for Ontology formats 1.005002102 metacpan
Bio::OntologyIO::Handlers::BaseSAXHandler 1.005002102 metacpan
Bio::OntologyIO::Handlers::InterProHandler XML handler class for InterProParser 1.005002102 metacpan
Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler parse an InterPro XML file and persist the resulting terms to a Biosql database 1.005002102 metacpan
Bio::OntologyIO::InterProParser Parser for InterPro xml files. 1.005002102 metacpan
Bio::OntologyIO::dagflat a base class parser for GO flat-file type formats 1.005002102 metacpan
Bio::OntologyIO::goflat a parser for the Gene Ontology flat-file format 1.005002102 metacpan
Bio::OntologyIO::obo a parser for OBO flat-file format from Gene Ontology Consortium 1.005002102 metacpan
Bio::OntologyIO::simplehierarchy a base class parser for simple hierarchy-by-indentation type formats 1.005002102 metacpan
Bio::OntologyIO::soflat a parser for the Sequence Ontology flat-file format 1.005002102 metacpan
Bio::Perl Functional access to BioPerl for people who don't know objects 1.005002102 metacpan
Bio::Phenotype::Correlate Representation of a correlating phenotype in a given species 1.005002102 metacpan
Bio::Phenotype::MeSH::Term A MeSH term 1.005002102 metacpan
Bio::Phenotype::MeSH::Twig Context for a MeSH term 1.005002102 metacpan
Bio::Phenotype::Measure Representation of context/value(-range)/unit triplets 1.005002102 metacpan
Bio::Phenotype::OMIM::MiniMIMentry Representation of a Mini MIM entry 1.005002102 metacpan
Bio::Phenotype::OMIM::OMIMentry represents OMIM (Online Mendelian Inheritance in Man) database entries 1.005002102 metacpan
Bio::Phenotype::OMIM::OMIMentryAllelicVariant Representation of a allelic variant of the OMIM database 1.005002102 metacpan
Bio::Phenotype::OMIM::OMIMparser parser for the OMIM database 1.005002102 metacpan
Bio::Phenotype::Phenotype A class for modeling phenotypes 1.005002102 metacpan
Bio::Phenotype::PhenotypeI An interface for classes modeling phenotypes 1.005002102 metacpan
Bio::PopGen::Genotype An implementation of GenotypeI which is just an allele container 1.005002102 metacpan
Bio::PopGen::GenotypeI A marker and alleles for a specific individual 1.005002102 metacpan
Bio::PopGen::HtSNP 1.005002102 metacpan
Bio::PopGen::IO Input individual,marker,allele information 1.005002102 metacpan
Bio::PopGen::IO::csv 1.005002102 metacpan
Bio::PopGen::IO::hapmap A parser for HapMap output data 1.005002102 metacpan
Bio::PopGen::IO::phase A parser for Phase format data 1.005002102 metacpan
Bio::PopGen::IO::prettybase Extract individual allele data from PrettyBase format 1.005002102 metacpan
Bio::PopGen::Individual An implementation of an Individual who has Genotype or Sequence Results 1.005002102 metacpan
Bio::PopGen::IndividualI An individual who has Genotype or Sequence Results 1.005002102 metacpan
Bio::PopGen::Marker A genetic marker which one uses to generate genotypes 1.005002102 metacpan
Bio::PopGen::MarkerI A Population Genetic conceptual marker 1.005002102 metacpan
Bio::PopGen::PopStats A collection of methods for calculating statistics about a population or sets of populations 1.005002102 metacpan
Bio::PopGen::Population A population of individuals 1.005002102 metacpan
Bio::PopGen::PopulationI Interface for Populations 1.005002102 metacpan
Bio::PopGen::Simulation::Coalescent A Coalescent simulation factory 1.005002102 metacpan
Bio::PopGen::Simulation::GeneticDrift A simple genetic drift simulation 1.005002102 metacpan
Bio::PopGen::Statistics Population Genetics statistical tests 1.005002102 metacpan
Bio::PopGen::TagHaplotype 1.005002102 metacpan
Bio::PopGen::Utilities Utilities for working with PopGen data and objects 1.005002102 metacpan
Bio::PrimarySeq Bioperl lightweight Sequence Object 1.005002102 metacpan
Bio::PrimarySeq::Fasta 1.005002102 metacpan
Bio::PrimarySeqI Interface definition for a Bio::PrimarySeq 1.005002102 metacpan
Bio::PullParserI A base module for fast 'pull' parsing 1.005002102 metacpan
Bio::Range Pure perl RangeI implementation 1.005002102 metacpan
Bio::RangeI Range interface 1.005002102 metacpan
Bio::Restriction::Analysis cutting sequences with restriction enzymes 1.005002102 metacpan
Bio::Restriction::Enzyme A single restriction endonuclease (cuts DNA at specific locations) 1.005002102 metacpan
Bio::Restriction::Enzyme::MultiCut A single restriction endonuclease 1.005002102 metacpan
Bio::Restriction::Enzyme::MultiSite A single restriction endonuclease 1.005002102 metacpan
Bio::Restriction::EnzymeCollection Set of restriction endonucleases 1.005002102 metacpan
Bio::Restriction::EnzymeI Interface class for restriction endonuclease 1.005002102 metacpan
Bio::Restriction::IO Handler for sequence variation IO Formats 1.005002102 metacpan
Bio::Restriction::IO::bairoch bairoch enzyme set 1.005002102 metacpan
Bio::Restriction::IO::base base enzyme set 1.005002102 metacpan
Bio::Restriction::IO::itype2 itype2 enzyme set 1.005002102 metacpan
Bio::Restriction::IO::withrefm withrefm enzyme set 1.005002102 metacpan
Bio::Root::Exception Generic exception objects for Bioperl 1.005002102 metacpan
Bio::Root::HTTPget module for fallback HTTP get operations when LWP:: is unavailable 1.005002102 metacpan
Bio::Root::IO module providing several methods often needed when dealing with file IO 1.005002102 metacpan
Bio::Root::Root Hash-based implementation of Bio::Root::RootI 1.005002102 metacpan
Bio::Root::RootI Abstract interface to root object code 1.005002102 metacpan
Bio::Root::Storable object serialisation methods 1.005002102 metacpan
Bio::Root::Version provide global, distribution-level versioning 1.005002102 metacpan
Bio::Search::BlastStatistics An object for Blast statistics 1.005002102 metacpan
Bio::Search::BlastUtils Utility functions for Bio::Search:: BLAST objects 1.005002102 metacpan
Bio::Search::DatabaseI Interface for a database used in a sequence search 1.005002102 metacpan
Bio::Search::GenericDatabase Generic implementation of Bio::Search::DatabaseI 1.005002102 metacpan
Bio::Search::GenericStatistics An object for statistics 1.005002102 metacpan
Bio::Search::HSP::BlastHSP Bioperl BLAST High-Scoring Pair object 1.005002102 metacpan
Bio::Search::HSP::FastaHSP HSP object for FASTA specific data 1.005002102 metacpan
Bio::Search::HSP::GenericHSP A "Generic" implementation of a High Scoring Pair 1.005002102 metacpan
Bio::Search::HSP::HMMERHSP A HSP object for HMMER results 1.005002102 metacpan
Bio::Search::HSP::HSPFactory A factory to create Bio::Search::HSP::HSPI objects 1.005002102 metacpan
Bio::Search::HSP::HSPI Interface for a High Scoring Pair in a similarity search result 1.005002102 metacpan
Bio::Search::HSP::HmmpfamHSP A parser and HSP object for hmmpfam hsps 1.005002102 metacpan
Bio::Search::HSP::PSLHSP A HSP for PSL output 1.005002102 metacpan
Bio::Search::HSP::PsiBlastHSP Bioperl BLAST High-Scoring Pair object 1.005002102 metacpan
Bio::Search::HSP::PullHSPI Bio::Search::HSP::HSPI interface for pull parsers. 1.005002102 metacpan
Bio::Search::HSP::WABAHSP HSP object suitable for describing WABA alignments 1.005002102 metacpan
Bio::Search::Hit::BlastHit Blast-specific subclass of Bio::Search::Hit::GenericHit 1.005002102 metacpan
Bio::Search::Hit::Fasta Hit object specific for Fasta-generated hits 1.005002102 metacpan
Bio::Search::Hit::GenericHit A generic implementation of the Bio::Search::Hit::HitI interface 1.005002102 metacpan
Bio::Search::Hit::HMMERHit A Hit module for HMMER hits 1.005002102 metacpan
Bio::Search::Hit::HitFactory A factory to create Bio::Search::Hit::HitI objects 1.005002102 metacpan
Bio::Search::Hit::HitI Interface for a hit in a similarity search result 1.005002102 metacpan
Bio::Search::Hit::HmmpfamHit A parser and hit object for hmmpfam hits 1.005002102 metacpan
Bio::Search::Hit::PsiBlastHit Bioperl BLAST Hit object 1.005002102 metacpan
Bio::Search::Hit::PullHitI Bio::Search::Hit::HitI interface for pull parsers. 1.005002102 metacpan
Bio::Search::Iteration::GenericIteration A generic implementation of the Bio::Search::Iteration::IterationI interface. 1.005002102 metacpan
Bio::Search::Iteration::IterationI Abstract interface to an iteration from an iterated search result, such as PSI-BLAST. 1.005002102 metacpan
Bio::Search::Processor DESCRIPTION of Object 1.005002102 metacpan
Bio::Search::Result::BlastResult Blast-specific subclass of Bio::Search::Result::GenericResult 1.005002102 metacpan
Bio::Search::Result::GenericResult Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results. 1.005002102 metacpan
Bio::Search::Result::HMMERResult A Result object for HMMER results 1.005002102 metacpan
Bio::Search::Result::HmmpfamResult A parser and result object for hmmpfam results 1.005002102 metacpan
Bio::Search::Result::PullResultI Bio::Search::Result::ResultI interface for 'pull' parsers 1.005002102 metacpan
Bio::Search::Result::ResultFactory A factory to create Bio::Search::Result::ResultI objects 1.005002102 metacpan
Bio::Search::Result::ResultI Abstract interface to Search Result objects 1.005002102 metacpan
Bio::Search::Result::WABAResult Result object for WABA alignment output 1.005002102 metacpan
Bio::Search::SearchUtils Utility functions for Bio::Search:: objects 1.005002102 metacpan
Bio::Search::StatisticsI A Base object for statistics 1.005002102 metacpan
Bio::SearchDist A perl wrapper around Sean Eddy's histogram object 1.005002102 metacpan
Bio::SearchIO Driver for parsing Sequence Database Searches (BLAST, FASTA, ...) 1.005002102 metacpan
Bio::SearchIO::EventHandlerI An abstract Event Handler for Search Result parsing 1.005002102 metacpan
Bio::SearchIO::FastHitEventBuilder Event Handler for SearchIO events. 1.005002102 metacpan
Bio::SearchIO::IteratedSearchResultEventBuilder Event Handler for SearchIO events. 1.005002102 metacpan
Bio::SearchIO::SearchResultEventBuilder Event Handler for SearchIO events. 1.005002102 metacpan
Bio::SearchIO::SearchWriterI Interface for outputting parsed Search results 1.005002102 metacpan
Bio::SearchIO::Writer::BSMLResultWriter BSML output writer 1.005002102 metacpan
Bio::SearchIO::Writer::GbrowseGFF Interface for outputting parsed search results in Gbrowse GFF format 1.005002102 metacpan
Bio::SearchIO::Writer::HSPTableWriter Tab-delimited data for Bio::Search::HSP::HSPI objects 1.005002102 metacpan
Bio::SearchIO::Writer::HTMLResultWriter write a Bio::Search::ResultI in HTML 1.005002102 metacpan
Bio::SearchIO::Writer::HitTableWriter Tab-delimited data for Bio::Search::Hit::HitI objects 1.005002102 metacpan
Bio::SearchIO::Writer::ResultTableWriter Outputs tab-delimited data for each Bio::Search::Result::ResultI object. 1.005002102 metacpan
Bio::SearchIO::Writer::TextResultWriter Object to implement writing a Bio::Search::ResultI in Text. 1.005002102 metacpan
Bio::SearchIO::axt a parser for axt format reports 1.005002102 metacpan
Bio::SearchIO::blast Event generator for event based parsing of blast reports 1.005002102 metacpan
Bio::SearchIO::blasttable Driver module for SearchIO for parsing NCBI -m 8/9 format 1.005002102 metacpan
Bio::SearchIO::blastxml A SearchIO implementation of NCBI Blast XML parsing. 1.005002102 metacpan
Bio::SearchIO::exonerate parser for Exonerate 1.005002102 metacpan
Bio::SearchIO::fasta A SearchIO parser for FASTA results 1.005002102 metacpan
Bio::SearchIO::hmmer A parser for HMMER output (hmmpfam, hmmsearch) 1.005002102 metacpan
Bio::SearchIO::hmmer_pull A parser for HMMER output 1.005002102 metacpan
Bio::SearchIO::megablast a driver module for Bio::SearchIO to parse megablast reports (format 0) 1.005002102 metacpan
Bio::SearchIO::psl A parser for PSL output (UCSC) 1.005002102 metacpan
Bio::SearchIO::sim4 parser for Sim4 alignments 1.005002102 metacpan
Bio::SearchIO::waba SearchIO parser for Jim Kent WABA program alignment output 1.005002102 metacpan
Bio::SearchIO::wise Parsing of wise output as alignments 1.005002102 metacpan
Bio::Seq Sequence object, with features 1.005002102 metacpan
Bio::Seq::BaseSeqProcessor Base implementation for a SequenceProcessor 1.005002102 metacpan
Bio::Seq::EncodedSeq subtype of L<Bio::LocatableSeq|Bio::LocatableSeq> to store DNA that encodes a protein 1.005002102 metacpan
Bio::Seq::LargeLocatableSeq LocatableSeq object that stores sequence as files in the tempdir 1.005002102 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 1.005002102 metacpan
Bio::Seq::LargeSeq SeqI compliant object that stores sequence as files in /tmp 1.005002102 metacpan
Bio::Seq::LargeSeqI Interface class for sequences that cache their residues in a temporary file 1.005002102 metacpan
Bio::Seq::Meta Generic superclass for sequence objects with residue-based meta information 1.005002102 metacpan
Bio::Seq::Meta::Array array-based generic implementation of a sequence class with residue-based meta information 1.005002102 metacpan
Bio::Seq::MetaI Interface for sequence objects with residue-based meta information 1.005002102 metacpan
Bio::Seq::PrimaryQual Bioperl lightweight Quality Object 1.005002102 metacpan
Bio::Seq::PrimedSeq A representation of a sequence and two primers flanking a target region 1.005002102 metacpan
Bio::Seq::QualI Interface definition for a Bio::Seq::Qual 1.005002102 metacpan
Bio::Seq::Quality Implementation of sequence with residue quality and trace values 1.005002102 metacpan
Bio::Seq::RichSeq Module implementing a sequence created from a rich sequence database entry 1.005002102 metacpan
Bio::Seq::RichSeqI interface for sequences from rich data sources, mostly databases 1.005002102 metacpan
Bio::Seq::SeqBuilder Configurable object builder for sequence stream parsers 1.005002102 metacpan
Bio::Seq::SeqFactory Instantiates a new Bio::PrimarySeqI (or derived class) through a factory 1.005002102 metacpan
Bio::Seq::SeqFastaSpeedFactory Instantiates a new Bio::PrimarySeqI (or derived class) through a factory 1.005002102 metacpan
Bio::Seq::SeqWithQuality Bioperl object packaging a sequence with its quality 1.005002102 metacpan
Bio::Seq::SequenceTrace Bioperl object packaging a sequence with its trace 1.005002102 metacpan
Bio::Seq::TraceI Interface definition for a Bio::Seq::Trace 1.005002102 metacpan
Bio::SeqAnalysisParserI Sequence analysis output parser interface 1.005002102 metacpan
Bio::SeqFeature::Annotated PLEASE PUT SOMETHING HERE 1.005002102 metacpan
Bio::SeqFeature::AnnotationAdaptor integrates SeqFeatureIs annotation 1.005002102 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. 1.005002102 metacpan
Bio::SeqFeature::CollectionI An interface for a collection of SeqFeatureI objects. 1.005002102 metacpan
Bio::SeqFeature::Computation Computation SeqFeature 1.005002102 metacpan
Bio::SeqFeature::FeaturePair hold pair feature information e.g. blast hits 1.005002102 metacpan
Bio::SeqFeature::Gene::Exon a feature representing an exon 1.005002102 metacpan
Bio::SeqFeature::Gene::ExonI Interface for a feature representing an exon 1.005002102 metacpan
Bio::SeqFeature::Gene::GeneStructure A feature representing an arbitrarily complex structure of a gene 1.005002102 metacpan
Bio::SeqFeature::Gene::GeneStructureI A feature representing an arbitrarily complex structure of a gene 1.005002102 metacpan
Bio::SeqFeature::Gene::Intron An intron feature 1.005002102 metacpan
Bio::SeqFeature::Gene::NC_Feature 1.005002102 metacpan
Bio::SeqFeature::Gene::Poly_A_site poly A feature 1.005002102 metacpan
Bio::SeqFeature::Gene::Promoter Describes a promoter 1.005002102 metacpan
Bio::SeqFeature::Gene::Transcript A feature representing a transcript 1.005002102 metacpan
Bio::SeqFeature::Gene::TranscriptI Interface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site. 1.005002102 metacpan
Bio::SeqFeature::Gene::UTR A feature representing an untranslated region that is part of a transcriptional unit 1.005002102 metacpan
Bio::SeqFeature::Generic Generic SeqFeature 1.005002102 metacpan
Bio::SeqFeature::PositionProxy handle features when truncation/revcom sequences span a feature 1.005002102 metacpan
Bio::SeqFeature::Primer Primer Generic SeqFeature 1.005002102 metacpan
Bio::SeqFeature::SiRNA::Oligo Perl object for small inhibitory RNAs. 1.005002102 metacpan
Bio::SeqFeature::SiRNA::Pair Perl object for small inhibitory RNA (SiRNA) oligo pairs 1.005002102 metacpan
Bio::SeqFeature::Similarity A sequence feature based on similarity 1.005002102 metacpan
Bio::SeqFeature::SimilarityPair Sequence feature based on the similarity of two sequences. 1.005002102 metacpan
Bio::SeqFeature::Tools::FeatureNamer generates unique persistent names for features 1.005002102 metacpan
Bio::SeqFeature::Tools::IDHandler maps $seq_feature-E<gt>primary_tag 1.005002102 metacpan
Bio::SeqFeature::Tools::TypeMapper maps $seq_feature-E<gt>primary_tag 1.005002102 metacpan
Bio::SeqFeature::Tools::Unflattener turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy 1.005002102 metacpan
Bio::SeqFeature::TypedSeqFeatureI a strongly typed SeqFeature 1.005002102 metacpan
Bio::SeqFeatureI Abstract interface of a Sequence Feature 1.005002102 metacpan
Bio::SeqI 1.005002102 metacpan
Bio::SeqIO Handler for SeqIO Formats 1.005002102 metacpan
Bio::SeqIO::FTHelper Helper class for Embl/Genbank feature tables 1.005002102 metacpan
Bio::SeqIO::MultiFile Treating a set of files as a single input stream 1.005002102 metacpan
Bio::SeqIO::abi abi trace sequence input/output stream 1.005002102 metacpan
Bio::SeqIO::ace ace sequence input/output stream 1.005002102 metacpan
Bio::SeqIO::agave AGAVE sequence output stream. 1.005002102 metacpan
Bio::SeqIO::alf alf trace sequence input/output stream 1.005002102 metacpan
Bio::SeqIO::asciitree asciitree sequence input/output stream 1.005002102 metacpan
Bio::SeqIO::bsml BSML sequence input/output stream 1.005002102 metacpan
Bio::SeqIO::bsml_sax BSML sequence input/output stream using SAX 1.005002102 metacpan
Bio::SeqIO::chadoxml chadoxml sequence output stream 1.005002102 metacpan
Bio::SeqIO::chaos chaos sequence input/output stream 1.005002102 metacpan
Bio::SeqIO::chaosxml chaosxml sequence input/output stream 1.005002102 metacpan
Bio::SeqIO::ctf ctf trace sequence input/output stream 1.005002102 metacpan
Bio::SeqIO::embl EMBL sequence input/output stream 1.005002102 metacpan
Bio::SeqIO::entrezgene Entrez Gene ASN1 parser 1.005002102 metacpan
Bio::SeqIO::excel sequence input/output stream from a MSExcel-formatted table 1.005002102 metacpan
Bio::SeqIO::exp exp trace sequence input/output stream 1.005002102 metacpan
Bio::SeqIO::fasta fasta sequence input/output stream 1.005002102 metacpan
Bio::SeqIO::fastq fastq sequence input/output stream 1.005002102 metacpan
Bio::SeqIO::game a class for parsing and writing game-XML 1.005002102 metacpan
Bio::SeqIO::game::featHandler a class for handling feature elements 1.005002102 metacpan
Bio::SeqIO::game::gameHandler PerlSAX handler for game-XML 1.005002102 metacpan
Bio::SeqIO::game::gameSubs a base class for game-XML parsing 1.005002102 metacpan
Bio::SeqIO::game::gameWriter a class for writing game-XML 1.005002102 metacpan
Bio::SeqIO::game::seqHandler a class for handling game-XML sequences 1.005002102 metacpan
Bio::SeqIO::gcg GCG sequence input/output stream 1.005002102 metacpan
Bio::SeqIO::genbank GenBank sequence input/output stream 1.005002102 metacpan
Bio::SeqIO::interpro InterProScan XML input/output stream 1.005002102 metacpan
Bio::SeqIO::kegg KEGG sequence input/output stream 1.005002102 metacpan
Bio::SeqIO::largefasta method i/o on very large fasta sequence files 1.005002102 metacpan
Bio::SeqIO::lasergene Lasergene sequence file input/output stream 1.005002102 metacpan
Bio::SeqIO::locuslink LocusLink input/output stream 1.005002102 metacpan
Bio::SeqIO::metafasta metafasta sequence input/output stream 1.005002102 metacpan
Bio::SeqIO::phd .phd file input/output stream 1.005002102 metacpan
Bio::SeqIO::pir PIR sequence input/output stream 1.005002102 metacpan
Bio::SeqIO::pln pln trace sequence input/output stream 1.005002102 metacpan
Bio::SeqIO::qual .qual file input/output stream 1.005002102 metacpan
Bio::SeqIO::raw raw sequence file input/output stream 1.005002102 metacpan
Bio::SeqIO::scf .scf file input/output stream 1.005002102 metacpan
Bio::SeqIO::strider DNA strider sequence input/output stream 1.005002102 metacpan
Bio::SeqIO::swiss Swissprot sequence input/output stream 1.005002102 metacpan
Bio::SeqIO::tab nearly raw sequence file input/output stream. Reads/writes id"\t"sequence"\n" 1.005002102 metacpan
Bio::SeqIO::table sequence input/output stream from a delimited table 1.005002102 metacpan
Bio::SeqIO::tigr TIGR XML sequence input/output stream 1.005002102 metacpan
Bio::SeqIO::tigrxml Parse TIGR (new) XML 1.005002102 metacpan
Bio::SeqIO::tinyseq reading/writing sequences in NCBI TinySeq format 1.005002102 metacpan
Bio::SeqIO::tinyseq::tinyseqHandler XML event handlers to support NCBI TinySeq XML parsing 1.005002102 metacpan
Bio::SeqIO::ztr ztr trace sequence input/output stream 1.005002102 metacpan
Bio::SeqUtils Additional methods for PrimarySeq objects 1.005002102 metacpan
Bio::SimpleAlign Multiple alignments held as a set of sequences 1.005002102 metacpan
Bio::SimpleAnalysisI A simple interface to any (local or remote) analysis tool 1.005002102 metacpan
Bio::Species Generic species object 1.005002102 metacpan
Bio::Structure::Atom Bioperl structure Object, describes an Atom 1.005002102 metacpan
Bio::Structure::Chain Bioperl structure Object, describes a chain 1.005002102 metacpan
Bio::Structure::Entry Bioperl structure Object, describes the whole entry 1.005002102 metacpan
Bio::Structure::IO Handler for Structure Formats 1.005002102 metacpan
Bio::Structure::IO::pdb PDB input/output stream 1.005002102 metacpan
Bio::Structure::Model Bioperl structure Object, describes a Model 1.005002102 metacpan
Bio::Structure::Residue Bioperl structure Object, describes a Residue 1.005002102 metacpan
Bio::Structure::SecStr::DSSP::Res Module for parsing/accessing dssp output 1.005002102 metacpan
Bio::Structure::SecStr::STRIDE::Res Module for parsing/accessing stride output 1.005002102 metacpan
Bio::Structure::StructureI Abstract Interface for a Structure objects 1.005002102 metacpan
Bio::Symbol::Alphabet BSANE/BioCORBA compliant symbol list alphabet 1.005002102 metacpan
Bio::Symbol::AlphabetI A Symbol Alphabet 1.005002102 metacpan
Bio::Symbol::DNAAlphabet A ready made DNA alphabet 1.005002102 metacpan
Bio::Symbol::ProteinAlphabet A ready made Protein alphabet 1.005002102 metacpan
Bio::Symbol::Symbol A biological symbol 1.005002102 metacpan
Bio::Symbol::SymbolI Interface for a Symbol 1.005002102 metacpan
Bio::Taxon A node in a represented taxonomy 1.005002102 metacpan
Bio::Taxonomy representing Taxonomy. 1.005002102 metacpan
Bio::Taxonomy::FactoryI interface to define how to access NCBI Taxonoy 1.005002102 metacpan
Bio::Taxonomy::Node A node in a represented taxonomy 1.005002102 metacpan
Bio::Taxonomy::Taxon Generic Taxonomic Entity object 1.005002102 metacpan
Bio::Taxonomy::Tree An Organism Level Implementation of TreeI interface. 1.005002102 metacpan
Bio::Tools::AlignFactory Base object for alignment factories 1.005002102 metacpan
Bio::Tools::Alignment::Consed A module to work with objects from consed .ace files 1.005002102 metacpan
Bio::Tools::Alignment::Trim A kludge to do specialized trimming of sequence based on quality. 1.005002102 metacpan
Bio::Tools::Analysis::DNA::ESEfinder a wrapper around ESEfinder server 1.005002102 metacpan
Bio::Tools::Analysis::Protein::Domcut a wrapper around Domcut server 1.005002102 metacpan
Bio::Tools::Analysis::Protein::ELM a wrapper around the ELM server which predicts short functional motifs on amino acid sequences 1.005002102 metacpan
Bio::Tools::Analysis::Protein::GOR4 a wrapper around GOR4 protein secondary structure prediction server 1.005002102 metacpan
Bio::Tools::Analysis::Protein::HNN a wrapper around the HNN protein secondary structure prediction server 1.005002102 metacpan
Bio::Tools::Analysis::Protein::Mitoprot a wrapper around Mitoprot server 1.005002102 metacpan
Bio::Tools::Analysis::Protein::NetPhos a wrapper around NetPhos server 1.005002102 metacpan
Bio::Tools::Analysis::Protein::Scansite a wrapper around the Scansite server 1.005002102 metacpan
Bio::Tools::Analysis::Protein::Sopma a wrapper around the Sopma protein secondary structure prediction server 1.005002102 metacpan
Bio::Tools::Analysis::SimpleAnalysisBase abstract superclass for SimpleAnalysis implementations 1.005002102 metacpan
Bio::Tools::AnalysisResult Base class for analysis result objects and parsers 1.005002102 metacpan
Bio::Tools::BPbl2seq Lightweight BLAST parser for pair-wise sequence alignment using the BLAST algorithm. 1.005002102 metacpan
Bio::Tools::BPlite Lightweight BLAST parser 1.005002102 metacpan
Bio::Tools::BPlite::HSP Blast report High Scoring Pair (HSP) 1.005002102 metacpan
Bio::Tools::BPlite::Iteration object for parsing single iteration of a PSIBLAST report 1.005002102 metacpan
Bio::Tools::BPlite::Sbjct A Blast Subject (database search Hit) 1.005002102 metacpan
Bio::Tools::BPpsilite Lightweight BLAST parser for (iterated) psiblast reports 1.005002102 metacpan
Bio::Tools::Blat parser for Blat program 1.005002102 metacpan
Bio::Tools::CodonTable Bioperl codon table object 1.005002102 metacpan
Bio::Tools::Coil parser for Coil output 1.005002102 metacpan
Bio::Tools::ECnumber representation of EC numbers (Enzyme Classification) 1.005002102 metacpan
Bio::Tools::EMBOSS::Palindrome parse EMBOSS palindrome output 1.005002102 metacpan
Bio::Tools::EPCR Parse ePCR output and make features 1.005002102 metacpan
Bio::Tools::ERPIN a parser for ERPIN output 1.005002102 metacpan
Bio::Tools::ESTScan Results of one ESTScan run 1.005002102 metacpan
Bio::Tools::Eponine Results of one Eponine run 1.005002102 metacpan
Bio::Tools::Est2Genome Parse est2genome output, makes simple Bio::SeqFeature::Generic objects 1.005002102 metacpan
Bio::Tools::Fgenesh parse results of one Fgenesh run 1.005002102 metacpan
Bio::Tools::FootPrinter write sequence features in FootPrinter format 1.005002102 metacpan
Bio::Tools::GFF A Bio::SeqAnalysisParserI compliant GFF format parser 1.005002102 metacpan
Bio::Tools::Gel Calculates relative electrophoretic migration distances 1.005002102 metacpan
Bio::Tools::Geneid Results of one geneid run 1.005002102 metacpan
Bio::Tools::Genemark Results of one Genemark run 1.005002102 metacpan
Bio::Tools::Genewise Results of one Genewise run 1.005002102 metacpan
Bio::Tools::Genomewise Results of one Genomewise run 1.005002102 metacpan
Bio::Tools::Genscan Results of one Genscan run 1.005002102 metacpan
Bio::Tools::Glimmer parser for GlimmerM/GlimmerHMM eukaryotic gene predictions 1.005002102 metacpan
Bio::Tools::Grail Results of one Grail run 1.005002102 metacpan
Bio::Tools::GuessSeqFormat Module for determining the sequence format of the contents of a file, a string, or through a filehandle. 1.005002102 metacpan
Bio::Tools::HMM Perl extension to perform Hidden Markov Model calculations 1.005002102 metacpan
Bio::Tools::HMMER::Domain One particular domain hit from HMMER 1.005002102 metacpan
Bio::Tools::HMMER::Results Object representing HMMER output results 1.005002102 metacpan
Bio::Tools::HMMER::Set Set of identical domains from HMMER matches 1.005002102 metacpan
Bio::Tools::Hmmpfam Parser for Hmmpfam program 1.005002102 metacpan
Bio::Tools::IUPAC Generates unique Seq objects from an ambiguous Seq object 1.005002102 metacpan
Bio::Tools::Lucy Object for analyzing the output from Lucy, a vector and quality trimming program from TIGR 1.005002102 metacpan
Bio::Tools::MZEF Results of one MZEF run 1.005002102 metacpan
Bio::Tools::OddCodes Object holding alternative alphabet coding for one protein sequence 1.005002102 metacpan
Bio::Tools::Phylo::Molphy parser for Molphy output 1.005002102 metacpan
Bio::Tools::Phylo::Molphy::Result container for data parsed from a ProtML run 1.005002102 metacpan
Bio::Tools::Phylo::PAML Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00 1.005002102 metacpan
Bio::Tools::Phylo::PAML::ModelResult A container for NSSite Model Result from PAML 1.005002102 metacpan
Bio::Tools::Phylo::PAML::Result A PAML result set object 1.005002102 metacpan
Bio::Tools::Phylo::Phylip::ProtDist parser for ProtDist output 1.005002102 metacpan
Bio::Tools::Prediction::Exon A predicted exon feature 1.005002102 metacpan
Bio::Tools::Prediction::Gene a predicted gene structure feature 1.005002102 metacpan
Bio::Tools::Primer3 Create input for and work with the output from the program primer3 1.005002102 metacpan
Bio::Tools::Primer::Assessor::Base base class for common assessor things 1.005002102 metacpan
Bio::Tools::Primer::AssessorI interface for assessing primer pairs 1.005002102 metacpan
Bio::Tools::Primer::Feature position of a single primer 1.005002102 metacpan
Bio::Tools::Primer::Pair two primers on left and right side 1.005002102 metacpan
Bio::Tools::Prints Parser for FingerPRINTScanII program 1.005002102 metacpan
Bio::Tools::Profile parse Profile output 1.005002102 metacpan
Bio::Tools::Promoterwise parser for Promoterwise tab format output 1.005002102 metacpan
Bio::Tools::PrositeScan Parser for ps_scan result 1.005002102 metacpan
Bio::Tools::Pseudowise Results of one Pseudowise run 1.005002102 metacpan
Bio::Tools::QRNA A Parser for qrna output 1.005002102 metacpan
Bio::Tools::RNAMotif A parser for RNAMotif output 1.005002102 metacpan
Bio::Tools::RandomDistFunctions A set of routines useful for generating random data in different distributions 1.005002102 metacpan
Bio::Tools::RepeatMasker a parser for RepeatMasker output 1.005002102 metacpan
Bio::Tools::RestrictionEnzyme Bioperl object for a restriction endonuclease (cuts DNA at specific locations) 1.005002102 metacpan
Bio::Tools::Run::GenericParameters An object for the parameters used to run programs 1.005002102 metacpan
Bio::Tools::Run::ParametersI A Base object for the parameters used to run programs 1.005002102 metacpan
Bio::Tools::Run::RemoteBlast Object for remote execution of the NCBI Blast via HTTP 1.005002102 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. 1.005002102 metacpan
Bio::Tools::Run::WrapperBase A Base object for wrappers around executables 1.005002102 metacpan
Bio::Tools::Seg parse C<seg> output 1.005002102 metacpan
Bio::Tools::SeqPattern represent a sequence pattern or motif 1.005002102 metacpan
Bio::Tools::SeqStats Object holding statistics for one particular sequence 1.005002102 metacpan
Bio::Tools::SeqWords Object holding n-mer statistics for a sequence 1.005002102 metacpan
Bio::Tools::SiRNA 1.005002102 metacpan
Bio::Tools::SiRNA::Ruleset::saigo Perl object implementing the Saigo group's rules for designing small inhibitory RNAs 1.005002102 metacpan
Bio::Tools::SiRNA::Ruleset::tuschl Perl object implementing the tuschl group's rules for designing small inhibitory RNAs 1.005002102 metacpan
Bio::Tools::Sigcleave Bioperl object for sigcleave analysis 1.005002102 metacpan
Bio::Tools::Signalp parser for Signalp output 1.005002102 metacpan
Bio::Tools::Sim4::Exon A single exon determined by an alignment 1.005002102 metacpan
Bio::Tools::Sim4::Results Results of one Sim4 run 1.005002102 metacpan
Bio::Tools::Spidey::Exon A single exon determined by an alignment 1.005002102 metacpan
Bio::Tools::Spidey::Results Results of a Spidey run 1.005002102 metacpan
Bio::Tools::Tmhmm parse TMHMM output (TransMembrane HMM) 1.005002102 metacpan
Bio::Tools::dpAlign Perl extension to do pairwise dynamic programming sequence alignment 1.005002102 metacpan
Bio::Tools::ipcress Parse ipcress output and make features 1.005002102 metacpan
Bio::Tools::isPcr Parse isPcr output and make features 1.005002102 metacpan
Bio::Tools::pICalculator calculate the isoelectric point of a protein 1.005002102 metacpan
Bio::Tools::pSW pairwise Smith Waterman object 1.005002102 metacpan
Bio::Tools::tRNAscanSE A parser for tRNAscan-SE output 1.005002102 metacpan
Bio::Tree::AlleleNode A Node with Alleles attached 1.005002102 metacpan
Bio::Tree::Compatible Testing compatibility of phylogenetic trees with nested taxa. 1.005002102 metacpan
Bio::Tree::DistanceFactory Construct a tree using distance based methods 1.005002102 metacpan
Bio::Tree::Draw::Cladogram Drawing phylogenetic trees in Encapsulated PostScript (EPS) format. 1.005002102 metacpan
Bio::Tree::Node A Simple Tree Node 1.005002102 metacpan
Bio::Tree::NodeI Interface describing a Tree Node 1.005002102 metacpan
Bio::Tree::NodeNHX A Simple Tree Node with support for NHX tags 1.005002102 metacpan
Bio::Tree::RandomFactory TreeFactory for generating Random Trees 1.005002102 metacpan
Bio::Tree::Statistics Calculate certain statistics for a Tree 1.005002102 metacpan
Bio::Tree::Tree An Implementation of TreeI interface. 1.005002102 metacpan
Bio::Tree::TreeFunctionsI Decorated Interface implementing basic Tree exploration methods 1.005002102 metacpan
Bio::Tree::TreeI A Tree object suitable for lots of things, designed originally for Phylogenetic Trees. 1.005002102 metacpan
Bio::TreeIO Parser for Tree files 1.005002102 metacpan
Bio::TreeIO::TreeEventBuilder Build Bio::Tree::Tree's and Bio::Tree::Node's from Events 1.005002102 metacpan
Bio::TreeIO::cluster A TreeIO driver module for parsing Algorithm::Cluster::treecluster() output 1.005002102 metacpan
Bio::TreeIO::lintree Parser for lintree output trees 1.005002102 metacpan
Bio::TreeIO::newick TreeIO implementation for parsing Newick/New Hampshire/PHYLIP format. 1.005002102 metacpan
Bio::TreeIO::nexus A TreeIO driver module for parsing Nexus tree output from PAUP 1.005002102 metacpan
Bio::TreeIO::nhx TreeIO implementation for parsing Newick/New Hampshire eXtendend (NHX) format. 1.005002102 metacpan
Bio::TreeIO::pag Bio::TreeIO driver for Pagel format 1.005002102 metacpan
Bio::TreeIO::svggraph A simple output format that converts a Tree object to an SVG output 1.005002102 metacpan
Bio::TreeIO::tabtree A simple output format which displays a tree as an ASCII drawing 1.005002102 metacpan
Bio::UpdateableSeqI Descendant of Bio::SeqI that allows updates 1.005002102 metacpan
Bio::Variation::AAChange Sequence change class for polypeptides 1.005002102 metacpan
Bio::Variation::AAReverseMutate point mutation and codon information from single amino acid changes 1.005002102 metacpan
Bio::Variation::Allele Sequence object with allele-specific attributes 1.005002102 metacpan
Bio::Variation::DNAMutation DNA level mutation class 1.005002102 metacpan
Bio::Variation::IO Handler for sequence variation IO Formats 1.005002102 metacpan
Bio::Variation::IO::flat flat file sequence variation input/output stream 1.005002102 metacpan
Bio::Variation::IO::xml XML sequence variation input/output stream 1.005002102 metacpan
Bio::Variation::RNAChange Sequence change class for RNA level 1.005002102 metacpan
Bio::Variation::SNP submitted SNP 1.005002102 metacpan
Bio::Variation::SeqDiff Container class for mutation/variant descriptions 1.005002102 metacpan
Bio::Variation::VariantI Sequence Change SeqFeature abstract class 1.005002102 metacpan
Bio::WebAgent A base class for Web (any protocol) access 1.005002102 metacpan
FeatureStore 1.005002102 metacpan

Other Files

Build.PL metacpan
Changes metacpan
MANIFEST metacpan
META.yml metacpan
Makefile.PL metacpan
README metacpan
doc/Deobfuscator/Build.PL metacpan
doc/Deobfuscator/MANIFEST metacpan
doc/Deobfuscator/META.yml metacpan
doc/Deobfuscator/Makefile.PL metacpan