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-1.007000_005/deobfuscator/Deobfuscator/lib/Deobfuscator.pm -- Around line 90: '=item' outside of any '=over'

use_strict

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

Error: Bio::CodonUsage::IO, Bio::DB::CUTG, Bio::DB::Flat, Bio::DB::SeqFeature::NormalizedFeatureI, Bio::DB::SeqFeature::NormalizedTableFeatureI, Bio::DB::SeqFeature::Store::DBI::Iterator, Bio::Location::Split, Bio::Matrix::PSM::SiteMatrixI, Bio::MolEvol::CodonModel, Bio::Phenotype::PhenotypeI, Bio::Search::BlastUtils, Bio::SearchIO::SearchWriterI, Bio::SearchIO::cross_match, Bio::SeqIO::game, Bio::Tools::Primer::Assessor::Base, Bio::Tools::Primer::AssessorI, Bio::Tools::Primer::Feature, Bio::Tools::Primer::Pair, Bio::Tools::dpAlign

consistent_version

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

Error: 1.007000_005,1.11

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/Graphics.pm, Bio/Align/PairwiseStatistics.pm, Bio/Align/ProteinStatistics.pm, Bio/Align/StatisticsI.pm, Bio/Align/Utilities.pm, Bio/AlignIO.pm, Bio/AlignIO/Handler/GenericAlignHandler.pm, Bio/AlignIO/arp.pm, Bio/AlignIO/bl2seq.pm, Bio/AlignIO/clustalw.pm, Bio/AlignIO/emboss.pm, Bio/AlignIO/fasta.pm, Bio/AlignIO/largemultifasta.pm, Bio/AlignIO/maf.pm, Bio/AlignIO/mase.pm, Bio/AlignIO/mega.pm, Bio/AlignIO/meme.pm, Bio/AlignIO/metafasta.pm, Bio/AlignIO/msf.pm, Bio/AlignIO/nexml.pm, Bio/AlignIO/nexus.pm, Bio/AlignIO/pfam.pm, Bio/AlignIO/phylip.pm, Bio/AlignIO/po.pm, Bio/AlignIO/proda.pm, Bio/AlignIO/prodom.pm, Bio/AlignIO/psi.pm, Bio/AlignIO/selex.pm, Bio/AlignIO/stockholm.pm, Bio/AlignIO/xmfa.pm, Bio/AnalysisI.pm, Bio/AnalysisI.pm, Bio/AnalysisParserI.pm, Bio/AnalysisResultI.pm, Bio/AnnotatableI.pm, Bio/Annotation/AnnotationFactory.pm, Bio/Annotation/Collection.pm, Bio/Annotation/Comment.pm, Bio/Annotation/DBLink.pm, Bio/Annotation/OntologyTerm.pm, Bio/Annotation/Reference.pm, Bio/Annotation/Relation.pm, Bio/Annotation/SimpleValue.pm, Bio/Annotation/StructuredValue.pm, Bio/Annotation/TagTree.pm, Bio/Annotation/Target.pm, Bio/Annotation/Tree.pm, Bio/Annotation/TypeManager.pm, Bio/AnnotationCollectionI.pm, Bio/AnnotationI.pm, Bio/Assembly/Contig.pm, Bio/Assembly/ContigAnalysis.pm, Bio/Assembly/IO.pm, Bio/Assembly/IO/ace.pm, Bio/Assembly/IO/bowtie.pm, Bio/Assembly/IO/maq.pm, Bio/Assembly/IO/phrap.pm, Bio/Assembly/IO/sam.pm, Bio/Assembly/IO/tigr.pm, Bio/Assembly/Scaffold.pm, Bio/Assembly/ScaffoldI.pm, Bio/Assembly/Singlet.pm, Bio/Assembly/Tools/ContigSpectrum.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/DB/Ace.pm, Bio/DB/BioFetch.pm, Bio/DB/CUTG.pm, Bio/DB/DBFetch.pm, Bio/DB/EMBL.pm, Bio/DB/EntrezGene.pm, Bio/DB/Expression.pm, Bio/DB/Expression/geo.pm, Bio/DB/Failover.pm, Bio/DB/Fasta.pm, Bio/DB/SeqFeature/Store/berkeleydb.pm, Bio/DB/FileCache.pm, Bio/DB/Flat.pm, Bio/DB/Flat/BDB.pm, Bio/DB/Flat/BDB/embl.pm, Bio/DB/Flat/BDB/fasta.pm, Bio/DB/Flat/BDB/genbank.pm, Bio/DB/Flat/BDB/swiss.pm, Bio/DB/Flat/BinarySearch.pm, Bio/DB/GFF.pm, Bio/DB/GFF/Adaptor/ace.pm, Bio/DB/GFF/Adaptor/berkeleydb.pm, Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm, Bio/DB/GFF/Adaptor/biofetch.pm, Bio/DB/GFF/Adaptor/biofetch_oracle.pm, Bio/DB/GFF/Adaptor/dbi.pm, Bio/DB/GFF/Adaptor/dbi/caching_handle.pm, Bio/DB/GFF/Adaptor/dbi/caching_handle.pm, Bio/DB/GFF/Adaptor/dbi/iterator.pm, Bio/DB/GFF/Adaptor/dbi/mysql.pm, Bio/DB/GFF/Adaptor/dbi/mysqlace.pm, Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm, Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm, Bio/DB/GFF/Adaptor/dbi/oracle.pm, Bio/DB/GFF/Adaptor/dbi/oracleace.pm, Bio/DB/GFF/Adaptor/dbi/pg.pm, Bio/DB/GFF/Adaptor/dbi/pg_fts.pm, Bio/DB/GFF/Adaptor/memory.pm, Bio/DB/GFF/Adaptor/memory/feature_serializer.pm, Bio/DB/GFF/Adaptor/memory/iterator.pm, Bio/DB/GFF/Aggregator.pm, Bio/DB/GFF/Aggregator/alignment.pm, Bio/DB/GFF/Aggregator/clone.pm, Bio/DB/GFF/Aggregator/coding.pm, Bio/DB/GFF/Aggregator/gene.pm, Bio/DB/GFF/Aggregator/match.pm, Bio/DB/GFF/Aggregator/none.pm, Bio/DB/GFF/Aggregator/orf.pm, Bio/DB/GFF/Aggregator/processed_transcript.pm, Bio/DB/GFF/Aggregator/so_transcript.pm, Bio/DB/GFF/Aggregator/transcript.pm, Bio/DB/GFF/Aggregator/ucsc_acembly.pm, Bio/DB/GFF/Aggregator/ucsc_ensgene.pm, Bio/DB/GFF/Aggregator/ucsc_genscan.pm, Bio/DB/GFF/Aggregator/ucsc_refgene.pm, Bio/DB/GFF/Aggregator/ucsc_sanger22.pm, Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm, Bio/DB/GFF/Aggregator/ucsc_softberry.pm, Bio/DB/GFF/Aggregator/ucsc_twinscan.pm, Bio/DB/GFF/Aggregator/ucsc_unigene.pm, Bio/DB/GFF/Featname.pm, Bio/DB/GFF/Feature.pm, Bio/DB/GFF.pm, Bio/DB/GFF/Homol.pm, Bio/DB/GFF.pm, Bio/DB/GFF/RelSegment.pm, Bio/DB/GFF/Segment.pm, Bio/DB/GFF/Typename.pm, Bio/DB/GFF/Util/Binning.pm, Bio/DB/GFF/Util/Rearrange.pm, Bio/DB/GenBank.pm, Bio/DB/GenPept.pm, Bio/DB/GenericWebAgent.pm, Bio/DB/HIV.pm, Bio/DB/HIV/HIVAnnotProcessor.pm, Bio/DB/HIV/HIVQueryHelper.pm, Bio/DB/InMemoryCache.pm, Bio/DB/IndexedBase.pm, Bio/DB/IndexedBase.pm, Bio/DB/LocationI.pm, Bio/DB/MeSH.pm, Bio/DB/NCBIHelper.pm, Bio/DB/Qual.pm, Bio/DB/Query/GenBank.pm, Bio/DB/Query/HIVQuery.pm, Bio/DB/Query/WebQuery.pm, Bio/DB/QueryI.pm, Bio/DB/RandomAccessI.pm, Bio/DB/RefSeq.pm, Bio/DB/ReferenceI.pm, Bio/DB/Registry.pm, Bio/DB/SeqFeature.pm, Bio/DB/SeqFeature/NormalizedFeature.pm, Bio/DB/SeqFeature/NormalizedFeatureI.pm, Bio/DB/SeqFeature/NormalizedTableFeatureI.pm, Bio/DB/SeqFeature/Segment.pm, Bio/DB/SeqFeature/Store.pm, Bio/DB/SeqFeature/Store/DBI/Iterator.pm, Bio/DB/SeqFeature/Store/DBI/Pg.pm, Bio/DB/SeqFeature/Store/DBI/SQLite.pm, Bio/DB/SeqFeature/Store/DBI/mysql.pm, Bio/DB/SeqFeature/Store/FeatureFileLoader.pm, Bio/DB/SeqFeature/Store.pm, Bio/DB/SeqFeature/Store/GFF2Loader.pm, Bio/DB/SeqFeature/Store/GFF3Loader.pm, Bio/DB/SeqFeature/Store/LoadHelper.pm, Bio/DB/SeqFeature/Store/Loader.pm, Bio/DB/SeqFeature/Store/bdb.pm, Bio/DB/SeqFeature/Store/berkeleydb.pm, Bio/DB/SeqFeature/Store/berkeleydb3.pm, Bio/DB/SeqFeature/Store/berkeleydb.pm, Bio/DB/SeqFeature/Store/memory.pm, Bio/DB/SeqFeature/Store/memory.pm, Bio/DB/SeqI.pm, Bio/DB/SeqVersion.pm, Bio/DB/SeqVersion/gi.pm, Bio/DB/SwissProt.pm, Bio/DB/TFBS.pm, Bio/DB/TFBS/transfac_pro.pm, Bio/DB/Taxonomy.pm, Bio/DB/Taxonomy/entrez.pm, Bio/DB/Taxonomy/flatfile.pm, Bio/DB/Taxonomy/greengenes.pm, Bio/DB/Taxonomy/list.pm, Bio/DB/Taxonomy/silva.pm, Bio/DB/Taxonomy/sqlite.pm, Bio/DB/Universal.pm, Bio/DB/UpdateableSeqI.pm, Bio/DB/WebDBSeqI.pm, Bio/DBLinkContainerI.pm, Bio/Das/FeatureTypeI.pm, Bio/Das/SegmentI.pm, Bio/DasI.pm, Bio/DescribableI.pm, Bio/Draw/Pictogram.pm, Bio/Event/EventGeneratorI.pm, Bio/Event/EventHandlerI.pm, Bio/Factory/AnalysisI.pm, Bio/Factory/ApplicationFactoryI.pm, Bio/Factory/DriverFactory.pm, Bio/Factory/FTLocationFactory.pm, Bio/Factory/LocationFactoryI.pm, Bio/Factory/MapFactoryI.pm, Bio/Factory/ObjectBuilderI.pm, Bio/Factory/ObjectFactory.pm, Bio/Factory/ObjectFactoryI.pm, Bio/Factory/SeqAnalysisParserFactory.pm, Bio/Factory/SeqAnalysisParserFactoryI.pm, Bio/Factory/SequenceFactoryI.pm, Bio/Factory/SequenceProcessorI.pm, Bio/Factory/SequenceStreamI.pm, Bio/Factory/TreeFactoryI.pm, Bio/FeatureHolderI.pm, Bio/HandlerBaseI.pm, Bio/IdCollectionI.pm, Bio/IdentifiableI.pm, Bio/Index/Abstract.pm, Bio/Index/AbstractSeq.pm, Bio/Index/Blast.pm, Bio/Index/BlastTable.pm, Bio/Index/EMBL.pm, Bio/Index/Fasta.pm, Bio/Index/Fastq.pm, Bio/Index/GenBank.pm, Bio/Index/Hmmer.pm, Bio/Index/Qual.pm, Bio/Index/Stockholm.pm, Bio/Index/SwissPfam.pm, Bio/Index/Swissprot.pm, Bio/LiveSeq/AARange.pm, Bio/LiveSeq/Chain.pm, Bio/LiveSeq/ChainI.pm, Bio/LiveSeq/DNA.pm, Bio/LiveSeq/Exon.pm, Bio/LiveSeq/Gene.pm, Bio/LiveSeq/IO/BioPerl.pm, Bio/LiveSeq/IO/Loader.pm, Bio/LiveSeq/Intron.pm, Bio/LiveSeq/Mutation.pm, Bio/LiveSeq/Mutator.pm, Bio/LiveSeq/Prim_Transcript.pm, Bio/LiveSeq/Range.pm, Bio/LiveSeq/Repeat_Region.pm, Bio/LiveSeq/Repeat_Unit.pm, Bio/LiveSeq/SeqI.pm, Bio/LiveSeq/Transcript.pm, Bio/LiveSeq/Translation.pm, Bio/Search/Tiling/MapTileUtils.pm, Bio/Location/Atomic.pm, Bio/Location/AvWithinCoordPolicy.pm, Bio/Location/CoordinatePolicyI.pm, Bio/Location/Fuzzy.pm, Bio/Location/FuzzyLocationI.pm, Bio/Location/NarrowestCoordPolicy.pm, Bio/Location/Simple.pm, Bio/Location/Split.pm, Bio/Location/SplitLocationI.pm, Bio/Location/WidestCoordPolicy.pm, Bio/LocationI.pm, Bio/Map/Clone.pm, Bio/Map/Contig.pm, Bio/Map/CytoMap.pm, Bio/Map/CytoMarker.pm, Bio/Map/CytoPosition.pm, Bio/Map/EntityI.pm, Bio/Map/FPCMarker.pm, Bio/Map/Gene.pm, Bio/Map/GeneMap.pm, Bio/Map/GenePosition.pm, Bio/Map/GeneRelative.pm, Bio/Map/LinkageMap.pm, Bio/Map/LinkagePosition.pm, Bio/Map/MapI.pm, Bio/Map/Mappable.pm, Bio/Map/MappableI.pm, Bio/Map/Marker.pm, Bio/Map/MarkerI.pm, Bio/Map/Microsatellite.pm, Bio/Map/OrderedPosition.pm, Bio/Map/OrderedPositionWithDistance.pm, Bio/Map/Physical.pm, Bio/Map/Position.pm, Bio/Map/PositionHandler.pm, Bio/Map/PositionHandlerI.pm, Bio/Map/PositionI.pm, Bio/Map/PositionWithSequence.pm, Bio/Map/Prediction.pm, Bio/Map/Relative.pm, Bio/Map/RelativeI.pm, Bio/Map/SimpleMap.pm, Bio/Map/TranscriptionFactor.pm, Bio/MapIO.pm, Bio/MapIO/fpc.pm, Bio/MapIO/mapmaker.pm, Bio/Matrix/Generic.pm, Bio/Matrix/IO.pm, Bio/Matrix/IO/mlagan.pm, Bio/Matrix/IO/phylip.pm, Bio/Matrix/IO/scoring.pm, Bio/Matrix/MatrixI.pm, Bio/Matrix/Mlagan.pm, Bio/Matrix/PSM/IO.pm, Bio/Matrix/PSM/IO/mast.pm, Bio/Matrix/PSM/IO/masta.pm, Bio/Matrix/PSM/IO/meme.pm, Bio/Matrix/PSM/IO/psiblast.pm, Bio/Matrix/PSM/IO/transfac.pm, Bio/Matrix/PSM/InstanceSite.pm, Bio/Matrix/PSM/InstanceSiteI.pm, Bio/Matrix/PSM/ProtMatrix.pm, Bio/Matrix/PSM/ProtPsm.pm, Bio/Matrix/PSM/Psm.pm, Bio/Matrix/PSM/PsmHeader.pm, Bio/Matrix/PSM/PsmHeaderI.pm, Bio/Matrix/PSM/PsmI.pm, Bio/Matrix/PSM/SiteMatrix.pm, Bio/Matrix/PSM/SiteMatrixI.pm, Bio/Matrix/PhylipDist.pm, Bio/Matrix/Scoring.pm, Bio/MolEvol/CodonModel.pm, Bio/Nexml/Factory.pm, Bio/NexmlIO.pm, Bio/Ontology/DocumentRegistry.pm, Bio/Ontology/GOterm.pm, Bio/Ontology/InterProTerm.pm, Bio/Ontology/OBOEngine.pm, Bio/Ontology/OBOterm.pm, Bio/Ontology/Ontology.pm, Bio/Ontology/OntologyEngineI.pm, Bio/Ontology/OntologyI.pm, Bio/Ontology/OntologyStore.pm, Bio/Ontology/Path.pm, Bio/Ontology/PathI.pm, Bio/Ontology/Relationship.pm, Bio/Ontology/RelationshipFactory.pm, Bio/Ontology/RelationshipI.pm, Bio/Ontology/RelationshipType.pm, Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm, Bio/Ontology/SimpleOntologyEngine.pm, Bio/Ontology/Term.pm, Bio/Ontology/TermFactory.pm, Bio/Ontology/TermI.pm, Bio/OntologyIO.pm, Bio/OntologyIO/Handlers/BaseSAXHandler.pm, Bio/OntologyIO/Handlers/InterProHandler.pm, Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm, Bio/OntologyIO/InterProParser.pm, Bio/OntologyIO/dagflat.pm, Bio/OntologyIO/goflat.pm, Bio/OntologyIO/obo.pm, Bio/OntologyIO/simplehierarchy.pm, Bio/OntologyIO/soflat.pm, Bio/ParameterBaseI.pm, Bio/Perl.pm, Bio/Phenotype/Correlate.pm, Bio/Phenotype/MeSH/Term.pm, Bio/Phenotype/MeSH/Twig.pm, Bio/Phenotype/Measure.pm, Bio/Phenotype/OMIM/MiniMIMentry.pm, Bio/Phenotype/OMIM/OMIMentry.pm, Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm, Bio/Phenotype/OMIM/OMIMparser.pm, Bio/Phenotype/Phenotype.pm, Bio/Phenotype/PhenotypeI.pm, Bio/PhyloNetwork.pm, Bio/PhyloNetwork/Factory.pm, Bio/PhyloNetwork/FactoryX.pm, Bio/PhyloNetwork/GraphViz.pm, Bio/PhyloNetwork/RandomFactory.pm, Bio/PhyloNetwork/TreeFactory.pm, Bio/PhyloNetwork/TreeFactoryMulti.pm, Bio/PhyloNetwork/TreeFactoryX.pm, Bio/PhyloNetwork/muVector.pm, Bio/PopGen/Genotype.pm, Bio/PopGen/GenotypeI.pm, Bio/PopGen/HtSNP.pm, Bio/PopGen/IO.pm, Bio/PopGen/IO/csv.pm, Bio/PopGen/IO/hapmap.pm, Bio/PopGen/IO/phase.pm, Bio/PopGen/IO/prettybase.pm, Bio/PopGen/Individual.pm, Bio/PopGen/IndividualI.pm, Bio/PopGen/Marker.pm, Bio/PopGen/MarkerI.pm, Bio/PopGen/PopStats.pm, Bio/PopGen/Population.pm, Bio/PopGen/PopulationI.pm, Bio/PopGen/Simulation/Coalescent.pm, Bio/PopGen/Simulation/GeneticDrift.pm, Bio/PopGen/Statistics.pm, Bio/PopGen/TagHaplotype.pm, Bio/PopGen/Utilities.pm, Bio/PrimarySeq.pm, Bio/DB/Fasta.pm, Bio/PrimarySeqI.pm, Bio/PullParserI.pm, Bio/Range.pm, Bio/RangeI.pm, Bio/Restriction/Analysis.pm, Bio/Restriction/Enzyme.pm, Bio/Restriction/Enzyme/MultiCut.pm, Bio/Restriction/Enzyme/MultiSite.pm, Bio/Restriction/EnzymeCollection.pm, Bio/Restriction/EnzymeI.pm, Bio/Restriction/IO.pm, Bio/Restriction/IO/bairoch.pm, Bio/Restriction/IO/base.pm, Bio/Restriction/IO/itype2.pm, Bio/Restriction/IO/prototype.pm, Bio/Restriction/IO/withrefm.pm, Bio/Root/Build.pm, Bio/Root/Exception.pm, Bio/Root/HTTPget.pm, Bio/Root/IO.pm, Bio/Root/Root.pm, Bio/Root/RootI.pm, Bio/Root/Storable.pm, Bio/Root/Test.pm, Bio/Root/TestObject.pm, Bio/Root/Utilities.pm, Bio/Root/Version.pm, Bio/Search/BlastStatistics.pm, Bio/Search/BlastUtils.pm, Bio/Search/DatabaseI.pm, Bio/Search/GenericDatabase.pm, Bio/Search/GenericStatistics.pm, Bio/Search/HSP/BlastHSP.pm, Bio/Search/HSP/BlastPullHSP.pm, Bio/Search/HSP/FastaHSP.pm, Bio/Search/HSP/GenericHSP.pm, Bio/Search/HSP/HMMERHSP.pm, Bio/Search/HSP/HSPFactory.pm, Bio/Search/Tiling/MapTileUtils.pm, Bio/Search/HSP/HmmpfamHSP.pm, Bio/Search/HSP/ModelHSP.pm, Bio/Search/HSP/PSLHSP.pm, Bio/Search/HSP/PsiBlastHSP.pm, Bio/Search/HSP/PullHSPI.pm, Bio/Search/HSP/WABAHSP.pm, Bio/Search/Hit/BlastHit.pm, Bio/Search/Hit/BlastPullHit.pm, Bio/Search/Hit/Fasta.pm, Bio/Search/Hit/GenericHit.pm, Bio/Search/Hit/HMMERHit.pm, Bio/Search/Hit/HitFactory.pm, Bio/Search/Hit/HitI.pm, Bio/Search/Hit/HmmpfamHit.pm, Bio/Search/Hit/ModelHit.pm, Bio/Search/Hit/PsiBlastHit.pm, Bio/Search/Hit/PullHitI.pm, Bio/Search/Hit/hmmer3Hit.pm, Bio/Search/Iteration/GenericIteration.pm, Bio/Search/Iteration/IterationI.pm, Bio/Search/Processor.pm, Bio/Search/Result/BlastPullResult.pm, Bio/Search/Result/BlastResult.pm, Bio/Search/Result/CrossMatchResult.pm, Bio/Search/Result/GenericResult.pm, Bio/Search/Result/HMMERResult.pm, Bio/Search/Result/HmmpfamResult.pm, Bio/Search/Result/INFERNALResult.pm, Bio/Search/Result/PullResultI.pm, Bio/Search/Result/ResultFactory.pm, Bio/Search/Result/ResultI.pm, Bio/Search/Result/WABAResult.pm, Bio/Search/Result/hmmer3Result.pm, Bio/Search/SearchUtils.pm, Bio/Search/StatisticsI.pm, Bio/Search/Tiling/MapTileUtils.pm, Bio/Search/Tiling/MapTiling.pm, Bio/Search/Tiling/TilingI.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/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/blast_pull.pm, Bio/SearchIO/blasttable.pm, Bio/SearchIO/cross_match.pm, Bio/SearchIO/erpin.pm, Bio/SearchIO/exonerate.pm, Bio/SearchIO/fasta.pm, Bio/SearchIO/gmap_f9.pm, Bio/SearchIO/hmmer.pm, Bio/SearchIO/hmmer2.pm, Bio/SearchIO/hmmer3.pm, Bio/SearchIO/hmmer_pull.pm, Bio/SearchIO/infernal.pm, Bio/SearchIO/megablast.pm, Bio/SearchIO/psl.pm, Bio/SearchIO/rnamotif.pm, Bio/SearchIO/sim4.pm, Bio/SearchIO/waba.pm, Bio/SearchIO/wise.pm, Bio/Seq.pm, Bio/Seq/BaseSeqProcessor.pm, Bio/Seq/EncodedSeq.pm, Bio/Seq/LargeLocatableSeq.pm, Bio/Seq/LargePrimarySeq.pm, Bio/Seq/LargeSeq.pm, Bio/Seq/LargeSeqI.pm, Bio/Seq/Meta.pm, Bio/Seq/Meta/Array.pm, Bio/Seq/MetaI.pm, Bio/Seq/PrimaryQual.pm, Bio/DB/Qual.pm, Bio/Seq/PrimedSeq.pm, Bio/Seq/QualI.pm, Bio/Seq/Quality.pm, Bio/Seq/RichSeq.pm, Bio/Seq/RichSeqI.pm, Bio/Seq/SeqBuilder.pm, Bio/Seq/SeqFactory.pm, Bio/Seq/SeqFastaSpeedFactory.pm, Bio/Seq/SeqWithQuality.pm, Bio/Seq/SequenceTrace.pm, Bio/Seq/SimulatedRead.pm, Bio/Seq/TraceI.pm, Bio/SeqAnalysisParserI.pm, Bio/SeqEvolution/DNAPoint.pm, Bio/SeqEvolution/EvolutionI.pm, Bio/SeqEvolution/Factory.pm, Bio/SeqFeature/Amplicon.pm, Bio/SeqFeature/AnnotationAdaptor.pm, Bio/SeqFeature/Collection.pm, Bio/SeqFeature/CollectionI.pm, Bio/SeqFeature/Computation.pm, Bio/SeqFeature/FeaturePair.pm, Bio/SeqFeature/Gene/Exon.pm, Bio/SeqFeature/Gene/ExonI.pm, Bio/SeqFeature/Gene/GeneStructure.pm, Bio/SeqFeature/Gene/GeneStructureI.pm, Bio/SeqFeature/Gene/Intron.pm, Bio/SeqFeature/Gene/NC_Feature.pm, Bio/SeqFeature/Gene/Poly_A_site.pm, Bio/SeqFeature/Gene/Promoter.pm, Bio/SeqFeature/Gene/Transcript.pm, Bio/SeqFeature/Gene/TranscriptI.pm, Bio/SeqFeature/Gene/UTR.pm, Bio/SeqFeature/Generic.pm, Bio/SeqFeature/Lite.pm, Bio/SeqFeature/PositionProxy.pm, Bio/SeqFeature/Primer.pm, Bio/SeqFeature/SiRNA/Oligo.pm, Bio/SeqFeature/SiRNA/Pair.pm, Bio/SeqFeature/Similarity.pm, Bio/SeqFeature/SimilarityPair.pm, Bio/SeqFeature/SubSeq.pm, Bio/SeqFeature/Tools/FeatureNamer.pm, Bio/SeqFeature/Tools/IDHandler.pm, Bio/SeqFeature/Tools/TypeMapper.pm, Bio/SeqFeature/Tools/Unflattener.pm, Bio/SeqFeature/TypedSeqFeatureI.pm, Bio/SeqFeatureI.pm, Bio/SeqI.pm, Bio/SeqIO.pm, Bio/SeqIO/FTHelper.pm, Bio/SeqIO/Handler/GenericRichSeqHandler.pm, Bio/SeqIO/MultiFile.pm, Bio/SeqIO/abi.pm, Bio/SeqIO/ace.pm, Bio/SeqIO/agave.pm, Bio/SeqIO/alf.pm, Bio/SeqIO/asciitree.pm, Bio/SeqIO/bsml.pm, Bio/SeqIO/bsml_sax.pm, Bio/SeqIO/chadoxml.pm, Bio/SeqIO/chaos.pm, Bio/SeqIO/chaosxml.pm, Bio/SeqIO/ctf.pm, Bio/SeqIO/embl.pm, Bio/SeqIO/embldriver.pm, Bio/SeqIO/entrezgene.pm, Bio/SeqIO/excel.pm, Bio/SeqIO/exp.pm, Bio/SeqIO/fasta.pm, Bio/SeqIO/fastq.pm, Bio/SeqIO/flybase_chadoxml.pm, Bio/SeqIO/game.pm, Bio/SeqIO/game/featHandler.pm, Bio/SeqIO/game/gameHandler.pm, Bio/SeqIO/game/gameSubs.pm, Bio/SeqIO/game/gameWriter.pm, Bio/SeqIO/game/seqHandler.pm, Bio/SeqIO/gbdriver.pm, Bio/SeqIO/gbxml.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/mbsout.pm, Bio/SeqIO/metafasta.pm, Bio/SeqIO/msout.pm, Bio/SeqIO/nexml.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/seqxml.pm, Bio/SeqIO/strider.pm, Bio/SeqIO/swiss.pm, Bio/SeqIO/swissdriver.pm, Bio/SeqIO/tab.pm, Bio/SeqIO/table.pm, Bio/SeqIO/tigr.pm, Bio/SeqIO/tigrxml.pm, Bio/SeqIO/tinyseq.pm, Bio/SeqIO/tinyseq/tinyseqHandler.pm, Bio/SeqIO/ztr.pm, Bio/SeqUtils.pm, Bio/SimpleAlign.pm, Bio/SimpleAnalysisI.pm, Bio/Species.pm, Bio/Structure/Atom.pm, Bio/Structure/Chain.pm, Bio/Structure/Entry.pm, Bio/Structure/IO.pm, Bio/Structure/IO/pdb.pm, Bio/Structure/Model.pm, Bio/Structure/Residue.pm, Bio/Structure/SecStr/DSSP/Res.pm, Bio/Structure/SecStr/STRIDE/Res.pm, Bio/Structure/StructureI.pm, Bio/Symbol/Alphabet.pm, Bio/Symbol/AlphabetI.pm, Bio/Symbol/DNAAlphabet.pm, Bio/Symbol/ProteinAlphabet.pm, Bio/Symbol/Symbol.pm, Bio/Symbol/SymbolI.pm, Bio/Taxon.pm, Bio/Taxonomy.pm, Bio/Taxonomy/FactoryI.pm, Bio/Taxonomy/Node.pm, Bio/Taxonomy/Taxon.pm, Bio/Taxonomy/Tree.pm, Bio/Tools/AlignFactory.pm, Bio/Tools/Alignment/Consed.pm, Bio/Tools/Alignment/Trim.pm, Bio/Tools/AmpliconSearch.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/NetPhos.pm, Bio/Tools/Analysis/Protein/Scansite.pm, Bio/Tools/Analysis/Protein/Sopma.pm, Bio/Tools/Analysis/SimpleAnalysisBase.pm, Bio/Tools/AnalysisResult.pm, Bio/Tools/Blat.pm, Bio/Tools/CodonTable.pm, Bio/Tools/Coil.pm, Bio/Tools/ECnumber.pm, Bio/Tools/EMBOSS/Palindrome.pm, Bio/Tools/EPCR.pm, Bio/Tools/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/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/Match.pm, Bio/Tools/OddCodes.pm, Bio/Tools/Phylo/Gerp.pm, Bio/Tools/Phylo/Gumby.pm, Bio/Tools/Phylo/Molphy.pm, Bio/Tools/Phylo/Molphy/Result.pm, Bio/Tools/Phylo/PAML.pm, Bio/Tools/Phylo/PAML/Codeml.pm, Bio/Tools/Phylo/PAML/ModelResult.pm, Bio/Tools/Phylo/PAML/Result.pm, Bio/Tools/Phylo/Phylip/ProtDist.pm, Bio/Tools/Prediction/Exon.pm, Bio/Tools/Prediction/Gene.pm, Bio/Tools/Primer3.pm, Bio/Tools/Primer/Assessor/Base.pm, Bio/Tools/Primer/AssessorI.pm, Bio/Tools/Primer/Feature.pm, Bio/Tools/Primer/Pair.pm, Bio/Tools/Prints.pm, Bio/Tools/Profile.pm, Bio/Tools/Promoterwise.pm, Bio/Tools/PrositeScan.pm, Bio/Tools/Protparam.pm, Bio/Tools/Pseudowise.pm, Bio/Tools/QRNA.pm, Bio/Tools/RandomDistFunctions.pm, Bio/Tools/RepeatMasker.pm, Bio/Tools/Run/GenericParameters.pm, Bio/Tools/Run/ParametersI.pm, Bio/Tools/Run/RemoteBlast.pm, Bio/Tools/Seg.pm, Bio/Tools/SeqPattern.pm, Bio/Tools/SeqPattern/Backtranslate.pm, Bio/Tools/SeqStats.pm, Bio/Tools/SeqWords.pm, Bio/Tools/SiRNA.pm, Bio/Tools/SiRNA/Ruleset/saigo.pm, Bio/Tools/SiRNA/Ruleset/tuschl.pm, Bio/Tools/Sigcleave.pm, Bio/Tools/Signalp.pm, Bio/Tools/Signalp/ExtendedSignalp.pm, Bio/Tools/Sim4/Exon.pm, Bio/Tools/Sim4/Results.pm, Bio/Tools/Spidey/Exon.pm, Bio/Tools/Spidey/Results.pm, Bio/Tools/TandemRepeatsFinder.pm, Bio/Tools/TargetP.pm, Bio/Tools/Tmhmm.pm, Bio/Tools/dpAlign.pm, Bio/Tools/ipcress.pm, Bio/Tools/isPcr.pm, Bio/Tools/pICalculator.pm, Bio/Tools/pSW.pm, Bio/Tools/tRNAscanSE.pm, Bio/Tree/AlleleNode.pm, Bio/Tree/AnnotatableNode.pm, Bio/Tree/Compatible.pm, Bio/Tree/DistanceFactory.pm, Bio/Tree/Draw/Cladogram.pm, Bio/Tree/Node.pm, Bio/Tree/NodeI.pm, Bio/Tree/NodeNHX.pm, Bio/Tree/RandomFactory.pm, Bio/Tree/Statistics.pm, Bio/Tree/Tree.pm, Bio/Tree/TreeFunctionsI.pm, Bio/Tree/TreeI.pm, Bio/TreeIO.pm, Bio/TreeIO/NewickParser.pm, Bio/TreeIO/TreeEventBuilder.pm, Bio/TreeIO/cluster.pm, Bio/TreeIO/lintree.pm, Bio/TreeIO/newick.pm, Bio/TreeIO/nexml.pm, Bio/TreeIO/nexus.pm, Bio/TreeIO/nhx.pm, Bio/TreeIO/pag.pm, Bio/TreeIO/phyloxml.pm, Bio/TreeIO/svggraph.pm, Bio/TreeIO/tabtree.pm, Bio/UpdateableSeqI.pm, Bio/Variation/AAChange.pm, Bio/Variation/AAReverseMutate.pm, Bio/Variation/Allele.pm, Bio/Variation/DNAMutation.pm, Bio/Variation/IO.pm, Bio/Variation/IO/flat.pm, Bio/Variation/IO/xml.pm, Bio/Variation/RNAChange.pm, Bio/Variation/SNP.pm, Bio/Variation/SeqDiff.pm, Bio/Variation/VariantI.pm, Bio/WebAgent.pm, Bio/DB/GFF/Adaptor/berkeleydb.pm

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::AlignIO, Bio::AlignIO::arp, Bio::AlignIO::bl2seq, Bio::AlignIO::clustalw, Bio::AlignIO::emboss, Bio::AlignIO::fasta, Bio::AlignIO::largemultifasta, Bio::AlignIO::maf, Bio::AlignIO::mase, Bio::AlignIO::mega, Bio::AlignIO::meme, Bio::AlignIO::metafasta, Bio::AlignIO::msf, Bio::AlignIO::nexml, Bio::AlignIO::nexus, Bio::AlignIO::pfam, Bio::AlignIO::phylip, Bio::AlignIO::po, Bio::AlignIO::proda, Bio::AlignIO::prodom, Bio::AlignIO::psi, Bio::AlignIO::selex, Bio::AlignIO::stockholm, Bio::AlignIO::xmfa, Bio::AnalysisI, Bio::AnalysisParserI, Bio::AnalysisResultI, Bio::AnnotatableI, Bio::Annotation::AnnotationFactory, Bio::Annotation::Collection, Bio::Annotation::Comment, Bio::Annotation::DBLink, Bio::Annotation::OntologyTerm, Bio::Annotation::Reference, Bio::Annotation::Relation, Bio::Annotation::SimpleValue, Bio::Annotation::StructuredValue, Bio::Annotation::TagTree, Bio::Annotation::Target, Bio::Annotation::Tree, Bio::Annotation::TypeManager, Bio::AnnotationCollectionI, Bio::AnnotationI, Bio::Assembly::Contig, Bio::Assembly::ContigAnalysis, Bio::Assembly::IO, Bio::Assembly::IO::ace, Bio::Assembly::IO::maq, Bio::Assembly::IO::phrap, Bio::Assembly::IO::tigr, Bio::Assembly::Scaffold, Bio::Assembly::ScaffoldI, Bio::Assembly::Singlet, Bio::Assembly::Tools::ContigSpectrum, Bio::Cluster::ClusterFactory, Bio::Cluster::FamilyI, Bio::Cluster::UniGene, Bio::Cluster::UniGeneI, Bio::ClusterI, Bio::ClusterIO, Bio::ClusterIO::dbsnp, Bio::ClusterIO::unigene, Bio::CodonUsage::IO, Bio::CodonUsage::Table, Bio::DB::Ace, Bio::DB::BioFetch, Bio::DB::CUTG, Bio::DB::DBFetch, Bio::DB::EMBL, Bio::DB::EntrezGene, Bio::DB::Expression, Bio::DB::Expression::geo, Bio::DB::Failover, Bio::DB::FileCache, Bio::DB::Flat, Bio::DB::Flat::BDB, Bio::DB::Flat::BDB::embl, Bio::DB::Flat::BDB::fasta, Bio::DB::Flat::BDB::genbank, Bio::DB::Flat::BDB::swiss, Bio::DB::Flat::BinarySearch, Bio::DB::GFF, Bio::DB::GFF::Adaptor::ace, Bio::DB::GFF::Adaptor::berkeleydb, Bio::DB::GFF::Adaptor::berkeleydb::iterator, Bio::DB::GFF::Adaptor::biofetch, Bio::DB::GFF::Adaptor::biofetch_oracle, Bio::DB::GFF::Adaptor::dbi, Bio::DB::GFF::Adaptor::dbi::caching_handle, Bio::DB::GFF::Adaptor::dbi::iterator, Bio::DB::GFF::Adaptor::dbi::mysql, Bio::DB::GFF::Adaptor::dbi::mysqlace, Bio::DB::GFF::Adaptor::dbi::mysqlcmap, Bio::DB::GFF::Adaptor::dbi::mysqlopt, Bio::DB::GFF::Adaptor::dbi::oracle, Bio::DB::GFF::Adaptor::dbi::oracleace, Bio::DB::GFF::Adaptor::dbi::pg, Bio::DB::GFF::Adaptor::dbi::pg_fts, Bio::DB::GFF::Adaptor::memory, Bio::DB::GFF::Adaptor::memory::feature_serializer, Bio::DB::GFF::Adaptor::memory::iterator, Bio::DB::GFF::Aggregator, Bio::DB::GFF::Aggregator::alignment, Bio::DB::GFF::Aggregator::clone, Bio::DB::GFF::Aggregator::coding, Bio::DB::GFF::Aggregator::gene, Bio::DB::GFF::Aggregator::match, Bio::DB::GFF::Aggregator::none, Bio::DB::GFF::Aggregator::orf, Bio::DB::GFF::Aggregator::processed_transcript, Bio::DB::GFF::Aggregator::so_transcript, Bio::DB::GFF::Aggregator::transcript, Bio::DB::GFF::Aggregator::ucsc_acembly, Bio::DB::GFF::Aggregator::ucsc_ensgene, Bio::DB::GFF::Aggregator::ucsc_genscan, Bio::DB::GFF::Aggregator::ucsc_refgene, Bio::DB::GFF::Aggregator::ucsc_sanger22, Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo, Bio::DB::GFF::Aggregator::ucsc_softberry, Bio::DB::GFF::Aggregator::ucsc_twinscan, Bio::DB::GFF::Aggregator::ucsc_unigene, Bio::DB::GFF::Featname, Bio::DB::GFF::Feature, Bio::DB::GFF::Homol, Bio::DB::GFF::RelSegment, Bio::DB::GFF::Segment, Bio::DB::GFF::Typename, Bio::DB::GFF::Util::Binning, Bio::DB::GFF::Util::Rearrange, Bio::DB::GenBank, Bio::DB::GenPept, Bio::DB::HIV::HIVAnnotProcessor, Bio::DB::HIV::HIVQueryHelper, Bio::DB::InMemoryCache, Bio::DB::Indexed::Stream, Bio::DB::LocationI, Bio::DB::MeSH, Bio::DB::NCBIHelper, Bio::DB::Query::GenBank, Bio::DB::Query::HIVQuery, Bio::DB::Query::WebQuery, Bio::DB::QueryI, Bio::DB::RandomAccessI, Bio::DB::RefSeq, Bio::DB::ReferenceI, Bio::DB::Registry, Bio::DB::SeqFeature, Bio::DB::SeqFeature::NormalizedFeature, Bio::DB::SeqFeature::NormalizedFeatureI, Bio::DB::SeqFeature::NormalizedTableFeatureI, Bio::DB::SeqFeature::Segment, Bio::DB::SeqFeature::Store::DBI::Iterator, Bio::DB::SeqFeature::Store::DBI::Pg, Bio::DB::SeqFeature::Store::DBI::SQLite, Bio::DB::SeqFeature::Store::DBI::mysql, Bio::DB::SeqFeature::Store::FeatureFileLoader, Bio::DB::SeqFeature::Store::GFF2Loader, Bio::DB::SeqFeature::Store::GFF3Loader, Bio::DB::SeqFeature::Store::LoadHelper, Bio::DB::SeqFeature::Store::Loader, Bio::DB::SeqFeature::Store::bdb, Bio::DB::SeqFeature::Store::berkeleydb, Bio::DB::SeqFeature::Store::berkeleydb3, Bio::DB::SeqFeature::Store::memory::Iterator, Bio::DB::SeqI, Bio::DB::SeqVersion, Bio::DB::SeqVersion::gi, Bio::DB::SwissProt, Bio::DB::TFBS, Bio::DB::TFBS::transfac_pro, Bio::DB::Taxonomy, Bio::DB::Taxonomy::entrez, Bio::DB::Taxonomy::flatfile, Bio::DB::Taxonomy::greengenes, Bio::DB::Taxonomy::list, Bio::DB::Taxonomy::silva, Bio::DB::Taxonomy::sqlite, Bio::DB::Universal, Bio::DB::UpdateableSeqI, Bio::DB::WebDBSeqI, Bio::DBLinkContainerI, Bio::Das::FeatureTypeI, Bio::Das::SegmentI, Bio::DasI, Bio::DescribableI, Bio::Draw::Pictogram, Bio::Event::EventGeneratorI, Bio::Event::EventHandlerI, Bio::Factory::AnalysisI, Bio::Factory::ApplicationFactoryI, Bio::Factory::DriverFactory, Bio::Factory::FTLocationFactory, Bio::Factory::LocationFactoryI, Bio::Factory::MapFactoryI, Bio::Factory::ObjectBuilderI, Bio::Factory::ObjectFactory, Bio::Factory::ObjectFactoryI, Bio::Factory::SeqAnalysisParserFactory, Bio::Factory::SeqAnalysisParserFactoryI, Bio::Factory::SequenceFactoryI, Bio::Factory::SequenceProcessorI, Bio::Factory::SequenceStreamI, Bio::Factory::TreeFactoryI, Bio::FeatureHolderI, Bio::IdCollectionI, Bio::IdentifiableI, Bio::Index::Abstract, Bio::Index::AbstractSeq, Bio::Index::Blast, Bio::Index::BlastTable, Bio::Index::EMBL, Bio::Index::Fastq, Bio::Index::GenBank, Bio::Index::Hmmer, Bio::Index::Qual, Bio::Index::Stockholm, Bio::Index::SwissPfam, Bio::Index::Swissprot, Bio::LiveSeq::AARange, Bio::LiveSeq::Chain, Bio::LiveSeq::ChainI, Bio::LiveSeq::DNA, Bio::LiveSeq::Exon, Bio::LiveSeq::Gene, Bio::LiveSeq::IO::BioPerl, Bio::LiveSeq::IO::Loader, Bio::LiveSeq::Intron, Bio::LiveSeq::Mutation, Bio::LiveSeq::Mutator, Bio::LiveSeq::Prim_Transcript, Bio::LiveSeq::Range, Bio::LiveSeq::Repeat_Region, Bio::LiveSeq::Repeat_Unit, Bio::LiveSeq::SeqI, Bio::LiveSeq::Transcript, Bio::LiveSeq::Translation, Bio::Location::Atomic, Bio::Location::AvWithinCoordPolicy, Bio::Location::CoordinatePolicyI, Bio::Location::Fuzzy, Bio::Location::FuzzyLocationI, Bio::Location::NarrowestCoordPolicy, Bio::Location::Simple, Bio::Location::Split, Bio::Location::SplitLocationI, Bio::Location::WidestCoordPolicy, Bio::LocationI, Bio::Map::Clone, Bio::Map::Contig, Bio::Map::CytoMap, Bio::Map::CytoMarker, Bio::Map::CytoPosition, Bio::Map::EntityI, Bio::Map::FPCMarker, Bio::Map::Gene, Bio::Map::GeneMap, Bio::Map::GenePosition, Bio::Map::GeneRelative, Bio::Map::LinkageMap, Bio::Map::LinkagePosition, Bio::Map::MapI, Bio::Map::Mappable, Bio::Map::MappableI, Bio::Map::Marker, Bio::Map::MarkerI, Bio::Map::Microsatellite, Bio::Map::OrderedPosition, Bio::Map::OrderedPositionWithDistance, Bio::Map::Physical, Bio::Map::Position, Bio::Map::PositionHandler, Bio::Map::PositionHandlerI, Bio::Map::PositionI, Bio::Map::PositionWithSequence, Bio::Map::Prediction, Bio::Map::Relative, Bio::Map::RelativeI, Bio::Map::SimpleMap, Bio::Map::TranscriptionFactor, Bio::MapIO, Bio::MapIO::fpc, Bio::MapIO::mapmaker, Bio::Matrix::Generic, Bio::Matrix::IO, Bio::Matrix::IO::mlagan, Bio::Matrix::IO::phylip, Bio::Matrix::IO::scoring, Bio::Matrix::MatrixI, Bio::Matrix::Mlagan, Bio::Matrix::PSM::IO, Bio::Matrix::PSM::IO::mast, Bio::Matrix::PSM::IO::masta, Bio::Matrix::PSM::IO::meme, Bio::Matrix::PSM::IO::psiblast, Bio::Matrix::PSM::IO::transfac, Bio::Matrix::PSM::InstanceSite, Bio::Matrix::PSM::InstanceSiteI, Bio::Matrix::PSM::ProtMatrix, Bio::Matrix::PSM::ProtPsm, Bio::Matrix::PSM::Psm, Bio::Matrix::PSM::PsmHeader, Bio::Matrix::PSM::PsmHeaderI, Bio::Matrix::PSM::PsmI, Bio::Matrix::PSM::SiteMatrix, Bio::Matrix::PSM::SiteMatrixI, Bio::Matrix::PhylipDist, Bio::Matrix::Scoring, Bio::MolEvol::CodonModel, Bio::Nexml::Factory, Bio::NexmlIO, Bio::Ontology::DocumentRegistry, Bio::Ontology::GOterm, Bio::Ontology::InterProTerm, Bio::Ontology::OBOEngine, Bio::Ontology::OBOterm, Bio::Ontology::Ontology, Bio::Ontology::OntologyEngineI, Bio::Ontology::OntologyI, Bio::Ontology::OntologyStore, Bio::Ontology::Path, Bio::Ontology::PathI, Bio::Ontology::Relationship, Bio::Ontology::RelationshipFactory, Bio::Ontology::RelationshipI, Bio::Ontology::RelationshipType, Bio::Ontology::SimpleGOEngine::GraphAdaptor, Bio::Ontology::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::PrimarySeq::Fasta, Bio::PrimarySeqI, Bio::PullParserI, Bio::Range, Bio::RangeI, Bio::Restriction::Analysis, Bio::Restriction::Enzyme::MultiCut, Bio::Restriction::Enzyme::MultiSite, Bio::Restriction::EnzymeCollection, Bio::Restriction::EnzymeI, Bio::Restriction::IO, Bio::Restriction::IO::bairoch, Bio::Restriction::IO::base, Bio::Restriction::IO::itype2, Bio::Restriction::IO::prototype, Bio::Root::Exception, Bio::Root::IO, Bio::Root::Root, Bio::Root::RootI, Bio::Root::Storable, Bio::Root::TestObject, Bio::Root::Utilities, Bio::Root::Version, Bio::Search::BlastStatistics, Bio::Search::BlastUtils, Bio::Search::DatabaseI, Bio::Search::GenericDatabase, Bio::Search::GenericStatistics, Bio::Search::HSP::BlastHSP, Bio::Search::HSP::BlastPullHSP, Bio::Search::HSP::FastaHSP, Bio::Search::HSP::GenericHSP, Bio::Search::HSP::HMMERHSP, Bio::Search::HSP::HSPFactory, Bio::Search::HSP::HmmpfamHSP, Bio::Search::HSP::ModelHSP, Bio::Search::HSP::PSLHSP, Bio::Search::HSP::PsiBlastHSP, Bio::Search::HSP::PullHSPI, Bio::Search::HSP::WABAHSP, Bio::Search::Hit::BlastHit, Bio::Search::Hit::BlastPullHit, Bio::Search::Hit::Fasta, Bio::Search::Hit::GenericHit, Bio::Search::Hit::HMMERHit, Bio::Search::Hit::HitFactory, Bio::Search::Hit::HitI, Bio::Search::Hit::HmmpfamHit, Bio::Search::Hit::ModelHit, Bio::Search::Hit::PsiBlastHit, Bio::Search::Hit::PullHitI, Bio::Search::Hit::hmmer3Hit, Bio::Search::Iteration::GenericIteration, Bio::Search::Iteration::IterationI, Bio::Search::Processor, Bio::Search::Result::BlastPullResult, Bio::Search::Result::BlastResult, Bio::Search::Result::CrossMatchResult, Bio::Search::Result::GenericResult, Bio::Search::Result::HMMERResult, Bio::Search::Result::HmmpfamResult, Bio::Search::Result::PullResultI, Bio::Search::Result::ResultFactory, Bio::Search::Result::ResultI, Bio::Search::Result::WABAResult, Bio::Search::Result::hmmer3Result, Bio::Search::SearchUtils, Bio::Search::StatisticsI, Bio::SearchDist, Bio::SearchIO::EventHandlerI, Bio::SearchIO::FastHitEventBuilder, Bio::SearchIO::IteratedSearchResultEventBuilder, Bio::SearchIO::SearchResultEventBuilder, Bio::SearchIO::SearchWriterI, 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::blast_pull, Bio::SearchIO::blasttable, Bio::SearchIO::cross_match, Bio::SearchIO::erpin, Bio::SearchIO::exonerate, Bio::SearchIO::fasta, Bio::SearchIO::hmmer, Bio::SearchIO::hmmer2, Bio::SearchIO::hmmer3, Bio::SearchIO::hmmer_pull, Bio::SearchIO::infernal, Bio::SearchIO::megablast, Bio::SearchIO::psl, Bio::SearchIO::rnamotif, Bio::SearchIO::sim4, Bio::SearchIO::waba, Bio::SearchIO::wise, Bio::Seq, Bio::Seq::BaseSeqProcessor, Bio::Seq::EncodedSeq, Bio::Seq::LargeLocatableSeq, Bio::Seq::LargePrimarySeq, Bio::Seq::LargeSeq, Bio::Seq::LargeSeqI, Bio::Seq::Meta, Bio::Seq::Meta::Array, Bio::Seq::MetaI, Bio::Seq::PrimaryQual, Bio::Seq::PrimaryQual::Qual, Bio::Seq::PrimedSeq, Bio::Seq::QualI, Bio::Seq::Quality, Bio::Seq::RichSeq, Bio::Seq::RichSeqI, Bio::Seq::SeqBuilder, Bio::Seq::SeqFactory, Bio::Seq::SeqFastaSpeedFactory, Bio::Seq::SeqWithQuality, Bio::Seq::SequenceTrace, Bio::Seq::TraceI, Bio::SeqAnalysisParserI, Bio::SeqEvolution::DNAPoint, Bio::SeqEvolution::EvolutionI, Bio::SeqEvolution::Factory, Bio::SeqFeature::Amplicon, Bio::SeqFeature::AnnotationAdaptor, Bio::SeqFeature::Collection, Bio::SeqFeature::CollectionI, Bio::SeqFeature::Computation, Bio::SeqFeature::FeaturePair, Bio::SeqFeature::Gene::Exon, Bio::SeqFeature::Gene::ExonI, Bio::SeqFeature::Gene::GeneStructure, Bio::SeqFeature::Gene::GeneStructureI, Bio::SeqFeature::Gene::Intron, Bio::SeqFeature::Gene::NC_Feature, Bio::SeqFeature::Gene::Poly_A_site, Bio::SeqFeature::Gene::Promoter, Bio::SeqFeature::Gene::Transcript, Bio::SeqFeature::Gene::TranscriptI, Bio::SeqFeature::Gene::UTR, Bio::SeqFeature::Generic, Bio::SeqFeature::Lite, Bio::SeqFeature::PositionProxy, Bio::SeqFeature::Primer, Bio::SeqFeature::Similarity, Bio::SeqFeature::SimilarityPair, Bio::SeqFeature::SubSeq, 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::FTHelper, Bio::SeqIO::MultiFile, Bio::SeqIO::abi, Bio::SeqIO::ace, Bio::SeqIO::agave, Bio::SeqIO::alf, Bio::SeqIO::asciitree, Bio::SeqIO::bsml, Bio::SeqIO::bsml_sax, Bio::SeqIO::chadoxml, Bio::SeqIO::chaos, Bio::SeqIO::chaosxml, Bio::SeqIO::ctf, Bio::SeqIO::embl, Bio::SeqIO::embldriver, Bio::SeqIO::entrezgene, Bio::SeqIO::excel, Bio::SeqIO::exp, Bio::SeqIO::fastq, Bio::SeqIO::flybase_chadoxml, Bio::SeqIO::game, Bio::SeqIO::game::featHandler, Bio::SeqIO::game::gameHandler, Bio::SeqIO::game::gameSubs, Bio::SeqIO::game::gameWriter, Bio::SeqIO::game::seqHandler, Bio::SeqIO::gbxml, Bio::SeqIO::gcg, Bio::SeqIO::genbank, Bio::SeqIO::interpro, Bio::SeqIO::kegg, Bio::SeqIO::largefasta, Bio::SeqIO::lasergene, Bio::SeqIO::locuslink, Bio::SeqIO::mbsout, Bio::SeqIO::metafasta, Bio::SeqIO::msout, Bio::SeqIO::nexml, Bio::SeqIO::phd, Bio::SeqIO::pir, Bio::SeqIO::pln, Bio::SeqIO::qual, Bio::SeqIO::raw, Bio::SeqIO::scf, Bio::SeqIO::seqxml, Bio::SeqIO::swiss, Bio::SeqIO::swissdriver, Bio::SeqIO::tab, Bio::SeqIO::table, Bio::SeqIO::tigr, Bio::SeqIO::tigrxml, Bio::SeqIO::tinyseq, Bio::SeqIO::ztr, Bio::SimpleAnalysisI, 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::NetPhos, Bio::Tools::Analysis::Protein::Scansite, Bio::Tools::Analysis::Protein::Sopma, Bio::Tools::Analysis::SimpleAnalysisBase, Bio::Tools::AnalysisResult, Bio::Tools::Blat, Bio::Tools::CodonTable, Bio::Tools::Coil, Bio::Tools::ECnumber, Bio::Tools::EMBOSS::Palindrome, Bio::Tools::EPCR, Bio::Tools::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::HMMER::Domain, Bio::Tools::HMMER::Results, Bio::Tools::HMMER::Set, Bio::Tools::Hmmpfam, Bio::Tools::IUPAC, Bio::Tools::Lucy, Bio::Tools::MZEF, Bio::Tools::Match, Bio::Tools::OddCodes, Bio::Tools::Phylo::Gerp, Bio::Tools::Phylo::Gumby, Bio::Tools::Phylo::Molphy, Bio::Tools::Phylo::Molphy::Result, Bio::Tools::Phylo::PAML, Bio::Tools::Phylo::PAML::Codeml, Bio::Tools::Phylo::PAML::ModelResult, Bio::Tools::Phylo::PAML::Result, Bio::Tools::Phylo::Phylip::ProtDist, Bio::Tools::Prediction::Exon, Bio::Tools::Prediction::Gene, Bio::Tools::Primer3, Bio::Tools::Primer::Assessor::Base, Bio::Tools::Primer::AssessorI, Bio::Tools::Primer::Feature, Bio::Tools::Primer::Pair, Bio::Tools::Prints, Bio::Tools::Profile, Bio::Tools::Promoterwise, Bio::Tools::PrositeScan, Bio::Tools::Protparam, Bio::Tools::Pseudowise, Bio::Tools::QRNA, Bio::Tools::RandomDistFunctions, Bio::Tools::RepeatMasker, Bio::Tools::Run::GenericParameters, Bio::Tools::Run::ParametersI, Bio::Tools::Seg, Bio::Tools::SeqPattern, Bio::Tools::SeqStats, Bio::Tools::SeqWords, Bio::Tools::Sigcleave, Bio::Tools::Signalp, Bio::Tools::Signalp::ExtendedSignalp, Bio::Tools::Sim4::Exon, Bio::Tools::Sim4::Results, Bio::Tools::Spidey::Exon, Bio::Tools::Spidey::Results, Bio::Tools::TandemRepeatsFinder, Bio::Tools::TargetP, Bio::Tools::Tmhmm, Bio::Tools::dpAlign, Bio::Tools::ipcress, Bio::Tools::isPcr, Bio::Tools::pICalculator, Bio::Tools::pSW, Bio::Tools::tRNAscanSE, Bio::Tree::AlleleNode, Bio::Tree::AnnotatableNode, Bio::Tree::Compatible, Bio::Tree::DistanceFactory, Bio::Tree::Draw::Cladogram, Bio::Tree::Node, Bio::Tree::NodeI, Bio::Tree::NodeNHX, Bio::Tree::RandomFactory, Bio::Tree::Statistics, Bio::Tree::Tree, Bio::Tree::TreeFunctionsI, Bio::Tree::TreeI, Bio::TreeIO, Bio::TreeIO::NewickParser, Bio::TreeIO::TreeEventBuilder, Bio::TreeIO::cluster, Bio::TreeIO::lintree, Bio::TreeIO::newick, Bio::TreeIO::nexml, Bio::TreeIO::nexus, Bio::TreeIO::nhx, Bio::TreeIO::pag, Bio::TreeIO::phyloxml, Bio::TreeIO::svggraph, Bio::TreeIO::tabtree, Bio::UpdateableSeqI, Bio::Variation::AAChange, Bio::Variation::AAReverseMutate, Bio::Variation::Allele, Bio::Variation::DNAMutation, Bio::Variation::IO, Bio::Variation::IO::flat, Bio::Variation::IO::xml, Bio::Variation::RNAChange, Bio::Variation::SNP, Bio::Variation::SeqDiff, Bio::Variation::VariantI, Bio::WebAgent

meta_yml_has_repository_resource

Add a 'repository' resource to the META.yml via 'meta_add' accessor (for Module::Build) or META_ADD parameter (for ExtUtils::MakeMaker).

Modules

Name Abstract Version View
Bio::Align::AlignI An interface for describing sequence alignments. metacpan
Bio::Align::DNAStatistics Calculate some statistics for a DNA alignment metacpan
Bio::Align::Graphics Graphic Rendering of Bio::Align::AlignI Objects metacpan
Bio::Align::PairwiseStatistics Base statistic object for Pairwise Alignments metacpan
Bio::Align::ProteinStatistics Calculate Protein Alignment statistics (mostly distances) metacpan
Bio::Align::StatisticsI Calculate some statistics for an alignment metacpan
Bio::Align::Utilities A collection of utilities regarding converting and manipulating alignment objects metacpan
Bio::AlignIO Handler for AlignIO Formats metacpan
Bio::AlignIO::Handler::GenericAlignHandler Bio::HandlerI-based generic data handler class for alignment-based data metacpan
Bio::AlignIO::arp ARP MSA Sequence input/output stream metacpan
Bio::AlignIO::bl2seq bl2seq sequence input/output stream metacpan
Bio::AlignIO::clustalw clustalw sequence input/output stream metacpan
Bio::AlignIO::emboss Parse EMBOSS alignment output (from applications water and needle) metacpan
Bio::AlignIO::fasta fasta MSA Sequence input/output stream metacpan
Bio::AlignIO::largemultifasta Largemultifasta MSA Sequence input/output stream metacpan
Bio::AlignIO::maf Multiple Alignment Format sequence input stream metacpan
Bio::AlignIO::mase mase sequence input/output stream metacpan
Bio::AlignIO::mega Parse and Create MEGA format data files metacpan
Bio::AlignIO::meme meme sequence input/output stream metacpan
Bio::AlignIO::metafasta Metafasta MSA Sequence input/output stream metacpan
Bio::AlignIO::msf msf sequence input/output stream metacpan
Bio::AlignIO::nexml NeXML format sequence alignment input/output stream driver metacpan
Bio::AlignIO::nexus NEXUS format sequence input/output stream metacpan
Bio::AlignIO::pfam pfam sequence input/output stream metacpan
Bio::AlignIO::phylip PHYLIP format sequence input/output stream metacpan
Bio::AlignIO::po po MSA Sequence input/output stream metacpan
Bio::AlignIO::proda proda sequence input/output stream metacpan
Bio::AlignIO::prodom prodom sequence input/output stream metacpan
Bio::AlignIO::psi Read/Write PSI-BLAST profile alignment files metacpan
Bio::AlignIO::selex selex sequence input/output stream metacpan
Bio::AlignIO::stockholm stockholm sequence input/output stream metacpan
Bio::AlignIO::xmfa XMFA MSA Sequence input/output stream metacpan
Bio::AnalysisI An interface to any (local or remote) analysis tool metacpan
Bio::AnalysisI::JobI metacpan
Bio::AnalysisParserI Generic analysis output parser interface metacpan
Bio::AnalysisResultI Interface for analysis result objects metacpan
Bio::AnnotatableI the base interface an annotatable object must implement metacpan
Bio::Annotation::AnnotationFactory Instantiates a new Bio::AnnotationI (or derived class) through a factory metacpan
Bio::Annotation::Collection Default Perl implementation of AnnotationCollectionI metacpan
Bio::Annotation::Comment A comment object, holding text metacpan
Bio::Annotation::DBLink untyped links between databases metacpan
Bio::Annotation::OntologyTerm An ontology term adapted to AnnotationI metacpan
Bio::Annotation::Reference Specialised DBLink object for Literature References metacpan
Bio::Annotation::Relation Relationship (pairwise) with other objects SeqI and NodeI; metacpan
Bio::Annotation::SimpleValue A simple scalar metacpan
Bio::Annotation::StructuredValue A scalar with embedded structured information metacpan
Bio::Annotation::TagTree AnnotationI with tree-like hierarchal key-value relationships ('structured tags') that can be represented as simple text. metacpan
Bio::Annotation::Target Provides an object which represents a target (ie, a similarity hit) from one object to something in another database metacpan
Bio::Annotation::Tree Provide a tree as an annotation to a Bio::AnnotatableI object metacpan
Bio::Annotation::TypeManager Manages types for annotation collections metacpan
Bio::AnnotationCollectionI Interface for annotation collections metacpan
Bio::AnnotationI Annotation interface metacpan
Bio::Assembly::Contig Perl module to hold and manipulate sequence assembly contigs. metacpan
Bio::Assembly::ContigAnalysis metacpan
Bio::Assembly::IO Handler for Assembly::IO Formats metacpan
Bio::Assembly::IO::ace module to load ACE files from various assembly programs metacpan
Bio::Assembly::IO::bowtie An IO module for assemblies in Bowtie format *BETA* metacpan
Bio::Assembly::IO::maq Driver to read assembly files in maq format *BETA* metacpan
Bio::Assembly::IO::phrap driver to load phrap.out files. metacpan
Bio::Assembly::IO::sam An IO module for assemblies in Sam format *BETA* metacpan
Bio::Assembly::IO::tigr Driver to read and write assembly files in the TIGR Assembler v2 default format. metacpan
Bio::Assembly::Scaffold Perl module to hold and manipulate sequence assembly data. metacpan
Bio::Assembly::ScaffoldI Abstract Inteface of Sequence Assemblies metacpan
Bio::Assembly::Singlet Perl module to hold and manipulate singlets from sequence assembly contigs. metacpan
Bio::Assembly::Tools::ContigSpectrum create and manipulate contig spectra metacpan
Bio::Cluster::ClusterFactory Instantiates a new Bio::ClusterI (or derived class) through a factory metacpan
Bio::Cluster::FamilyI Family Interface metacpan
Bio::Cluster::SequenceFamily Sequence Family object metacpan
Bio::Cluster::UniGene UniGene object metacpan
Bio::Cluster::UniGeneI abstract interface of UniGene object metacpan
Bio::ClusterI Cluster Interface metacpan
Bio::ClusterIO Handler for Cluster Formats metacpan
Bio::ClusterIO::dbsnp dbSNP input stream metacpan
Bio::ClusterIO::unigene UniGene input stream metacpan
Bio::CodonUsage::IO for reading and writing codon usage tables to file metacpan
Bio::CodonUsage::Table for access to the Codon usage Database at http://www.kazusa.or.jp/codon. metacpan
Bio::DB::Ace Database object interface to ACeDB servers metacpan
Bio::DB::BioFetch Database object interface to BioFetch retrieval metacpan
Bio::DB::CUTG for access to the Codon usage Database at http://www.kazusa.or.jp/codon. metacpan
Bio::DB::DBFetch Database object for retrieving using the dbfetch script metacpan
Bio::DB::EMBL Database object interface for EMBL entry retrieval metacpan
Bio::DB::EntrezGene Database object interface to Entrez Gene metacpan
Bio::DB::Expression DESCRIPTION of Object metacpan
Bio::DB::Expression::geo *** DESCRIPTION of Class metacpan
Bio::DB::Failover A Bio::DB::RandomAccessI compliant class which wraps a prioritized list of DBs metacpan
Bio::DB::Fasta Fast indexed access to fasta files metacpan
Bio::DB::Fasta::Subdir metacpan
Bio::DB::FileCache In file cache for BioSeq objects metacpan
Bio::DB::Flat Interface for indexed flat files metacpan
Bio::DB::Flat::BDB Interface for BioHackathon standard BDB-indexed flat file metacpan
Bio::DB::Flat::BDB::embl embl adaptor for Open-bio standard BDB-indexed flat file metacpan
Bio::DB::Flat::BDB::fasta fasta adaptor for Open-bio standard BDB-indexed flat file metacpan
Bio::DB::Flat::BDB::genbank genbank adaptor for Open-bio standard BDB-indexed flat file metacpan
Bio::DB::Flat::BDB::swiss swissprot adaptor for Open-bio standard BDB-indexed flat file metacpan
Bio::DB::Flat::BinarySearch BinarySearch search indexing system for sequence files metacpan
Bio::DB::GFF Storage and retrieval of sequence annotation data metacpan
Bio::DB::GFF::Adaptor::ace ace interface (for multiple inheritance) metacpan
Bio::DB::GFF::Adaptor::berkeleydb Bio::DB::GFF database adaptor for in-memory databases metacpan
Bio::DB::GFF::Adaptor::berkeleydb::iterator iterator for Bio::DB::GFF::Adaptor::berkeleydb metacpan
Bio::DB::GFF::Adaptor::biofetch Cache BioFetch objects in a Bio::DB::GFF database metacpan
Bio::DB::GFF::Adaptor::biofetch_oracle Cache BioFetch objects in a Bio::DB::GFF database metacpan
Bio::DB::GFF::Adaptor::dbi Database adaptor for DBI (SQL) databases metacpan
Bio::DB::GFF::Adaptor::dbi::caching_handle Cache for database handles metacpan
Bio::DB::GFF::Adaptor::dbi::faux_dbh metacpan
Bio::DB::GFF::Adaptor::dbi::iterator iterator for Bio::DB::GFF::Adaptor::dbi metacpan
Bio::DB::GFF::Adaptor::dbi::mysql Database adaptor for a specific mysql schema metacpan
Bio::DB::GFF::Adaptor::dbi::mysqlace Unholy union between mysql GFF database and acedb database metacpan
Bio::DB::GFF::Adaptor::dbi::mysqlcmap Database adaptor for an integraded CMap/GBrowse mysql schema metacpan
Bio::DB::GFF::Adaptor::dbi::mysqlopt Deprecated database adaptor metacpan
Bio::DB::GFF::Adaptor::dbi::oracle Database adaptor for a specific oracle schema metacpan
Bio::DB::GFF::Adaptor::dbi::oracleace Unholy union between oracle GFF database and acedb database metacpan
Bio::DB::GFF::Adaptor::dbi::pg Database adaptor for a specific postgres schema metacpan
Bio::DB::GFF::Adaptor::dbi::pg_fts Database adaptor for a specific postgres schema with a TSearch2 implementation metacpan
Bio::DB::GFF::Adaptor::memory Bio::DB::GFF database adaptor for in-memory databases metacpan
Bio::DB::GFF::Adaptor::memory::feature_serializer utility methods for serializing and deserializing GFF features metacpan
Bio::DB::GFF::Adaptor::memory::iterator iterator for Bio::DB::GFF::Adaptor::memory metacpan
Bio::DB::GFF::Aggregator Aggregate GFF groups into composite features metacpan
Bio::DB::GFF::Aggregator::alignment Alignment aggregator metacpan
Bio::DB::GFF::Aggregator::clone Clone aggregator metacpan
Bio::DB::GFF::Aggregator::coding The Coding Region Aggregator metacpan
Bio::DB::GFF::Aggregator::gene Sequence Ontology Geene metacpan
Bio::DB::GFF::Aggregator::match Match aggregator metacpan
Bio::DB::GFF::Aggregator::none No aggregation metacpan
Bio::DB::GFF::Aggregator::orf An aggregator for orf regions metacpan
Bio::DB::GFF::Aggregator::processed_transcript Sequence Ontology Transcript metacpan
Bio::DB::GFF::Aggregator::so_transcript Sequence Ontology Transcript metacpan
Bio::DB::GFF::Aggregator::transcript Transcript aggregator metacpan
Bio::DB::GFF::Aggregator::ucsc_acembly UCSC acembly aggregator metacpan
Bio::DB::GFF::Aggregator::ucsc_ensgene UCSC ensGene aggregator metacpan
Bio::DB::GFF::Aggregator::ucsc_genscan UCSC genscan aggregator metacpan
Bio::DB::GFF::Aggregator::ucsc_refgene UCSC refGene aggregator metacpan
Bio::DB::GFF::Aggregator::ucsc_sanger22 UCSC sanger22 aggregator metacpan
Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo UCSC sanger22pseudo aggregator metacpan
Bio::DB::GFF::Aggregator::ucsc_softberry UCSC softberry aggregator metacpan
Bio::DB::GFF::Aggregator::ucsc_twinscan UCSC twinscan aggregator metacpan
Bio::DB::GFF::Aggregator::ucsc_unigene UCSC UniGene aggregator metacpan
Bio::DB::GFF::Featname The name of a feature metacpan
Bio::DB::GFF::Feature A relative segment identified by a feature type metacpan
Bio::DB::GFF::FeatureIterator metacpan
Bio::DB::GFF::Homol A segment of DNA that is homologous to another metacpan
Bio::DB::GFF::ID_Iterator metacpan
Bio::DB::GFF::RelSegment Sequence segment with relative coordinate support metacpan
Bio::DB::GFF::Segment Simple DNA segment object metacpan
Bio::DB::GFF::Typename The name of a feature type metacpan
Bio::DB::GFF::Util::Binning binning utility for Bio::DB::GFF index metacpan
Bio::DB::GFF::Util::Rearrange rearrange utility metacpan
Bio::DB::GenBank Database object interface to GenBank metacpan
Bio::DB::GenPept Database object interface to GenPept metacpan
Bio::DB::GenericWebAgent helper base class for parameter-based remote server access and response retrieval. metacpan
Bio::DB::HIV Database object interface to the Los Alamos HIV Sequence Database metacpan
Bio::DB::HIV::HIVAnnotProcessor metacpan
Bio::DB::HIV::HIVQueryHelper Routines and packages used by Bio::DB::HIV and Bio::DB::Query::HIVQuery metacpan
Bio::DB::InMemoryCache Abstract interface for a sequence database metacpan
Bio::DB::Indexed::Stream metacpan
Bio::DB::IndexedBase Base class for modules using indexed sequence files metacpan
Bio::DB::LocationI A RandomAccessI-like abstract interface for retrieving location data from a sequence database and returning Bio::LocationI objects metacpan
Bio::DB::MeSH Term retrieval from a Web MeSH database metacpan
Bio::DB::NCBIHelper A collection of routines useful for queries to NCBI databases. metacpan
Bio::DB::Qual Fast indexed access to quality files metacpan
Bio::DB::Query::GenBank Build a GenBank Entrez Query metacpan
Bio::DB::Query::HIVQuery Query interface to the Los Alamos HIV Sequence Database metacpan
Bio::DB::Query::WebQuery Helper class for web-based sequence queryies metacpan
Bio::DB::QueryI Object Interface to queryable sequence databases metacpan
Bio::DB::RandomAccessI Abstract interface for a sequence database metacpan
Bio::DB::RefSeq Database object interface for RefSeq retrieval metacpan
Bio::DB::ReferenceI A RandomAccessI-like abstract interface for retrieving Reference data from a sequence database and returning Bio::Annotation::Reference objects metacpan
Bio::DB::Registry Access to the Open Bio Database Access registry scheme metacpan
Bio::DB::SeqFeature Normalized feature for use with Bio::DB::SeqFeature::Store metacpan
Bio::DB::SeqFeature::NormalizedFeature Normalized feature for use with Bio::DB::SeqFeature::Store metacpan
Bio::DB::SeqFeature::NormalizedFeatureI Interface for normalized features metacpan
Bio::DB::SeqFeature::NormalizedTableFeatureI Interface for normalized features whose hierarchy is stored in a table metacpan
Bio::DB::SeqFeature::Segment Location-based access to genome annotation data metacpan
Bio::DB::SeqFeature::Store Storage and retrieval of sequence annotation data metacpan
Bio::DB::SeqFeature::Store::DBI::Iterator utility methods for creating and iterating over SeqFeature records metacpan
Bio::DB::SeqFeature::Store::DBI::Pg PostgreSQL implementation of Bio::DB::SeqFeature::Store metacpan
Bio::DB::SeqFeature::Store::DBI::SQLite SQLite implementation of Bio::DB::SeqFeature::Store metacpan
Bio::DB::SeqFeature::Store::DBI::mysql Mysql implementation of Bio::DB::SeqFeature::Store metacpan
Bio::DB::SeqFeature::Store::FeatureFileLoader feature file loader for Bio::DB::SeqFeature::Store metacpan
Bio::DB::SeqFeature::Store::FeatureIterator metacpan
Bio::DB::SeqFeature::Store::GFF2Loader GFF2 file loader for Bio::DB::SeqFeature::Store metacpan
Bio::DB::SeqFeature::Store::GFF3Loader GFF3 file loader for Bio::DB::SeqFeature::Store metacpan
Bio::DB::SeqFeature::Store::LoadHelper Internal utility for Bio::DB::SeqFeature::Store 1.11 metacpan
Bio::DB::SeqFeature::Store::Loader Loader metacpan
Bio::DB::SeqFeature::Store::bdb fetch and store objects from a BerkeleyDB metacpan
Bio::DB::SeqFeature::Store::berkeleydb Storage and retrieval of sequence annotation data in Berkeleydb files metacpan
Bio::DB::SeqFeature::Store::berkeleydb3 Storage and retrieval of sequence annotation data in Berkeleydb files metacpan
Bio::DB::SeqFeature::Store::berkeleydb::Iterator metacpan
Bio::DB::SeqFeature::Store::memory In-memory implementation of Bio::DB::SeqFeature::Store metacpan
Bio::DB::SeqFeature::Store::memory::Iterator metacpan
Bio::DB::SeqI Abstract Interface for Sequence databases metacpan
Bio::DB::SeqVersion front end to querying databases for identifier versions metacpan
Bio::DB::SeqVersion::gi interface to NCBI Sequence Revision History page metacpan
Bio::DB::SwissProt Database object interface to SwissProt retrieval metacpan
Bio::DB::TFBS Access to a Transcription Factor Binding Site database metacpan
Bio::DB::TFBS::transfac_pro An implementation of Bio::DB::TFBS which uses local flat files for transfac pro metacpan
Bio::DB::Taxonomy Access to a taxonomy database metacpan
Bio::DB::Taxonomy::entrez Taxonomy Entrez driver metacpan
Bio::DB::Taxonomy::flatfile Use the NCBI taxonomy from local indexed flat files metacpan
Bio::DB::Taxonomy::greengenes Use the Greengenes taxonomy metacpan
Bio::DB::Taxonomy::list An implementation of Bio::DB::Taxonomy that accepts lists of words to build a database metacpan
Bio::DB::Taxonomy::silva Use the Silva taxonomy metacpan
Bio::DB::Taxonomy::sqlite SQLite-based implementation of Bio::DB::Taxonomy::flatfile metacpan
Bio::DB::Universal Artificial database that delegates to specific databases metacpan
Bio::DB::UpdateableSeqI An interface for writing to a database of sequences. metacpan
Bio::DB::WebDBSeqI Object Interface to generalize Web Databases for retrieving sequences metacpan
Bio::DBLinkContainerI Abstract interface for any object wanting to use database cross references metacpan
Bio::Das::FeatureTypeI Simple interface to Sequence Ontology feature types metacpan
Bio::Das::SegmentI DAS-style access to a feature database metacpan
Bio::DasI DAS-style access to a feature database metacpan
Bio::DescribableI interface for objects with human readable names and descriptions metacpan
Bio::Draw::Pictogram generate SVG output of Pictogram display for consensus motifs metacpan
Bio::Event::EventGeneratorI This interface describes the basic event generator class. metacpan
Bio::Event::EventHandlerI An Event Handler Interface metacpan
Bio::Factory::AnalysisI An interface to analysis tool factory metacpan
Bio::Factory::ApplicationFactoryI Interface class for Application Factories metacpan
Bio::Factory::DriverFactory Base class for factory classes loading drivers metacpan
Bio::Factory::FTLocationFactory A FeatureTable Location Parser metacpan
Bio::Factory::LocationFactoryI A factory interface for generating locations from a string metacpan
Bio::Factory::MapFactoryI A Factory for getting markers metacpan
Bio::Factory::ObjectBuilderI Interface for an object builder metacpan
Bio::Factory::ObjectFactory Instantiates a new Bio::Root::RootI (or derived class) through a factory metacpan
Bio::Factory::ObjectFactoryI A General object creator factory metacpan
Bio::Factory::SeqAnalysisParserFactory class capable of creating SeqAnalysisParserI compliant parsers metacpan
Bio::Factory::SeqAnalysisParserFactoryI interface describing objects capable of creating SeqAnalysisParserI compliant parsers metacpan
Bio::Factory::SequenceFactoryI This interface allows for generic building of sequences in factories which create sequences (like SeqIO) metacpan
Bio::Factory::SequenceProcessorI Interface for chained sequence processing algorithms metacpan
Bio::Factory::SequenceStreamI Interface describing the basics of a Sequence Stream. metacpan
Bio::Factory::TreeFactoryI Factory Interface for getting and writing trees from/to a data stream metacpan
Bio::FeatureHolderI the base interface an object with features must implement metacpan
Bio::HandlerBaseI Interface class for handler methods which interact with any event-driven parsers (drivers). metacpan
Bio::IdCollectionI interface for objects with multiple identifiers metacpan
Bio::IdentifiableI interface for objects with identifiers metacpan
Bio::Index::Abstract Abstract interface for indexing a flat file metacpan
Bio::Index::AbstractSeq base class for AbstractSeq metacpan
Bio::Index::Blast Indexes Blast reports and supports retrieval based on query accession(s) metacpan
Bio::Index::BlastTable Indexes tabular Blast reports (-m 8 or -m 9 format) and supports retrieval based on query accession(s) metacpan
Bio::Index::EMBL Interface for indexing (multiple) EMBL/Swissprot .dat files (i.e. flat file EMBL/Swissprot format). metacpan
Bio::Index::Fasta Interface for indexing (multiple) fasta files metacpan
Bio::Index::Fastq Interface for indexing (multiple) fastq files metacpan
Bio::Index::GenBank Interface for indexing one or more GenBank files (i.e. flat file GenBank format). metacpan
Bio::Index::Hmmer indexes HMMER reports and supports retreival based on query metacpan
Bio::Index::Qual Interface for indexing (multiple) fasta qual files metacpan
Bio::Index::Stockholm metacpan
Bio::Index::SwissPfam Interface for indexing swisspfam files metacpan
Bio::Index::Swissprot Interface for indexing one or more Swissprot files. metacpan
Bio::LiveSeq::AARange AARange abstract class for LiveSeq metacpan
Bio::LiveSeq::Chain DoubleChain DataStructure for Perl metacpan
Bio::LiveSeq::ChainI Double linked chain data structure metacpan
Bio::LiveSeq::DNA DNA object for LiveSeq metacpan
Bio::LiveSeq::Exon Range abstract class for LiveSeq metacpan
Bio::LiveSeq::Gene Range abstract class for LiveSeq metacpan
Bio::LiveSeq::IO::BioPerl Loader for LiveSeq from EMBL entries with BioPerl metacpan
Bio::LiveSeq::IO::Loader Parent Loader for LiveSeq metacpan
Bio::LiveSeq::Intron Range abstract class for LiveSeq metacpan
Bio::LiveSeq::Mutation Mutation event descriptor class metacpan
Bio::LiveSeq::Mutator Package mutating LiveSequences metacpan
Bio::LiveSeq::Prim_Transcript Prim_Transcript class for LiveSeq metacpan
Bio::LiveSeq::Range Range abstract class for LiveSeq metacpan
Bio::LiveSeq::Repeat_Region Repeat_Region class for LiveSeq metacpan
Bio::LiveSeq::Repeat_Unit Repeat_Unit class for LiveSeq metacpan
Bio::LiveSeq::SeqI Abstract sequence interface class for LiveSeq metacpan
Bio::LiveSeq::Transcript Transcript class for LiveSeq metacpan
Bio::LiveSeq::Translation Translation class for LiveSeq metacpan
Bio::LocatableSeq metacpan
Bio::Location::Atomic Implementation of a Atomic Location on a Sequence metacpan
Bio::Location::AvWithinCoordPolicy class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise metacpan
Bio::Location::CoordinatePolicyI Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location metacpan
Bio::Location::Fuzzy Implementation of a Location on a Sequence which has unclear start and/or end locations metacpan
Bio::Location::FuzzyLocationI Abstract interface of a Location on a Sequence which has unclear start/end location metacpan
Bio::Location::NarrowestCoordPolicy class implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range metacpan
Bio::Location::Simple Implementation of a Simple Location on a Sequence metacpan
Bio::Location::Split Implementation of a Location on a Sequence which has multiple locations (start/end points) metacpan
Bio::Location::SplitLocationI Abstract interface of a Location on a Sequence which has multiple locations (start/end points) metacpan
Bio::Location::WidestCoordPolicy class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable range metacpan
Bio::LocationI Abstract interface of a Location on a Sequence metacpan
Bio::Map::Clone An central map object representing a clone metacpan
Bio::Map::Contig A MapI implementation handling the contigs of a Physical Map (such as FPC) metacpan
Bio::Map::CytoMap A Bio::MapI compliant map implementation handling cytogenic bands metacpan
Bio::Map::CytoMarker An object representing a marker. metacpan
Bio::Map::CytoPosition Marker class with cytogenetic band storing attributes metacpan
Bio::Map::EntityI An Entity Interface metacpan
Bio::Map::FPCMarker An central map object representing a marker metacpan
Bio::Map::Gene An gene modelled as a mappable element. metacpan
Bio::Map::GeneMap A MapI implementation to represent the area around a gene metacpan
Bio::Map::GenePosition A typed position, suitable for modelling the various regions of a gene. metacpan
Bio::Map::GeneRelative Represents being relative to named sub-regions of a gene. metacpan
Bio::Map::LinkageMap A representation of a genetic linkage map. metacpan
Bio::Map::LinkagePosition Create a Position for a Marker that will be placed on a Bio::Map::LinkageMap metacpan
Bio::Map::MapI Interface for describing Map objects in bioperl metacpan
Bio::Map::Mappable An object representing a generic map element that can have multiple locations in several maps. metacpan
Bio::Map::MappableI An object that can be placed in a map metacpan
Bio::Map::Marker An central map object representing a generic marker that can have multiple location in several maps. metacpan
Bio::Map::MarkerI Interface for basic marker functionality metacpan
Bio::Map::Microsatellite An object representing a Microsatellite marker. metacpan
Bio::Map::OrderedPosition Abstracts the notion of a member of an ordered list of markers. Each marker is a certain distance from the one in the ordered list before it. metacpan
Bio::Map::OrderedPositionWithDistance Abstracts the notion of a member of an ordered list of markers. Each marker is a certain distance from the one in the ordered list before it. metacpan
Bio::Map::Physical A class for handling a Physical Map (such as FPC) metacpan
Bio::Map::Position A single position of a Marker, or the range over which that marker lies, in a Map metacpan
Bio::Map::PositionHandler A Position Handler Implementation metacpan
Bio::Map::PositionHandlerI A Position Handler Interface metacpan
Bio::Map::PositionI Abstracts the notion of a position having a value in the context of a marker and a Map metacpan
Bio::Map::PositionWithSequence A position with a sequence. metacpan
Bio::Map::Prediction An object representing the predictions of something that can have multiple locations in several maps. metacpan
Bio::Map::Relative Represents what a Position's coordiantes are relative to. metacpan
Bio::Map::RelativeI Interface for describing what a Position's coordiantes are relative to. metacpan
Bio::Map::SimpleMap A MapI implementation handling the basics of a Map metacpan
Bio::Map::TranscriptionFactor A transcription factor modelled as a mappable element metacpan
Bio::MapIO A Map Factory object metacpan
Bio::MapIO::fpc A FPC Map reader metacpan
Bio::MapIO::mapmaker A Mapmaker Map reader metacpan
Bio::Matrix::Generic A generic matrix implementation metacpan
Bio::Matrix::IO A factory for Matrix parsing metacpan
Bio::Matrix::IO::mlagan A parser for the mlagan substitution matrix metacpan
Bio::Matrix::IO::phylip A parser for PHYLIP distance matricies metacpan
Bio::Matrix::IO::scoring A parser for PAM/BLOSUM matricies metacpan
Bio::Matrix::MatrixI An interface for describing a Matrix metacpan
Bio::Matrix::Mlagan A generic matrix with mlagan fields metacpan
Bio::Matrix::PSM::IO PSM parser metacpan
Bio::Matrix::PSM::IO::mast PSM mast parser implementation metacpan
Bio::Matrix::PSM::IO::masta motif fasta format parser metacpan
Bio::Matrix::PSM::IO::meme PSM meme parser implementation metacpan
Bio::Matrix::PSM::IO::psiblast PSM psiblast parser metacpan
Bio::Matrix::PSM::IO::transfac PSM transfac parser metacpan
Bio::Matrix::PSM::InstanceSite A PSM site occurance metacpan
Bio::Matrix::PSM::InstanceSiteI InstanceSite interface, holds an instance of a PSM metacpan
Bio::Matrix::PSM::ProtMatrix SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) with log-odds scoring information. metacpan
Bio::Matrix::PSM::ProtPsm handle combination of site matricies metacpan
Bio::Matrix::PSM::Psm handle combination of site matricies metacpan
Bio::Matrix::PSM::PsmHeader PSM mast parser implementation metacpan
Bio::Matrix::PSM::PsmHeaderI handles the header data from a PSM file metacpan
Bio::Matrix::PSM::PsmI abstract interface to handler of site matricies metacpan
Bio::Matrix::PSM::SiteMatrix SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds metacpan
Bio::Matrix::PSM::SiteMatrixI SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds metacpan
Bio::Matrix::PhylipDist A Phylip Distance Matrix object metacpan
Bio::Matrix::Scoring Object which can hold scoring matrix information metacpan
Bio::MolEvol::CodonModel Codon Evolution Models metacpan
Bio::Nexml::Factory A factory module for creating BioPerl and Bio::Phylo objects from/to nexml documents metacpan
Bio::NexmlIO stream handler for NeXML documents metacpan
Bio::Ontology::DocumentRegistry Keep track of where to find ontologies. Allows lookups by name. metacpan
Bio::Ontology::GOterm representation of GO terms metacpan
Bio::Ontology::InterProTerm Implementation of InterProI term interface metacpan
Bio::Ontology::OBOEngine An Ontology Engine for OBO style flat file format from the Gene Ontology Consortium metacpan
Bio::Ontology::OBOterm representation of OBO terms metacpan
Bio::Ontology::Ontology standard implementation of an Ontology metacpan
Bio::Ontology::OntologyEngineI Interface a minimal Ontology implementation should satisfy metacpan
Bio::Ontology::OntologyI Interface for an ontology implementation metacpan
Bio::Ontology::OntologyStore A repository of ontologies metacpan
Bio::Ontology::Path a path for an ontology term graph metacpan
Bio::Ontology::PathI Interface for a path between ontology terms metacpan
Bio::Ontology::Relationship a relationship for an ontology metacpan
Bio::Ontology::RelationshipFactory Instantiates a new Bio::Ontology::RelationshipI (or derived class) through a factory metacpan
Bio::Ontology::RelationshipI Interface for a relationship between ontology terms metacpan
Bio::Ontology::RelationshipType a relationship type for an ontology metacpan
Bio::Ontology::SimpleGOEngine::GraphAdaptor Graph adaptor for Bio::Ontology::SimpleGOEngine metacpan
Bio::Ontology::SimpleOntologyEngine Implementation of OntologyEngineI interface metacpan
Bio::Ontology::Term implementation of the interface for ontology terms metacpan
Bio::Ontology::TermFactory Instantiates a new Bio::Ontology::TermI (or derived class) through a factory metacpan
Bio::Ontology::TermI interface for ontology terms metacpan
Bio::OntologyIO Parser factory for Ontology formats metacpan
Bio::OntologyIO::Handlers::BaseSAXHandler metacpan
Bio::OntologyIO::Handlers::InterProHandler XML handler class for InterProParser metacpan
Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler parse an InterPro XML file and persist the resulting terms to a Biosql database metacpan
Bio::OntologyIO::InterProParser Parser for InterPro xml files. metacpan
Bio::OntologyIO::dagflat a base class parser for GO flat-file type formats metacpan
Bio::OntologyIO::goflat a parser for the Gene Ontology flat-file format metacpan
Bio::OntologyIO::obo metacpan
Bio::OntologyIO::simplehierarchy a base class parser for simple hierarchy-by-indentation type formats metacpan
Bio::OntologyIO::soflat a parser for the Sequence Ontology flat-file format metacpan
Bio::ParameterBaseI Simple interface class for any parameter-related data such as IDs, database name, program arguments, and other odds and ends. metacpan
Bio::Perl Functional access to BioPerl for people who don't know objects metacpan
Bio::Phenotype::Correlate Representation of a correlating phenotype in a given species metacpan
Bio::Phenotype::MeSH::Term A MeSH term metacpan
Bio::Phenotype::MeSH::Twig Context for a MeSH term metacpan
Bio::Phenotype::Measure Representation of context/value(-range)/unit triplets metacpan
Bio::Phenotype::OMIM::MiniMIMentry Representation of a Mini MIM entry metacpan
Bio::Phenotype::OMIM::OMIMentry represents OMIM (Online Mendelian Inheritance in Man) database entries metacpan
Bio::Phenotype::OMIM::OMIMentryAllelicVariant Representation of a allelic variant of the OMIM database metacpan
Bio::Phenotype::OMIM::OMIMparser parser for the OMIM database metacpan
Bio::Phenotype::Phenotype A class for modeling phenotypes metacpan
Bio::Phenotype::PhenotypeI An interface for classes modeling phenotypes metacpan
Bio::PhyloNetwork Module to compute with Phylogenetic Networks metacpan
Bio::PhyloNetwork::Factory Module to sequentially generate Phylogenetic Networks metacpan
Bio::PhyloNetwork::FactoryX Module to sequentially generate Phylogenetic Networks metacpan
Bio::PhyloNetwork::GraphViz Interface between PhyloNetwork and GraphViz metacpan
Bio::PhyloNetwork::RandomFactory Module to generate random Phylogenetic Networks metacpan
Bio::PhyloNetwork::TreeFactory Module to sequentially generate Phylogenetic Trees metacpan
Bio::PhyloNetwork::TreeFactoryMulti Module to sequentially generate Phylogenetic Trees metacpan
Bio::PhyloNetwork::TreeFactoryX Module to sequentially generate Phylogenetic Trees metacpan
Bio::PhyloNetwork::muVector Module to compute with vectors of arbitrary dimension metacpan
Bio::PopGen::Genotype An implementation of GenotypeI which is just an allele container metacpan
Bio::PopGen::GenotypeI A marker and alleles for a specific individual metacpan
Bio::PopGen::HtSNP metacpan
Bio::PopGen::IO Input individual,marker,allele information metacpan
Bio::PopGen::IO::csv metacpan
Bio::PopGen::IO::hapmap A parser for HapMap output data metacpan
Bio::PopGen::IO::phase A parser for Phase format data metacpan
Bio::PopGen::IO::prettybase Extract individual allele data from PrettyBase format metacpan
Bio::PopGen::Individual An implementation of an Individual who has Genotype or Sequence Results metacpan
Bio::PopGen::IndividualI An individual who has Genotype or Sequence Results metacpan
Bio::PopGen::Marker A genetic marker which one uses to generate genotypes metacpan
Bio::PopGen::MarkerI A Population Genetic conceptual marker metacpan
Bio::PopGen::PopStats A collection of methods for calculating statistics about a population or sets of populations metacpan
Bio::PopGen::Population A population of individuals metacpan
Bio::PopGen::PopulationI Interface for Populations metacpan
Bio::PopGen::Simulation::Coalescent A Coalescent simulation factory metacpan
Bio::PopGen::Simulation::GeneticDrift A simple genetic drift simulation metacpan
Bio::PopGen::Statistics Population Genetics statistical tests metacpan
Bio::PopGen::TagHaplotype metacpan
Bio::PopGen::Utilities Utilities for working with PopGen data and objects metacpan
Bio::PrimarySeq Bioperl lightweight sequence object metacpan
Bio::PrimarySeq::Fasta metacpan
Bio::PrimarySeqI Interface definition for a Bio::PrimarySeq metacpan
Bio::PullParserI A base module for fast 'pull' parsing metacpan
Bio::Range Pure perl RangeI implementation metacpan
Bio::RangeI Range interface metacpan
Bio::Restriction::Analysis cutting sequences with restriction enzymes metacpan
Bio::Restriction::Enzyme A single restriction endonuclease (cuts DNA at specific locations) metacpan
Bio::Restriction::Enzyme::MultiCut A single restriction endonuclease metacpan
Bio::Restriction::Enzyme::MultiSite A single restriction endonuclease metacpan
Bio::Restriction::EnzymeCollection Set of restriction endonucleases metacpan
Bio::Restriction::EnzymeI Interface class for restriction endonuclease metacpan
Bio::Restriction::IO Handler for sequence variation IO Formats metacpan
Bio::Restriction::IO::bairoch bairoch enzyme set metacpan
Bio::Restriction::IO::base base enzyme set metacpan
Bio::Restriction::IO::itype2 itype2 enzyme set metacpan
Bio::Restriction::IO::prototype prototype enzyme set metacpan
Bio::Restriction::IO::withrefm withrefm enzyme set metacpan
Bio::Root::Build 1.007000_005 metacpan
Bio::Root::Exception metacpan
Bio::Root::HTTPget module for fallback HTTP get operations when LWP:: is unavailable metacpan
Bio::Root::IO metacpan
Bio::Root::Root metacpan
Bio::Root::RootI metacpan
Bio::Root::Storable metacpan
Bio::Root::Test metacpan
Bio::Root::TestObject metacpan
Bio::Root::Utilities metacpan
Bio::Root::Version 1.007000_005 metacpan
Bio::Search::BlastStatistics An object for Blast statistics metacpan
Bio::Search::BlastUtils Utility functions for Bio::Search:: BLAST objects metacpan
Bio::Search::DatabaseI Interface for a database used in a sequence search metacpan
Bio::Search::GenericDatabase Generic implementation of Bio::Search::DatabaseI metacpan
Bio::Search::GenericStatistics An object for statistics metacpan
Bio::Search::HSP::BlastHSP Bioperl BLAST High-Scoring Pair object metacpan
Bio::Search::HSP::BlastPullHSP A parser and HSP object for BlastN hsps metacpan
Bio::Search::HSP::FastaHSP HSP object for FASTA specific data metacpan
Bio::Search::HSP::GenericHSP A "Generic" implementation of a High Scoring Pair metacpan
Bio::Search::HSP::HMMERHSP A HSP object for HMMER results metacpan
Bio::Search::HSP::HSPFactory A factory to create Bio::Search::HSP::HSPI objects metacpan
Bio::Search::HSP::HSPI metacpan
Bio::Search::HSP::HmmpfamHSP A parser and HSP object for hmmpfam hsps metacpan
Bio::Search::HSP::ModelHSP A HSP object for model-based searches metacpan
Bio::Search::HSP::PSLHSP A HSP for PSL output metacpan
Bio::Search::HSP::PsiBlastHSP Bioperl BLAST High-Scoring Pair object metacpan
Bio::Search::HSP::PullHSPI Bio::Search::HSP::HSPI interface for pull parsers. metacpan
Bio::Search::HSP::WABAHSP HSP object suitable for describing WABA alignments metacpan
Bio::Search::Hit::BlastHit Blast-specific subclass of Bio::Search::Hit::GenericHit metacpan
Bio::Search::Hit::BlastPullHit A parser and hit object for BLASTN hits metacpan
Bio::Search::Hit::Fasta Hit object specific for Fasta-generated hits metacpan
Bio::Search::Hit::GenericHit A generic implementation of the Bio::Search::Hit::HitI interface metacpan
Bio::Search::Hit::HMMERHit A Hit module for HMMER hits metacpan
Bio::Search::Hit::HitFactory A factory to create Bio::Search::Hit::HitI objects metacpan
Bio::Search::Hit::HitI Interface for a hit in a similarity search result metacpan
Bio::Search::Hit::HmmpfamHit A parser and hit object for hmmpfam hits metacpan
Bio::Search::Hit::ModelHit A model-based implementation of the Bio::Search::Hit::HitI interface metacpan
Bio::Search::Hit::PsiBlastHit Bioperl BLAST Hit object metacpan
Bio::Search::Hit::PullHitI Bio::Search::Hit::HitI interface for pull parsers. metacpan
Bio::Search::Hit::hmmer3Hit DESCRIPTION of Object metacpan
Bio::Search::Iteration::GenericIteration A generic implementation of the Bio::Search::Iteration::IterationI interface. metacpan
Bio::Search::Iteration::IterationI Abstract interface to an iteration from an iterated search result, such as PSI-BLAST. metacpan
Bio::Search::Processor DESCRIPTION of Object metacpan
Bio::Search::Result::BlastPullResult A parser and result object for BLASTN results metacpan
Bio::Search::Result::BlastResult Blast-specific subclass of Bio::Search::Result::GenericResult metacpan
Bio::Search::Result::CrossMatchResult CrossMatch-specific subclass of Bio::Search::Result::GenericResult metacpan
Bio::Search::Result::GenericResult Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results. metacpan
Bio::Search::Result::HMMERResult A Result object for HMMER results metacpan
Bio::Search::Result::HmmpfamResult A parser and result object for hmmpfam results metacpan
Bio::Search::Result::INFERNALResult A Result object for INFERNAL results metacpan
Bio::Search::Result::PullResultI Bio::Search::Result::ResultI interface for 'pull' parsers metacpan
Bio::Search::Result::ResultFactory A factory to create Bio::Search::Result::ResultI objects metacpan
Bio::Search::Result::ResultI Abstract interface to Search Result objects metacpan
Bio::Search::Result::WABAResult Result object for WABA alignment output metacpan
Bio::Search::Result::hmmer3Result DESCRIPTION of Object metacpan
Bio::Search::SearchUtils Utility functions for Bio::Search:: objects metacpan
Bio::Search::StatisticsI A Base object for statistics metacpan
Bio::Search::Tiling::MapTileUtils utilities for manipulating closed intervals for an HSP tiling algorithm metacpan
Bio::Search::Tiling::MapTiling An implementation of an HSP tiling algorithm, with methods to obtain frequently-requested statistics metacpan
Bio::Search::Tiling::TilingI Abstract interface for an HSP tiling module metacpan
Bio::SearchDist A perl wrapper around Sean Eddy's histogram object metacpan
Bio::SearchIO Driver for parsing Sequence Database Searches (BLAST, FASTA, ...) metacpan
Bio::SearchIO::EventHandlerI An abstract Event Handler for Search Result parsing metacpan
Bio::SearchIO::FastHitEventBuilder Event Handler for SearchIO events. metacpan
Bio::SearchIO::IteratedSearchResultEventBuilder Event Handler for SearchIO events. metacpan
Bio::SearchIO::SearchResultEventBuilder Event Handler for SearchIO events. metacpan
Bio::SearchIO::SearchWriterI Interface for outputting parsed Search results metacpan
Bio::SearchIO::Writer::GbrowseGFF Interface for outputting parsed search results in Gbrowse GFF format metacpan
Bio::SearchIO::Writer::HSPTableWriter Tab-delimited data for Bio::Search::HSP::HSPI objects metacpan
Bio::SearchIO::Writer::HTMLResultWriter write a Bio::Search::ResultI in HTML metacpan
Bio::SearchIO::Writer::HitTableWriter Tab-delimited data for Bio::Search::Hit::HitI objects metacpan
Bio::SearchIO::Writer::ResultTableWriter Outputs tab-delimited data for each Bio::Search::Result::ResultI object. metacpan
Bio::SearchIO::Writer::TextResultWriter Object to implement writing a Bio::Search::ResultI in Text. metacpan
Bio::SearchIO::axt a parser for axt format reports metacpan
Bio::SearchIO::blast Event generator for event based parsing of blast reports metacpan
Bio::SearchIO::blast_pull A parser for BLAST output metacpan
Bio::SearchIO::blasttable Driver module for SearchIO for parsing NCBI -m 8/9 format metacpan
Bio::SearchIO::cross_match CrossMatch-specific subclass of Bio::SearchIO metacpan
Bio::SearchIO::erpin SearchIO-based ERPIN parser metacpan
Bio::SearchIO::exonerate parser for Exonerate metacpan
Bio::SearchIO::fasta A SearchIO parser for FASTA results metacpan
Bio::SearchIO::gmap_f9 Event generator for parsing gmap reports (Z format) metacpan
Bio::SearchIO::hmmer A parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam) metacpan
Bio::SearchIO::hmmer2 A parser for HMMER output (hmmpfam, hmmsearch) metacpan
Bio::SearchIO::hmmer3 metacpan
Bio::SearchIO::hmmer_pull A parser for HMMER output metacpan
Bio::SearchIO::infernal SearchIO-based Infernal parser metacpan
Bio::SearchIO::megablast a driver module for Bio::SearchIO to parse megablast reports (format 0) metacpan
Bio::SearchIO::psl A parser for PSL output (UCSC) metacpan
Bio::SearchIO::rnamotif SearchIO-based RNAMotif parser metacpan
Bio::SearchIO::sim4 parser for Sim4 alignments metacpan
Bio::SearchIO::waba SearchIO parser for Jim Kent WABA program alignment output metacpan
Bio::SearchIO::wise Parsing of wise output as alignments metacpan
Bio::Seq Sequence object, with features metacpan
Bio::Seq::BaseSeqProcessor Base implementation for a SequenceProcessor metacpan
Bio::Seq::EncodedSeq subtype of L<Bio::LocatableSeq|Bio::LocatableSeq> to store DNA that encodes a protein metacpan
Bio::Seq::LargeLocatableSeq LocatableSeq object that stores sequence as files in the tempdir metacpan
Bio::Seq::LargePrimarySeq PrimarySeq object that stores sequence as files in the tempdir (as found by File::Temp) or the default method in Bio::Root::Root metacpan
Bio::Seq::LargeSeq SeqI compliant object that stores sequence as files in /tmp metacpan
Bio::Seq::LargeSeqI Interface class for sequences that cache their residues in a temporary file metacpan
Bio::Seq::Meta Generic superclass for sequence objects with residue-based meta information metacpan
Bio::Seq::Meta::Array array-based generic implementation of a sequence class with residue-based meta information metacpan
Bio::Seq::MetaI Interface for sequence objects with residue-based meta information metacpan
Bio::Seq::PrimaryQual Bioperl lightweight Quality Object metacpan
Bio::Seq::PrimaryQual::Qual metacpan
Bio::Seq::PrimedSeq A sequence and a pair of primers matching on it metacpan
Bio::Seq::QualI Interface definition for a Bio::Seq::Qual metacpan
Bio::Seq::Quality Implementation of sequence with residue quality and trace values metacpan
Bio::Seq::RichSeq Module implementing a sequence created from a rich sequence database entry metacpan
Bio::Seq::RichSeqI interface for sequences from rich data sources, mostly databases metacpan
Bio::Seq::SeqBuilder Configurable object builder for sequence stream parsers metacpan
Bio::Seq::SeqFactory Instantiation of generic Bio::PrimarySeqI (or derived) objects through a factory metacpan
Bio::Seq::SeqFastaSpeedFactory Rapid creation of Bio::Seq objects through a factory metacpan
Bio::Seq::SeqWithQuality Bioperl object packaging a sequence with its quality. Deprecated class, use Bio::Seq::Quality instead! metacpan
Bio::Seq::SequenceTrace Bioperl object packaging a sequence with its trace metacpan
Bio::Seq::SimulatedRead Read with sequencing errors taken from a reference sequence metacpan
Bio::Seq::TraceI Interface definition for a Bio::Seq::Trace metacpan
Bio::SeqAnalysisParserI Sequence analysis output parser interface metacpan
Bio::SeqEvolution::DNAPoint evolve a sequence by point mutations metacpan
Bio::SeqEvolution::EvolutionI the interface for evolving sequences metacpan
Bio::SeqEvolution::Factory Factory object to instantiate sequence evolving classes metacpan
Bio::SeqFeature::Amplicon Amplicon feature metacpan
Bio::SeqFeature::AnnotationAdaptor integrates SeqFeatureIs annotation metacpan
Bio::SeqFeature::Collection A container class for SeqFeatures suitable for performing operations such as finding features within a range, that match a certain feature type, etc. metacpan
Bio::SeqFeature::CollectionI An interface for a collection of SeqFeatureI objects. metacpan
Bio::SeqFeature::Computation Computation SeqFeature metacpan
Bio::SeqFeature::FeaturePair hold pair feature information e.g. blast hits metacpan
Bio::SeqFeature::Gene::Exon a feature representing an exon metacpan
Bio::SeqFeature::Gene::ExonI Interface for a feature representing an exon metacpan
Bio::SeqFeature::Gene::GeneStructure A feature representing an arbitrarily complex structure of a gene metacpan
Bio::SeqFeature::Gene::GeneStructureI A feature representing an arbitrarily complex structure of a gene metacpan
Bio::SeqFeature::Gene::Intron An intron feature metacpan
Bio::SeqFeature::Gene::NC_Feature metacpan
Bio::SeqFeature::Gene::Poly_A_site poly A feature metacpan
Bio::SeqFeature::Gene::Promoter Describes a promoter metacpan
Bio::SeqFeature::Gene::Transcript A feature representing a transcript metacpan
Bio::SeqFeature::Gene::TranscriptI Interface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site. metacpan
Bio::SeqFeature::Gene::UTR A feature representing an untranslated region that is part of a transcriptional unit metacpan
Bio::SeqFeature::Generic Generic SeqFeature metacpan
Bio::SeqFeature::Lite Lightweight Bio::SeqFeatureI class metacpan
Bio::SeqFeature::PositionProxy handle features when truncation/revcom sequences span a feature metacpan
Bio::SeqFeature::Primer Primer Generic SeqFeature metacpan
Bio::SeqFeature::SiRNA::Oligo Perl object for small inhibitory RNAs. metacpan
Bio::SeqFeature::SiRNA::Pair Perl object for small inhibitory RNA (SiRNA) oligo pairs metacpan
Bio::SeqFeature::Similarity A sequence feature based on similarity metacpan
Bio::SeqFeature::SimilarityPair Sequence feature based on the similarity of two sequences. metacpan
Bio::SeqFeature::SubSeq Feature representing a subsequence metacpan
Bio::SeqFeature::Tools::FeatureNamer generates unique persistent names for features metacpan
Bio::SeqFeature::Tools::IDHandler maps $seq_feature-E<gt>primary_tag metacpan
Bio::SeqFeature::Tools::TypeMapper maps $seq_feature-E<gt>primary_tag metacpan
Bio::SeqFeature::Tools::Unflattener turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy metacpan
Bio::SeqFeature::TypedSeqFeatureI a strongly typed SeqFeature metacpan
Bio::SeqFeatureI Abstract interface of a Sequence Feature metacpan
Bio::SeqI [Developers] Abstract Interface of Sequence (with features) metacpan
Bio::SeqIO Handler for SeqIO Formats metacpan
Bio::SeqIO::FTHelper Helper class for EMBL/Genbank feature tables metacpan
Bio::SeqIO::Handler::GenericRichSeqHandler Bio::HandlerI-based data handler for GenBank/EMBL/UniProt (and other) sequence data metacpan
Bio::SeqIO::MultiFile Treating a set of files as a single input stream metacpan
Bio::SeqIO::abi abi trace sequence input/output stream metacpan
Bio::SeqIO::ace ace sequence input/output stream metacpan
Bio::SeqIO::agave AGAVE sequence output stream. metacpan
Bio::SeqIO::alf alf trace sequence input/output stream metacpan
Bio::SeqIO::asciitree asciitree sequence input/output stream metacpan
Bio::SeqIO::bsml BSML sequence input/output stream metacpan
Bio::SeqIO::bsml_sax BSML sequence input/output stream using SAX metacpan
Bio::SeqIO::chadoxml chadoxml sequence output stream metacpan
Bio::SeqIO::chaos chaos sequence input/output stream metacpan
Bio::SeqIO::chaosxml chaosxml sequence input/output stream metacpan
Bio::SeqIO::ctf ctf trace sequence input/output stream metacpan
Bio::SeqIO::embl EMBL sequence input/output stream metacpan
Bio::SeqIO::embldriver EMBL sequence input/output stream metacpan
Bio::SeqIO::entrezgene Entrez Gene ASN1 parser metacpan
Bio::SeqIO::excel sequence input/output stream from a MSExcel-formatted table metacpan
Bio::SeqIO::exp exp trace sequence input/output stream metacpan
Bio::SeqIO::fasta fasta sequence input/output stream metacpan
Bio::SeqIO::fastq fastq sequence input/output stream metacpan
Bio::SeqIO::flybase_chadoxml FlyBase variant of chadoxml with sequence output stream metacpan
Bio::SeqIO::game a class for parsing and writing game-XML metacpan
Bio::SeqIO::game::featHandler a class for handling feature elements metacpan
Bio::SeqIO::game::gameHandler PerlSAX handler for game-XML metacpan
Bio::SeqIO::game::gameSubs a base class for game-XML parsing metacpan
Bio::SeqIO::game::gameWriter a class for writing game-XML metacpan
Bio::SeqIO::game::seqHandler a class for handling game-XML sequences metacpan
Bio::SeqIO::gbdriver GenBank handler-based push parser metacpan
Bio::SeqIO::gbxml GenBank sequence input/output stream using SAX metacpan
Bio::SeqIO::gcg GCG sequence input/output stream metacpan
Bio::SeqIO::genbank GenBank sequence input/output stream metacpan
Bio::SeqIO::interpro InterProScan XML input/output stream metacpan
Bio::SeqIO::kegg KEGG sequence input/output stream metacpan
Bio::SeqIO::largefasta method i/o on very large fasta sequence files metacpan
Bio::SeqIO::lasergene Lasergene sequence file input/output stream metacpan
Bio::SeqIO::locuslink LocusLink input/output stream metacpan
Bio::SeqIO::mbsout input stream for output by Teshima et al.'s mbs. metacpan
Bio::SeqIO::metafasta metafasta sequence input/output stream metacpan
Bio::SeqIO::msout input stream for output by Hudson's ms metacpan
Bio::SeqIO::nexml NeXML sequence input/output stream metacpan
Bio::SeqIO::phd phd file input/output stream metacpan
Bio::SeqIO::pir PIR sequence input/output stream metacpan
Bio::SeqIO::pln pln trace sequence input/output stream metacpan
Bio::SeqIO::qual .qual file input/output stream metacpan
Bio::SeqIO::raw raw sequence file input/output stream metacpan
Bio::SeqIO::scf .scf file input/output stream metacpan
Bio::SeqIO::seqxml SeqXML sequence input/output stream metacpan
Bio::SeqIO::strider DNA strider sequence input/output stream metacpan
Bio::SeqIO::swiss Swissprot sequence input/output stream metacpan
Bio::SeqIO::swissdriver SwissProt/UniProt handler-based push parser metacpan
Bio::SeqIO::tab nearly raw sequence file input/output stream. Reads/writes id"\t"sequence"\n" metacpan
Bio::SeqIO::table sequence input/output stream from a delimited table metacpan
Bio::SeqIO::tigr TIGR XML sequence input/output stream metacpan
Bio::SeqIO::tigrxml Parse TIGR (new) XML metacpan
Bio::SeqIO::tinyseq reading/writing sequences in NCBI TinySeq format metacpan
Bio::SeqIO::tinyseq::tinyseqHandler XML event handlers to support NCBI TinySeq XML parsing metacpan
Bio::SeqIO::ztr ztr trace sequence input/output stream metacpan
Bio::SeqUtils Additional methods for PrimarySeq objects metacpan
Bio::SimpleAlign Multiple alignments held as a set of sequences metacpan
Bio::SimpleAnalysisI A simple interface to any (local or remote) analysis tool metacpan
Bio::Species Generic species object. metacpan
Bio::Structure::Atom Bioperl structure Object, describes an Atom metacpan
Bio::Structure::Chain Bioperl structure Object, describes a chain metacpan
Bio::Structure::Entry Bioperl structure Object, describes the whole entry metacpan
Bio::Structure::IO Handler for Structure Formats metacpan
Bio::Structure::IO::pdb PDB input/output stream metacpan
Bio::Structure::Model Bioperl structure Object, describes a Model metacpan
Bio::Structure::Residue Bioperl structure Object, describes a Residue metacpan
Bio::Structure::SecStr::DSSP::Res Module for parsing/accessing dssp output metacpan
Bio::Structure::SecStr::STRIDE::Res Module for parsing/accessing stride output metacpan
Bio::Structure::StructureI Abstract Interface for a Structure objects metacpan
Bio::Symbol::Alphabet BSANE/BioCORBA compliant symbol list alphabet metacpan
Bio::Symbol::AlphabetI A Symbol Alphabet metacpan
Bio::Symbol::DNAAlphabet A ready made DNA alphabet metacpan
Bio::Symbol::ProteinAlphabet A ready made Protein alphabet metacpan
Bio::Symbol::Symbol A biological symbol metacpan
Bio::Symbol::SymbolI Interface for a Symbol metacpan
Bio::Taxon A node in a represented taxonomy metacpan
Bio::Taxonomy representing Taxonomy. metacpan
Bio::Taxonomy::FactoryI interface to define how to access NCBI Taxonoy metacpan
Bio::Taxonomy::Node A node in a represented taxonomy metacpan
Bio::Taxonomy::Taxon Generic Taxonomic Entity object metacpan
Bio::Taxonomy::Tree An Organism Level Implementation of TreeI interface. metacpan
Bio::Tools::AlignFactory Base object for alignment factories metacpan
Bio::Tools::Alignment::Consed A module to work with objects from consed .ace files metacpan
Bio::Tools::Alignment::Trim A kludge to do specialized trimming of sequence based on quality. metacpan
Bio::Tools::AmpliconSearch Find amplicons in a template using degenerate PCR primers metacpan
Bio::Tools::Analysis::DNA::ESEfinder a wrapper around ESEfinder server metacpan
Bio::Tools::Analysis::Protein::Domcut a wrapper around Domcut server metacpan
Bio::Tools::Analysis::Protein::ELM a wrapper around the ELM server which predicts short functional motifs on amino acid sequences metacpan
Bio::Tools::Analysis::Protein::GOR4 a wrapper around GOR4 protein secondary structure prediction server metacpan
Bio::Tools::Analysis::Protein::HNN a wrapper around the HNN protein secondary structure prediction server metacpan
Bio::Tools::Analysis::Protein::NetPhos a wrapper around NetPhos server metacpan
Bio::Tools::Analysis::Protein::Scansite a wrapper around the Scansite server metacpan
Bio::Tools::Analysis::Protein::Sopma a wrapper around the Sopma protein secondary structure prediction server metacpan
Bio::Tools::Analysis::SimpleAnalysisBase abstract superclass for SimpleAnalysis implementations metacpan
Bio::Tools::AnalysisResult Base class for analysis result objects and parsers metacpan
Bio::Tools::Blat parser for Blat program metacpan
Bio::Tools::CodonTable Codon table object metacpan
Bio::Tools::Coil parser for Coil output metacpan
Bio::Tools::ECnumber representation of EC numbers (Enzyme Classification) metacpan
Bio::Tools::EMBOSS::Palindrome parse EMBOSS palindrome output metacpan
Bio::Tools::EPCR Parse ePCR output and make features metacpan
Bio::Tools::ESTScan Results of one ESTScan run metacpan
Bio::Tools::Eponine Results of one Eponine run metacpan
Bio::Tools::Est2Genome Parse est2genome output, makes simple Bio::SeqFeature::Generic objects metacpan
Bio::Tools::Fgenesh parse results of one Fgenesh run metacpan
Bio::Tools::FootPrinter write sequence features in FootPrinter format metacpan
Bio::Tools::GFF A Bio::SeqAnalysisParserI compliant GFF format parser metacpan
Bio::Tools::Gel Calculates relative electrophoretic migration distances metacpan
Bio::Tools::Geneid Results of one geneid run metacpan
Bio::Tools::Genemark Results of one Genemark run metacpan
Bio::Tools::Genewise Results of one Genewise run metacpan
Bio::Tools::Genomewise Results of one Genomewise run metacpan
Bio::Tools::Genscan Results of one Genscan run metacpan
Bio::Tools::Glimmer parser for Glimmer 2.X/3.X prokaryotic and GlimmerM/GlimmerHMM eukaryotic gene predictions metacpan
Bio::Tools::Grail Results of one Grail run metacpan
Bio::Tools::GuessSeqFormat Module for determining the sequence format of the contents of a file, a string, or through a filehandle. metacpan
Bio::Tools::HMMER::Domain One particular domain hit from HMMER metacpan
Bio::Tools::HMMER::Results Object representing HMMER output results metacpan
Bio::Tools::HMMER::Set Set of identical domains from HMMER matches metacpan
Bio::Tools::Hmmpfam Parser for Hmmpfam program metacpan
Bio::Tools::IUPAC Generates unique sequence objects or regular expressions from an ambiguous IUPAC sequence metacpan
Bio::Tools::Lucy Object for analyzing the output from Lucy, a vector and quality trimming program from TIGR metacpan
Bio::Tools::MZEF Results of one MZEF run metacpan
Bio::Tools::Match Parses output from Transfac's match(TM) metacpan
Bio::Tools::OddCodes Object holding alternative alphabet coding for one protein sequence metacpan
Bio::Tools::Phylo::Gerp Parses output from GERP metacpan
Bio::Tools::Phylo::Gumby Parses output from gumby metacpan
Bio::Tools::Phylo::Molphy parser for Molphy output metacpan
Bio::Tools::Phylo::Molphy::Result container for data parsed from a ProtML run metacpan
Bio::Tools::Phylo::PAML Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00 metacpan
Bio::Tools::Phylo::PAML::Codeml Parses output from the PAML program codeml. metacpan
Bio::Tools::Phylo::PAML::ModelResult A container for NSSite Model Result from PAML metacpan
Bio::Tools::Phylo::PAML::Result A PAML result set object metacpan
Bio::Tools::Phylo::Phylip::ProtDist parser for ProtDist output metacpan
Bio::Tools::Prediction::Exon A predicted exon feature metacpan
Bio::Tools::Prediction::Gene a predicted gene structure feature metacpan
Bio::Tools::Primer3 Create input for and work with the output from the program primer3 metacpan
Bio::Tools::Primer::Assessor::Base base class for common assessor things metacpan
Bio::Tools::Primer::AssessorI interface for assessing primer pairs metacpan
Bio::Tools::Primer::Feature position of a single primer metacpan
Bio::Tools::Primer::Pair two primers on left and right side metacpan
Bio::Tools::Prints Parser for FingerPRINTScanII program metacpan
Bio::Tools::Profile parse Profile output metacpan
Bio::Tools::Promoterwise parser for Promoterwise tab format output metacpan
Bio::Tools::PrositeScan Parser for ps_scan result metacpan
Bio::Tools::Protparam submit to and parse output from protparam ; metacpan
Bio::Tools::Pseudowise Results of one Pseudowise run metacpan
Bio::Tools::QRNA A Parser for qrna output metacpan
Bio::Tools::RandomDistFunctions A set of routines useful for generating random data in different distributions metacpan
Bio::Tools::RepeatMasker a parser for RepeatMasker output metacpan
Bio::Tools::Run::GenericParameters An object for the parameters used to run programs metacpan
Bio::Tools::Run::ParametersI A Base object for the parameters used to run programs metacpan
Bio::Tools::Run::RemoteBlast Object for remote execution of the NCBI Blast via HTTP metacpan
Bio::Tools::Seg parse C<seg> output metacpan
Bio::Tools::SeqPattern represent a sequence pattern or motif metacpan
Bio::Tools::SeqPattern::Backtranslate metacpan
Bio::Tools::SeqStats Object holding statistics for one particular sequence metacpan
Bio::Tools::SeqWords Object holding n-mer statistics for a sequence metacpan
Bio::Tools::SiRNA metacpan
Bio::Tools::SiRNA::Ruleset::saigo Perl object implementing the Saigo group's rules for designing small inhibitory RNAs metacpan
Bio::Tools::SiRNA::Ruleset::tuschl Perl object implementing the tuschl group's rules for designing small inhibitory RNAs metacpan
Bio::Tools::Sigcleave Bioperl object for sigcleave analysis metacpan
Bio::Tools::Signalp parser for Signalp output metacpan
Bio::Tools::Signalp::ExtendedSignalp enhanced parser for Signalp output metacpan
Bio::Tools::Sim4::Exon A single exon determined by an alignment metacpan
Bio::Tools::Sim4::Results Results of one Sim4 run metacpan
Bio::Tools::Spidey::Exon A single exon determined by an alignment metacpan
Bio::Tools::Spidey::Results Results of a Spidey run metacpan
Bio::Tools::TandemRepeatsFinder a parser for Tandem Repeats Finder output metacpan
Bio::Tools::TargetP Results of one TargetP run metacpan
Bio::Tools::Tmhmm parse TMHMM output (TransMembrane HMM) metacpan
Bio::Tools::dpAlign Perl extension to do pairwise dynamic programming sequence alignment metacpan
Bio::Tools::ipcress Parse ipcress output and make features metacpan
Bio::Tools::isPcr Parse isPcr output and make features metacpan
Bio::Tools::pICalculator calculate the isoelectric point of a protein metacpan
Bio::Tools::pSW pairwise Smith Waterman object metacpan
Bio::Tools::tRNAscanSE A parser for tRNAscan-SE output metacpan
Bio::Tree::AlleleNode A Node with Alleles attached metacpan
Bio::Tree::AnnotatableNode A Tree Node with support for annotation metacpan
Bio::Tree::Compatible Testing compatibility of phylogenetic trees with nested taxa. metacpan
Bio::Tree::DistanceFactory Construct a tree using distance based methods metacpan
Bio::Tree::Draw::Cladogram Drawing phylogenetic trees in Encapsulated PostScript (EPS) format. metacpan
Bio::Tree::Node A Simple Tree Node metacpan
Bio::Tree::NodeI Interface describing a Tree Node metacpan
Bio::Tree::NodeNHX A Simple Tree Node with support for NHX tags metacpan
Bio::Tree::RandomFactory TreeFactory for generating Random Trees metacpan
Bio::Tree::Statistics Calculate certain statistics for a Tree metacpan
Bio::Tree::Tree An implementation of the TreeI interface. metacpan
Bio::Tree::TreeFunctionsI Decorated Interface implementing basic Tree exploration methods metacpan
Bio::Tree::TreeI A Tree object suitable for lots of things, designed originally for Phylogenetic Trees. metacpan
Bio::TreeIO Parser for Tree files metacpan
Bio::TreeIO::NewickParser metacpan
Bio::TreeIO::TreeEventBuilder Build Bio::Tree::Tree's and Bio::Tree::Node's from Events metacpan
Bio::TreeIO::cluster A TreeIO driver module for parsing Algorithm::Cluster::treecluster() output metacpan
Bio::TreeIO::lintree Parser for lintree output trees metacpan
Bio::TreeIO::newick metacpan
Bio::TreeIO::nexml A TreeIO driver module for parsing NeXML tree files metacpan
Bio::TreeIO::nexus A TreeIO driver module for parsing Nexus tree output from PAUP metacpan
Bio::TreeIO::nhx TreeIO implementation for parsing Newick/New Hampshire eXtendend (NHX) format. metacpan
Bio::TreeIO::pag Bio::TreeIO driver for Pagel format metacpan
Bio::TreeIO::phyloxml TreeIO implementation for parsing PhyloXML format. metacpan
Bio::TreeIO::svggraph A simple output format that converts a Tree object to an SVG output metacpan
Bio::TreeIO::tabtree A simple output format which displays a tree as an ASCII drawing metacpan
Bio::UpdateableSeqI Descendant of Bio::SeqI that allows updates metacpan
Bio::Variation::AAChange Sequence change class for polypeptides metacpan
Bio::Variation::AAReverseMutate point mutation and codon information from single amino acid changes metacpan
Bio::Variation::Allele Sequence object with allele-specific attributes metacpan
Bio::Variation::DNAMutation DNA level mutation class metacpan
Bio::Variation::IO Handler for sequence variation IO Formats metacpan
Bio::Variation::IO::flat flat file sequence variation input/output stream metacpan
Bio::Variation::IO::xml XML sequence variation input/output stream metacpan
Bio::Variation::RNAChange Sequence change class for RNA level metacpan
Bio::Variation::SNP submitted SNP metacpan
Bio::Variation::SeqDiff Container class for mutation/variant descriptions metacpan
Bio::Variation::VariantI Sequence Change SeqFeature abstract class metacpan
Bio::WebAgent A base class for Web (any protocol) access metacpan
FeatureStore metacpan

Other Files

Build.PL metacpan
Changes metacpan
MANIFEST metacpan
META.json metacpan
META.yml metacpan
README.md metacpan
deobfuscator/Deobfuscator/Build.PL metacpan
deobfuscator/Deobfuscator/MANIFEST metacpan
deobfuscator/Deobfuscator/META.yml metacpan
deobfuscator/Deobfuscator/Makefile.PL metacpan