- Released by
- CJFIELDS
- Version
- Release Date
- 2016-11-06
- Kwalitee
- 140.62
- Core Kwalitee
- 90.62
- LINKS
BioPerl 1.007001
Files
- .travis.yml
- AUTHORS
- BUGS
- 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/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/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/iterator.pm
- Bio/DB/GFF/Adaptor/dbi/mysql.pm
- Bio/DB/GFF/Adaptor/dbi/mysqlace.pm
- Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm
- Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm
- Bio/DB/GFF/Adaptor/dbi/oracle.pm
- Bio/DB/GFF/Adaptor/dbi/oracleace.pm
- Bio/DB/GFF/Adaptor/dbi/pg.pm
- Bio/DB/GFF/Adaptor/dbi/pg_fts.pm
- Bio/DB/GFF/Adaptor/memory.pm
- Bio/DB/GFF/Adaptor/memory/feature_serializer.pm
- Bio/DB/GFF/Adaptor/memory/iterator.pm
- Bio/DB/GFF/Aggregator.pm
- Bio/DB/GFF/Aggregator/alignment.pm
- Bio/DB/GFF/Aggregator/clone.pm
- Bio/DB/GFF/Aggregator/coding.pm
- Bio/DB/GFF/Aggregator/gene.pm
- Bio/DB/GFF/Aggregator/match.pm
- Bio/DB/GFF/Aggregator/none.pm
- Bio/DB/GFF/Aggregator/orf.pm
- Bio/DB/GFF/Aggregator/processed_transcript.pm
- Bio/DB/GFF/Aggregator/so_transcript.pm
- Bio/DB/GFF/Aggregator/transcript.pm
- Bio/DB/GFF/Aggregator/ucsc_acembly.pm
- Bio/DB/GFF/Aggregator/ucsc_ensgene.pm
- Bio/DB/GFF/Aggregator/ucsc_genscan.pm
- Bio/DB/GFF/Aggregator/ucsc_refgene.pm
- Bio/DB/GFF/Aggregator/ucsc_sanger22.pm
- Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm
- Bio/DB/GFF/Aggregator/ucsc_softberry.pm
- Bio/DB/GFF/Aggregator/ucsc_twinscan.pm
- Bio/DB/GFF/Aggregator/ucsc_unigene.pm
- Bio/DB/GFF/Featname.pm
- Bio/DB/GFF/Feature.pm
- Bio/DB/GFF/Homol.pm
- Bio/DB/GFF/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/HIV/lanl-schema.xml
- Bio/DB/InMemoryCache.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/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/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/IO/README
- Bio/LiveSeq/Intron.pm
- Bio/LiveSeq/Mutation.pm
- Bio/LiveSeq/Mutator.pm
- Bio/LiveSeq/Prim_Transcript.pm
- Bio/LiveSeq/Range.pm
- Bio/LiveSeq/Repeat_Region.pm
- Bio/LiveSeq/Repeat_Unit.pm
- Bio/LiveSeq/SeqI.pm
- Bio/LiveSeq/Transcript.pm
- Bio/LiveSeq/Translation.pm
- Bio/LocatableSeq.pm
- Bio/Location/Atomic.pm
- Bio/Location/AvWithinCoordPolicy.pm
- Bio/Location/CoordinatePolicyI.pm
- Bio/Location/Fuzzy.pm
- Bio/Location/FuzzyLocationI.pm
- Bio/Location/NarrowestCoordPolicy.pm
- Bio/Location/Simple.pm
- Bio/Location/Split.pm
- Bio/Location/SplitLocationI.pm
- Bio/Location/WidestCoordPolicy.pm
- Bio/LocationI.pm
- Bio/Map/Clone.pm
- Bio/Map/Contig.pm
- Bio/Map/CytoMap.pm
- Bio/Map/CytoMarker.pm
- Bio/Map/CytoPosition.pm
- Bio/Map/EntityI.pm
- Bio/Map/FPCMarker.pm
- Bio/Map/Gene.pm
- Bio/Map/GeneMap.pm
- Bio/Map/GenePosition.pm
- Bio/Map/GeneRelative.pm
- Bio/Map/LinkageMap.pm
- Bio/Map/LinkagePosition.pm
- Bio/Map/MapI.pm
- Bio/Map/Mappable.pm
- Bio/Map/MappableI.pm
- Bio/Map/Marker.pm
- Bio/Map/MarkerI.pm
- Bio/Map/Microsatellite.pm
- Bio/Map/OrderedPosition.pm
- Bio/Map/OrderedPositionWithDistance.pm
- Bio/Map/Physical.pm
- Bio/Map/Position.pm
- Bio/Map/PositionHandler.pm
- Bio/Map/PositionHandlerI.pm
- Bio/Map/PositionI.pm
- Bio/Map/PositionWithSequence.pm
- Bio/Map/Prediction.pm
- Bio/Map/Relative.pm
- Bio/Map/RelativeI.pm
- Bio/Map/SimpleMap.pm
- Bio/Map/TranscriptionFactor.pm
- Bio/MapIO.pm
- Bio/MapIO/fpc.pm
- Bio/MapIO/mapmaker.pm
- Bio/Matrix/Generic.pm
- Bio/Matrix/IO.pm
- Bio/Matrix/IO/mlagan.pm
- Bio/Matrix/IO/phylip.pm
- Bio/Matrix/IO/scoring.pm
- Bio/Matrix/MatrixI.pm
- Bio/Matrix/Mlagan.pm
- Bio/Matrix/PSM/IO.pm
- Bio/Matrix/PSM/IO/mast.pm
- Bio/Matrix/PSM/IO/masta.pm
- Bio/Matrix/PSM/IO/meme.pm
- Bio/Matrix/PSM/IO/psiblast.pm
- Bio/Matrix/PSM/IO/transfac.pm
- Bio/Matrix/PSM/InstanceSite.pm
- Bio/Matrix/PSM/InstanceSiteI.pm
- Bio/Matrix/PSM/ProtMatrix.pm
- Bio/Matrix/PSM/ProtPsm.pm
- Bio/Matrix/PSM/Psm.pm
- Bio/Matrix/PSM/PsmHeader.pm
- Bio/Matrix/PSM/PsmHeaderI.pm
- Bio/Matrix/PSM/PsmI.pm
- Bio/Matrix/PSM/SiteMatrix.pm
- Bio/Matrix/PSM/SiteMatrixI.pm
- Bio/Matrix/PhylipDist.pm
- Bio/Matrix/Scoring.pm
- Bio/MolEvol/CodonModel.pm
- Bio/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/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/HSP/HSPI.pm
- Bio/Search/HSP/HmmpfamHSP.pm
- Bio/Search/HSP/ModelHSP.pm
- Bio/Search/HSP/PSLHSP.pm
- Bio/Search/HSP/PsiBlastHSP.pm
- Bio/Search/HSP/PullHSPI.pm
- Bio/Search/HSP/WABAHSP.pm
- Bio/Search/Hit/BlastHit.pm
- Bio/Search/Hit/BlastPullHit.pm
- Bio/Search/Hit/Fasta.pm
- Bio/Search/Hit/GenericHit.pm
- Bio/Search/Hit/HMMERHit.pm
- Bio/Search/Hit/HitFactory.pm
- Bio/Search/Hit/HitI.pm
- Bio/Search/Hit/HmmpfamHit.pm
- Bio/Search/Hit/ModelHit.pm
- Bio/Search/Hit/PsiBlastHit.pm
- Bio/Search/Hit/PullHitI.pm
- Bio/Search/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/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
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- Bio/Tools/Prints.pm
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- Bio/Tools/Promoterwise.pm
- Bio/Tools/PrositeScan.pm
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- Bio/Tools/Pseudowise.pm
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- Bio/Tools/RandomDistFunctions.pm
- Bio/Tools/RepeatMasker.pm
- Bio/Tools/Run/GenericParameters.pm
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- Bio/Tools/Run/README
- 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
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- Bio/Tools/Spidey/Exon.pm
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- 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
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- Bio/TreeIO/pag.pm
- Bio/TreeIO/phyloxml.pm
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- Bio/TreeIO/tabtree.pm
- Bio/UpdateableSeqI.pm
- Bio/Variation/AAChange.pm
- Bio/Variation/AAReverseMutate.pm
- Bio/Variation/Allele.pm
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- Bio/Variation/README
- Bio/Variation/RNAChange.pm
- Bio/Variation/SNP.pm
- Bio/Variation/SeqDiff.pm
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- Bio/WebAgent.pm
- BioPerl.pm
- Build.PL
- Changes
- DEPENDENCIES
- DEPRECATED
- INSTALL-WIN.md
- INSTALL.SKIP
- INSTALL.md
- LICENSE
- MANIFEST
- META.json
- META.yml
- README.md
- deobfuscator/Deobfuscator/Build.PL
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- deobfuscator/Deobfuscator/bin/run-deobfuscator-update.pl
- deobfuscator/Deobfuscator/cgi-bin/deob_detail.cgi
- deobfuscator/Deobfuscator/cgi-bin/deob_flowchart.png
- deobfuscator/Deobfuscator/cgi-bin/deob_help.html
- deobfuscator/Deobfuscator/cgi-bin/deob_interface.cgi
- deobfuscator/Deobfuscator/excluded_modules.txt
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- examples/Bio-DB-GFF/load_ucsc.pl
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- examples/bioperl.pl
- examples/cluster/dbsnp.pl
- examples/contributed/nmrpdb_parse.pl
- examples/contributed/prosite2perl.pl
- examples/contributed/rebase2list.pl
- examples/db/dbfetch
- examples/db/est_tissue_query.pl
- examples/db/gb2features.pl
- examples/db/getGenBank.pl
- examples/db/get_seqs.pl
- examples/db/rfetch.pl
- examples/db/use_registry.pl
- examples/generate_random_seq.pl
- examples/liveseq/change_gene.pl
- examples/longorf.pl
- examples/make_primers.pl
- examples/popgen/parse_calc_stats.pl
- examples/quality/svgtrace.pl
- examples/rev_and_trans.pl
- examples/revcom_dir.pl
- examples/root/README
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- examples/root/exceptions2.pl
- examples/root/exceptions3.pl
- examples/root/exceptions4.pl
- examples/searchio/blast_example.pl
- examples/searchio/custom_writer.pl
- examples/searchio/hitwriter.pl
- examples/searchio/hspwriter.pl
- examples/searchio/htmlwriter.pl
- examples/searchio/psiblast_features.pl
- examples/searchio/psiblast_iterations.pl
- examples/searchio/rawwriter.pl
- examples/searchio/resultwriter.pl
- examples/searchio/waba2gff.pl
- examples/searchio/waba2gff3.pl
- examples/sirna/TAG
- examples/sirna/rnai_finder.cgi
- examples/structure/structure-io.pl
- examples/subsequence.cgi
- examples/tk/gsequence.pl
- examples/tk/hitdisplay.pl
- examples/tools/extract_genes.pl
- examples/tools/gb_to_gff.pl
- examples/tools/gff2ps.pl
- examples/tools/parse_codeml.pl
- examples/tools/psw.pl
- examples/tools/reverse-translate.pl
- examples/tools/run_genscan.pl
- examples/tools/run_primer3.pl
- examples/tools/seq_pattern.pl
- examples/tools/standaloneblast.pl
- examples/tree/paup2phylip.pl
- ide/bioperl-mode/README
- ide/bioperl-mode/dist/Changes
- ide/bioperl-mode/dist/SKIP
- ide/bioperl-mode/dist/bioperl-mode-xemacs.tar
- ide/bioperl-mode/dist/bioperl-mode-xemacs.tar.md5
- ide/bioperl-mode/dist/bioperl-mode.tar
- ide/bioperl-mode/dist/bioperl-mode.tar.md5
- ide/bioperl-mode/dist/package-me
- ide/bioperl-mode/etc/images/bpmode-tool-dis.xpm
- ide/bioperl-mode/etc/images/bpmode-tool.xpm
- ide/bioperl-mode/site-lisp/bioperl-init.el
- ide/bioperl-mode/site-lisp/bioperl-mode.el
- ide/bioperl-mode/site-lisp/bioperl-skel.el
- ide/bioperl-mode/site-lisp/pod.el
- ide/bioperl.komodo
- maintenance/README
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- maintenance/big_split/file_classification.csv
- maintenance/big_split/rbuels_notes.txt
- maintenance/check_NAME.pl
- maintenance/check_URLs.pl
- maintenance/cvs2cl_by_file.pl
- maintenance/dependencies.pl
- maintenance/deprecated.pl
- maintenance/find_mod_deps.pl
- maintenance/module_usage.pl
- maintenance/modules.pl
- maintenance/ncbi_blast_switches.pl
- maintenance/perltidy.conf
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- maintenance/symlink_script.pl
- maintenance/version.pl
- models/README
- models/biblio.dia
- models/bio_liveseq_variation.dia
- models/bio_map.dia
- models/bio_restriction.dia
- models/bioperl.dia
- models/coordinatemapper.dia
- models/map_proposal.txt
- models/maps_and_markers.dia
- models/popgen.dia
- models/population_proposal.txt
- scripts/Bio-DB-GFF/README
- scripts/Bio-DB-GFF/bp_bulk_load_gff.pl
- scripts/Bio-DB-GFF/bp_fast_load_gff.pl
- scripts/Bio-DB-GFF/bp_genbank2gff.pl
- scripts/Bio-DB-GFF/bp_genbank2gff3.pl
- scripts/Bio-DB-GFF/bp_generate_histogram.pl
- scripts/Bio-DB-GFF/bp_load_gff.pl
- scripts/Bio-DB-GFF/bp_meta_gff.pl
- scripts/Bio-DB-GFF/bp_process_gadfly.pl
- scripts/Bio-DB-GFF/bp_process_sgd.pl
- scripts/Bio-DB-GFF/bp_process_wormbase.pl
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- scripts/seq/bp_unflatten_seq.pl
- scripts/seqstats/TAG
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- scripts/seqstats/bp_gccalc.pl
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- scripts/taxa/TAG
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- scripts/taxa/bp_local_taxonomydb_query.pl
- scripts/taxa/bp_query_entrez_taxa.pl
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- scripts/tree/TAG
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- scripts/utilities/README
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- scripts/utilities/bp_download_query_genbank.pl
- scripts/utilities/bp_find-blast-matches.pl
- scripts/utilities/bp_mask_by_search.pl
- scripts/utilities/bp_mrtrans.pl
- scripts/utilities/bp_mutate.pl
- scripts/utilities/bp_netinstall.pl
- scripts/utilities/bp_nrdb.pl
- scripts/utilities/bp_pairwise_kaks.pl
- scripts/utilities/bp_remote_blast.pl
- scripts/utilities/bp_revtrans-motif.pl
- scripts/utilities/bp_search2alnblocks.pl
- scripts/utilities/bp_search2gff.pl
- scripts/utilities/bp_search2tribe.pl
- scripts/utilities/bp_seq_length.pl
- scripts/utilities/bp_sreformat.pl
- t/Align/AlignStats.t
- t/Align/AlignUtil.t
- t/Align/Graphics.t
- t/Align/SimpleAlign.t
- t/Align/TreeBuild.t
- t/Align/Utilities.t
- t/AlignIO/AlignIO.t
- t/AlignIO/arp.t
- t/AlignIO/bl2seq.t
- t/AlignIO/clustalw.t
- t/AlignIO/emboss.t
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- t/AlignIO/largemultifasta.t
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- t/AlignIO/prodom.t
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- t/Annotation/Annotation.t
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- t/Assembly/ContigSpectrum.t
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- t/Cluster/UniGene.t
- t/ClusterIO/ClusterIO.t
- t/ClusterIO/SequenceFamily.t
- t/ClusterIO/unigene.t
- t/Draw/Pictogram.t
- t/LiveSeq/Chain.t
- t/LiveSeq/LiveSeq.t
- t/LiveSeq/Mutation.t
- t/LiveSeq/Mutator.t
- t/LocalDB/BioDBGFF.t
- t/LocalDB/Fasta.t
- t/LocalDB/Flat.t
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- t/LocalDB/Qual.t
- t/LocalDB/Registry.t
- t/LocalDB/SeqFeature.t
- t/LocalDB/Taxonomy/greengenes.t
- t/LocalDB/Taxonomy/silva.t
- t/LocalDB/Taxonomy/sqlite.t
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- t/Map/Cyto.t
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- t/Ontology/GOterm.t
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- t/Phenotype/Phenotype.t
- t/PodSyntax.t
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- t/PopGen/HtSNP.t
- t/PopGen/MK.t
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- t/RemoteDB/BioFetch.t
- t/RemoteDB/CUTG.t
- t/RemoteDB/EMBL.t
- t/RemoteDB/EntrezGene.t
- t/RemoteDB/GenBank.t
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- t/RemoteDB/HIV/HIV.t
- t/RemoteDB/HIV/HIVAnnotProcessor.t
- t/RemoteDB/HIV/HIVQuery.t
- t/RemoteDB/HIV/HIVQueryHelper.t
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- t/Restriction/Analysis-refac.t
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- t/data/nexml/trees.nexml.8.xml
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- t/data/nhmmer-3.1.out
- t/data/nhx-bacteria.nhx
- t/data/no-genes.genscan
- t/data/no_FH.embl
- t/data/no_cds_example.gb
- t/data/no_hsps.blastp
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- t/data/noninterleaved.phy
- t/data/nucmatrix.txt
- t/data/omim_genemap_test
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- t/data/popgen_saureus.dat
- t/data/popgen_saureus.multidat
- t/data/popstats.prettybase
- t/data/pre_rel9.swiss
- t/data/primedseq.fa
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- t/data/primer3_outfile.txt
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- t/data/sample_dataset.tigr
- t/data/sbay_c127.fas
- t/data/sbay_c545-yeast.BLASTZ.PSL
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- t/data/testdat.exonerate
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- t/data/tiny.stk
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- t/data/tol-2010-02-18.nhx
- t/data/traits.tab
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- t/data/transfac.dat
- t/data/transfac_pro/factor.dat
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- t/data/transfac_pro/matrix.dat
- t/data/transfac_pro/readme.txt
- t/data/transfac_pro/reference.dat
- t/data/transfac_pro/site.dat
- t/data/tree_nonewline.nexus
- t/data/trees.nexml.old.xml
- t/data/tricky.wublast
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- t/data/version2.scf
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- t/data/yeast.tRNAscanSE
- t/data/yn00.mlc
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- t/lib/Error.pm
- t/nexml.t
- travis_scripts/dependency_installs
- travis_scripts/trigger-dockerhub.sh
