- Released by
- SENDU
- Version
- Release Date
- 2006-11-17
- Kwalitee
- 134.38
- Core Kwalitee
- 87.5
- LINKS
bioperl 1.5.2_004-RC Deleted
Files
- AUTHORS
- BUGS
- Bio/Align/AlignI.pm
- Bio/Align/DNAStatistics.pm
- Bio/Align/PairwiseStatistics.pm
- Bio/Align/ProteinStatistics.pm
- Bio/Align/StatisticsI.pm
- Bio/Align/Utilities.pm
- Bio/AlignIO.pm
- Bio/AlignIO/bl2seq.pm
- Bio/AlignIO/clustalw.pm
- Bio/AlignIO/emboss.pm
- Bio/AlignIO/fasta.pm
- Bio/AlignIO/largemultifasta.pm
- Bio/AlignIO/maf.pm
- Bio/AlignIO/mase.pm
- Bio/AlignIO/mega.pm
- Bio/AlignIO/meme.pm
- Bio/AlignIO/metafasta.pm
- Bio/AlignIO/msf.pm
- Bio/AlignIO/nexus.pm
- Bio/AlignIO/pfam.pm
- Bio/AlignIO/phylip.pm
- Bio/AlignIO/po.pm
- Bio/AlignIO/prodom.pm
- Bio/AlignIO/psi.pm
- Bio/AlignIO/selex.pm
- Bio/AlignIO/stockholm.pm
- Bio/AnalysisI.pm
- Bio/AnalysisParserI.pm
- Bio/AnalysisResultI.pm
- Bio/AnnotatableI.pm
- Bio/Annotation/AnnotationFactory.pm
- Bio/Annotation/Collection.pm
- Bio/Annotation/Comment.pm
- Bio/Annotation/DBLink.pm
- Bio/Annotation/OntologyTerm.pm
- Bio/Annotation/Reference.pm
- Bio/Annotation/SimpleValue.pm
- Bio/Annotation/StructuredValue.pm
- Bio/Annotation/Target.pm
- Bio/Annotation/TypeManager.pm
- Bio/AnnotationCollectionI.pm
- Bio/AnnotationI.pm
- Bio/Assembly/Contig.pm
- Bio/Assembly/ContigAnalysis.pm
- Bio/Assembly/IO.pm
- Bio/Assembly/IO/ace.pm
- Bio/Assembly/IO/phrap.pm
- Bio/Assembly/Scaffold.pm
- Bio/Assembly/ScaffoldI.pm
- Bio/Assembly/Singlet.pm
- Bio/Biblio.pm
- Bio/Biblio/Article.pm
- Bio/Biblio/BiblioBase.pm
- Bio/Biblio/Book.pm
- Bio/Biblio/BookArticle.pm
- Bio/Biblio/IO.pm
- Bio/Biblio/IO/medline2ref.pm
- Bio/Biblio/IO/medlinexml.pm
- Bio/Biblio/IO/pubmed2ref.pm
- Bio/Biblio/IO/pubmedxml.pm
- Bio/Biblio/Journal.pm
- Bio/Biblio/JournalArticle.pm
- Bio/Biblio/MedlineArticle.pm
- Bio/Biblio/MedlineBook.pm
- Bio/Biblio/MedlineBookArticle.pm
- Bio/Biblio/MedlineJournal.pm
- Bio/Biblio/MedlineJournalArticle.pm
- Bio/Biblio/Organisation.pm
- Bio/Biblio/Patent.pm
- Bio/Biblio/Person.pm
- Bio/Biblio/Proceeding.pm
- Bio/Biblio/Provider.pm
- Bio/Biblio/PubmedArticle.pm
- Bio/Biblio/PubmedBookArticle.pm
- Bio/Biblio/PubmedJournalArticle.pm
- Bio/Biblio/Ref.pm
- Bio/Biblio/Service.pm
- Bio/Biblio/TechReport.pm
- Bio/Biblio/Thesis.pm
- Bio/Biblio/WebResource.pm
- Bio/Cluster/ClusterFactory.pm
- Bio/Cluster/FamilyI.pm
- Bio/Cluster/SequenceFamily.pm
- Bio/Cluster/UniGene.pm
- Bio/Cluster/UniGeneI.pm
- Bio/ClusterI.pm
- Bio/ClusterIO.pm
- Bio/ClusterIO/dbsnp.pm
- Bio/ClusterIO/unigene.pm
- Bio/CodonUsage/IO.pm
- Bio/CodonUsage/Table.pm
- Bio/Coordinate/Chain.pm
- Bio/Coordinate/Collection.pm
- Bio/Coordinate/ExtrapolatingPair.pm
- Bio/Coordinate/GeneMapper.pm
- Bio/Coordinate/Graph.pm
- Bio/Coordinate/MapperI.pm
- Bio/Coordinate/Pair.pm
- Bio/Coordinate/Result.pm
- Bio/Coordinate/Result/Gap.pm
- Bio/Coordinate/Result/Match.pm
- Bio/Coordinate/ResultI.pm
- Bio/Coordinate/Utils.pm
- Bio/DB/Ace.pm
- Bio/DB/Biblio/biofetch.pm
- Bio/DB/Biblio/eutils.pm
- Bio/DB/Biblio/pdf.pm
- Bio/DB/Biblio/soap.pm
- Bio/DB/BiblioI.pm
- Bio/DB/BioFetch.pm
- Bio/DB/CUTG.pm
- Bio/DB/DBFetch.pm
- Bio/DB/EMBL.pm
- Bio/DB/EUtilities.pm
- Bio/DB/EUtilities/Cookie.pm
- Bio/DB/EUtilities/ElinkData.pm
- Bio/DB/EUtilities/efetch.pm
- Bio/DB/EUtilities/egquery.pm
- Bio/DB/EUtilities/einfo.pm
- Bio/DB/EUtilities/elink.pm
- Bio/DB/EUtilities/epost.pm
- Bio/DB/EUtilities/esearch.pm
- Bio/DB/EUtilities/esummary.pm
- Bio/DB/EntrezGene.pm
- Bio/DB/Expression.pm
- Bio/DB/Expression/geo.pm
- Bio/DB/Failover.pm
- Bio/DB/Fasta.pm
- Bio/DB/FileCache.pm
- Bio/DB/Flat.pm
- Bio/DB/Flat/BDB.pm
- Bio/DB/Flat/BDB/embl.pm
- Bio/DB/Flat/BDB/fasta.pm
- Bio/DB/Flat/BDB/genbank.pm
- Bio/DB/Flat/BDB/swiss.pm
- Bio/DB/Flat/BDB/swissprot.pm
- Bio/DB/Flat/BinarySearch.pm
- Bio/DB/GDB.pm
- Bio/DB/GFF.pm
- Bio/DB/GFF/Adaptor/ace.pm
- Bio/DB/GFF/Adaptor/berkeleydb.pm
- Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm
- Bio/DB/GFF/Adaptor/biofetch.pm
- Bio/DB/GFF/Adaptor/biofetch_oracle.pm
- Bio/DB/GFF/Adaptor/dbi.pm
- Bio/DB/GFF/Adaptor/dbi/caching_handle.pm
- Bio/DB/GFF/Adaptor/dbi/iterator.pm
- Bio/DB/GFF/Adaptor/dbi/mysql.pm
- Bio/DB/GFF/Adaptor/dbi/mysqlace.pm
- Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm
- Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm
- Bio/DB/GFF/Adaptor/dbi/oracle.pm
- Bio/DB/GFF/Adaptor/dbi/oracleace.pm
- Bio/DB/GFF/Adaptor/dbi/pg.pm
- Bio/DB/GFF/Adaptor/dbi/pg_fts.pm
- Bio/DB/GFF/Adaptor/memory.pm
- Bio/DB/GFF/Adaptor/memory/feature_serializer.pm
- Bio/DB/GFF/Adaptor/memory/iterator.pm
- Bio/DB/GFF/Aggregator.pm
- Bio/DB/GFF/Aggregator/alignment.pm
- Bio/DB/GFF/Aggregator/clone.pm
- Bio/DB/GFF/Aggregator/coding.pm
- Bio/DB/GFF/Aggregator/match.pm
- Bio/DB/GFF/Aggregator/none.pm
- Bio/DB/GFF/Aggregator/processed_transcript.pm
- Bio/DB/GFF/Aggregator/so_transcript.pm
- Bio/DB/GFF/Aggregator/transcript.pm
- Bio/DB/GFF/Aggregator/ucsc_acembly.pm
- Bio/DB/GFF/Aggregator/ucsc_ensgene.pm
- Bio/DB/GFF/Aggregator/ucsc_genscan.pm
- Bio/DB/GFF/Aggregator/ucsc_refgene.pm
- Bio/DB/GFF/Aggregator/ucsc_sanger22.pm
- Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm
- Bio/DB/GFF/Aggregator/ucsc_softberry.pm
- Bio/DB/GFF/Aggregator/ucsc_twinscan.pm
- Bio/DB/GFF/Aggregator/ucsc_unigene.pm
- Bio/DB/GFF/Featname.pm
- Bio/DB/GFF/Feature.pm
- Bio/DB/GFF/Homol.pm
- Bio/DB/GFF/RelSegment.pm
- Bio/DB/GFF/Segment.pm
- Bio/DB/GFF/Typename.pm
- Bio/DB/GFF/Util/Binning.pm
- Bio/DB/GFF/Util/Rearrange.pm
- Bio/DB/GenBank.pm
- Bio/DB/GenPept.pm
- Bio/DB/GenericWebDBI.pm
- Bio/DB/InMemoryCache.pm
- Bio/DB/LocationI.pm
- Bio/DB/MeSH.pm
- Bio/DB/NCBIHelper.pm
- Bio/DB/Query/GenBank.pm
- Bio/DB/Query/WebQuery.pm
- Bio/DB/QueryI.pm
- Bio/DB/RandomAccessI.pm
- Bio/DB/RefSeq.pm
- Bio/DB/ReferenceI.pm
- Bio/DB/Registry.pm
- Bio/DB/SeqFeature.pm
- Bio/DB/SeqFeature/NormalizedFeature.pm
- Bio/DB/SeqFeature/NormalizedFeatureI.pm
- Bio/DB/SeqFeature/NormalizedTableFeatureI.pm
- Bio/DB/SeqFeature/Segment.pm
- Bio/DB/SeqFeature/Store.pm
- Bio/DB/SeqFeature/Store/DBI/Iterator.pm
- Bio/DB/SeqFeature/Store/DBI/mysql.pm
- Bio/DB/SeqFeature/Store/GFF3Loader.pm
- Bio/DB/SeqFeature/Store/bdb.pm
- Bio/DB/SeqFeature/Store/berkeleydb.pm
- Bio/DB/SeqFeature/Store/memory.pm
- Bio/DB/SeqHound.pm
- Bio/DB/SeqI.pm
- Bio/DB/SeqVersion.pm
- Bio/DB/SeqVersion/gi.pm
- Bio/DB/SwissProt.pm
- Bio/DB/Taxonomy.pm
- Bio/DB/Taxonomy/entrez.pm
- Bio/DB/Taxonomy/flatfile.pm
- Bio/DB/Taxonomy/list.pm
- Bio/DB/Universal.pm
- Bio/DB/UpdateableSeqI.pm
- Bio/DB/WebDBSeqI.pm
- Bio/DB/XEMBL.pm
- Bio/DB/XEMBLService.pm
- Bio/DBLinkContainerI.pm
- Bio/Das/FeatureTypeI.pm
- Bio/Das/SegmentI.pm
- Bio/DasI.pm
- Bio/DescribableI.pm
- Bio/Event/EventGeneratorI.pm
- Bio/Event/EventHandlerI.pm
- Bio/Expression/Contact.pm
- Bio/Expression/DataSet.pm
- Bio/Expression/FeatureGroup.pm
- Bio/Expression/FeatureGroup/FeatureGroupMas50.pm
- Bio/Expression/FeatureI.pm
- Bio/Expression/FeatureSet/FeatureSetMas50.pm
- Bio/Expression/Platform.pm
- Bio/Expression/ProbeI.pm
- Bio/Expression/Sample.pm
- Bio/Factory/AnalysisI.pm
- Bio/Factory/ApplicationFactoryI.pm
- Bio/Factory/DriverFactory.pm
- Bio/Factory/FTLocationFactory.pm
- Bio/Factory/HitFactoryI.pm
- Bio/Factory/LocationFactoryI.pm
- Bio/Factory/MapFactoryI.pm
- Bio/Factory/ObjectBuilderI.pm
- Bio/Factory/ObjectFactory.pm
- Bio/Factory/ObjectFactoryI.pm
- Bio/Factory/ResultFactoryI.pm
- Bio/Factory/SeqAnalysisParserFactory.pm
- Bio/Factory/SeqAnalysisParserFactoryI.pm
- Bio/Factory/SequenceFactoryI.pm
- Bio/Factory/SequenceProcessorI.pm
- Bio/Factory/SequenceStreamI.pm
- Bio/Factory/TreeFactoryI.pm
- Bio/FeatureHolderI.pm
- Bio/FeatureIO.pm
- Bio/FeatureIO/bed.pm
- Bio/FeatureIO/gff.pm
- Bio/FeatureIO/gtf.pm
- Bio/FeatureIO/interpro.pm
- Bio/FeatureIO/ptt.pm
- Bio/Graph/Edge.pm
- Bio/Graph/IO.pm
- Bio/Graph/IO/dip.pm
- Bio/Graph/IO/psi_xml.pm
- Bio/Graph/ProteinGraph.pm
- Bio/Graph/SimpleGraph.pm
- Bio/Graph/SimpleGraph/Traversal.pm
- Bio/Graphics.pm
- Bio/Graphics/ConfiguratorI.pm
- Bio/Graphics/Feature.pm
- Bio/Graphics/FeatureBase.pm
- Bio/Graphics/FeatureFile.pm
- Bio/Graphics/FeatureFile/Iterator.pm
- Bio/Graphics/Glyph.pm
- Bio/Graphics/Glyph/Factory.pm
- Bio/Graphics/Glyph/alignment.pm
- Bio/Graphics/Glyph/anchored_arrow.pm
- Bio/Graphics/Glyph/arrow.pm
- Bio/Graphics/Glyph/box.pm
- Bio/Graphics/Glyph/broken_line.pm
- Bio/Graphics/Glyph/cds.pm
- Bio/Graphics/Glyph/christmas_arrow.pm
- Bio/Graphics/Glyph/crossbox.pm
- Bio/Graphics/Glyph/dashed_line.pm
- Bio/Graphics/Glyph/diamond.pm
- Bio/Graphics/Glyph/dna.pm
- Bio/Graphics/Glyph/dot.pm
- Bio/Graphics/Glyph/dumbbell.pm
- Bio/Graphics/Glyph/ellipse.pm
- Bio/Graphics/Glyph/ex.pm
- Bio/Graphics/Glyph/extending_arrow.pm
- Bio/Graphics/Glyph/flag.pm
- Bio/Graphics/Glyph/gene.pm
- Bio/Graphics/Glyph/generic.pm
- Bio/Graphics/Glyph/graded_segments.pm
- Bio/Graphics/Glyph/group.pm
- Bio/Graphics/Glyph/heterogeneous_segments.pm
- Bio/Graphics/Glyph/image.pm
- Bio/Graphics/Glyph/lightning.pm
- Bio/Graphics/Glyph/line.pm
- Bio/Graphics/Glyph/merge_parts.pm
- Bio/Graphics/Glyph/merged_alignment.pm
- Bio/Graphics/Glyph/minmax.pm
- Bio/Graphics/Glyph/oval.pm
- Bio/Graphics/Glyph/pentagram.pm
- Bio/Graphics/Glyph/pinsertion.pm
- Bio/Graphics/Glyph/primers.pm
- Bio/Graphics/Glyph/processed_transcript.pm
- Bio/Graphics/Glyph/protein.pm
- Bio/Graphics/Glyph/ragged_ends.pm
- Bio/Graphics/Glyph/redgreen_box.pm
- Bio/Graphics/Glyph/redgreen_segment.pm
- Bio/Graphics/Glyph/repeating_shape.pm
- Bio/Graphics/Glyph/rndrect.pm
- Bio/Graphics/Glyph/ruler_arrow.pm
- Bio/Graphics/Glyph/saw_teeth.pm
- Bio/Graphics/Glyph/segmented_keyglyph.pm
- Bio/Graphics/Glyph/segments.pm
- Bio/Graphics/Glyph/so_transcript.pm
- Bio/Graphics/Glyph/span.pm
- Bio/Graphics/Glyph/splice_site.pm
- Bio/Graphics/Glyph/text_in_box.pm
- Bio/Graphics/Glyph/three_letters.pm
- Bio/Graphics/Glyph/tic_tac_toe.pm
- Bio/Graphics/Glyph/toomany.pm
- Bio/Graphics/Glyph/track.pm
- Bio/Graphics/Glyph/transcript.pm
- Bio/Graphics/Glyph/transcript2.pm
- Bio/Graphics/Glyph/translation.pm
- Bio/Graphics/Glyph/triangle.pm
- Bio/Graphics/Glyph/two_bolts.pm
- Bio/Graphics/Glyph/wave.pm
- Bio/Graphics/Glyph/weighted_arrow.pm
- Bio/Graphics/Glyph/whiskerplot.pm
- Bio/Graphics/Glyph/xyplot.pm
- Bio/Graphics/Panel.pm
- Bio/Graphics/Pictogram.pm
- Bio/Graphics/RendererI.pm
- Bio/Graphics/Util.pm
- Bio/IdCollectionI.pm
- Bio/IdentifiableI.pm
- Bio/Index/Abstract.pm
- Bio/Index/AbstractSeq.pm
- Bio/Index/Blast.pm
- Bio/Index/EMBL.pm
- Bio/Index/Fasta.pm
- Bio/Index/Fastq.pm
- Bio/Index/GenBank.pm
- Bio/Index/Hmmer.pm
- Bio/Index/Qual.pm
- Bio/Index/SwissPfam.pm
- Bio/Index/Swissprot.pm
- Bio/LiveSeq/AARange.pm
- Bio/LiveSeq/Chain.pm
- Bio/LiveSeq/ChainI.pm
- Bio/LiveSeq/DNA.pm
- Bio/LiveSeq/Exon.pm
- Bio/LiveSeq/Gene.pm
- Bio/LiveSeq/IO/BioPerl.pm
- Bio/LiveSeq/IO/Loader.pm
- Bio/LiveSeq/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/LinkageMap.pm
- Bio/Map/LinkagePosition.pm
- Bio/Map/MapI.pm
- Bio/Map/Mappable.pm
- Bio/Map/MappableI.pm
- Bio/Map/Marker.pm
- Bio/Map/MarkerI.pm
- Bio/Map/Microsatellite.pm
- Bio/Map/OrderedPosition.pm
- Bio/Map/OrderedPositionWithDistance.pm
- Bio/Map/Physical.pm
- Bio/Map/Position.pm
- Bio/Map/PositionHandler.pm
- Bio/Map/PositionHandlerI.pm
- Bio/Map/PositionI.pm
- Bio/Map/Relative.pm
- Bio/Map/RelativeI.pm
- Bio/Map/SimpleMap.pm
- Bio/MapIO.pm
- Bio/MapIO/fpc.pm
- Bio/MapIO/mapmaker.pm
- Bio/Matrix/Generic.pm
- Bio/Matrix/IO.pm
- Bio/Matrix/IO/phylip.pm
- Bio/Matrix/IO/scoring.pm
- Bio/Matrix/MatrixI.pm
- Bio/Matrix/PSM/IO.pm
- Bio/Matrix/PSM/IO/mast.pm
- Bio/Matrix/PSM/IO/masta.pm
- Bio/Matrix/PSM/IO/meme.pm
- Bio/Matrix/PSM/IO/psiblast.pm
- Bio/Matrix/PSM/IO/transfac.pm
- Bio/Matrix/PSM/InstanceSite.pm
- Bio/Matrix/PSM/InstanceSiteI.pm
- Bio/Matrix/PSM/ProtMatrix.pm
- Bio/Matrix/PSM/ProtPsm.pm
- Bio/Matrix/PSM/Psm.pm
- Bio/Matrix/PSM/PsmHeader.pm
- Bio/Matrix/PSM/PsmHeaderI.pm
- Bio/Matrix/PSM/PsmI.pm
- Bio/Matrix/PSM/SiteMatrix.pm
- Bio/Matrix/PSM/SiteMatrixI.pm
- Bio/Matrix/PhylipDist.pm
- Bio/Matrix/Scoring.pm
- Bio/Ontology/DocumentRegistry.pm
- Bio/Ontology/GOterm.pm
- Bio/Ontology/InterProTerm.pm
- Bio/Ontology/OBOEngine.pm
- Bio/Ontology/OBOterm.pm
- Bio/Ontology/Ontology.pm
- Bio/Ontology/OntologyEngineI.pm
- Bio/Ontology/OntologyI.pm
- Bio/Ontology/OntologyStore.pm
- Bio/Ontology/Path.pm
- Bio/Ontology/PathI.pm
- Bio/Ontology/Relationship.pm
- Bio/Ontology/RelationshipFactory.pm
- Bio/Ontology/RelationshipI.pm
- Bio/Ontology/RelationshipType.pm
- Bio/Ontology/SimpleGOEngine.pm
- Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm
- Bio/Ontology/SimpleGOEngine/GraphAdaptor02.pm
- Bio/Ontology/SimpleOntologyEngine.pm
- Bio/Ontology/Term.pm
- Bio/Ontology/TermFactory.pm
- Bio/Ontology/TermI.pm
- Bio/OntologyIO.pm
- Bio/OntologyIO/Handlers/BaseSAXHandler.pm
- Bio/OntologyIO/Handlers/InterProHandler.pm
- Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm
- Bio/OntologyIO/InterProParser.pm
- Bio/OntologyIO/dagflat.pm
- Bio/OntologyIO/goflat.pm
- Bio/OntologyIO/obo.pm
- Bio/OntologyIO/simplehierarchy.pm
- Bio/OntologyIO/soflat.pm
- Bio/Perl.pm
- Bio/Phenotype/Correlate.pm
- Bio/Phenotype/MeSH/Term.pm
- Bio/Phenotype/MeSH/Twig.pm
- Bio/Phenotype/Measure.pm
- Bio/Phenotype/OMIM/MiniMIMentry.pm
- Bio/Phenotype/OMIM/OMIMentry.pm
- Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm
- Bio/Phenotype/OMIM/OMIMparser.pm
- Bio/Phenotype/Phenotype.pm
- Bio/Phenotype/PhenotypeI.pm
- Bio/PopGen/Genotype.pm
- Bio/PopGen/GenotypeI.pm
- Bio/PopGen/HtSNP.pm
- Bio/PopGen/IO.pm
- Bio/PopGen/IO/csv.pm
- Bio/PopGen/IO/hapmap.pm
- Bio/PopGen/IO/phase.pm
- Bio/PopGen/IO/prettybase.pm
- Bio/PopGen/Individual.pm
- Bio/PopGen/IndividualI.pm
- Bio/PopGen/Marker.pm
- Bio/PopGen/MarkerI.pm
- Bio/PopGen/PopStats.pm
- Bio/PopGen/Population.pm
- Bio/PopGen/PopulationI.pm
- Bio/PopGen/Simulation/Coalescent.pm
- Bio/PopGen/Simulation/GeneticDrift.pm
- Bio/PopGen/Statistics.pm
- Bio/PopGen/TagHaplotype.pm
- Bio/PopGen/Utilities.pm
- Bio/PrimarySeq.pm
- Bio/PrimarySeqI.pm
- Bio/PullParserI.pm
- Bio/Range.pm
- Bio/RangeI.pm
- Bio/Restriction/Analysis.pm
- Bio/Restriction/Enzyme.pm
- Bio/Restriction/Enzyme/MultiCut.pm
- Bio/Restriction/Enzyme/MultiSite.pm
- Bio/Restriction/EnzymeCollection.pm
- Bio/Restriction/EnzymeI.pm
- Bio/Restriction/IO.pm
- Bio/Restriction/IO/bairoch.pm
- Bio/Restriction/IO/base.pm
- Bio/Restriction/IO/itype2.pm
- Bio/Restriction/IO/withrefm.pm
- Bio/Root/Exception.pm
- Bio/Root/HTTPget.pm
- Bio/Root/IO.pm
- Bio/Root/Root.pm
- Bio/Root/RootI.pm
- Bio/Root/Storable.pm
- Bio/Root/Version.pm
- Bio/Search/BlastStatistics.pm
- Bio/Search/BlastUtils.pm
- Bio/Search/DatabaseI.pm
- Bio/Search/GenericDatabase.pm
- Bio/Search/GenericStatistics.pm
- Bio/Search/HSP/BlastHSP.pm
- Bio/Search/HSP/FastaHSP.pm
- Bio/Search/HSP/GenericHSP.pm
- Bio/Search/HSP/HMMERHSP.pm
- Bio/Search/HSP/HSPFactory.pm
- Bio/Search/HSP/HSPI.pm
- Bio/Search/HSP/HmmpfamHSP.pm
- Bio/Search/HSP/PSLHSP.pm
- Bio/Search/HSP/PsiBlastHSP.pm
- Bio/Search/HSP/PullHSPI.pm
- Bio/Search/HSP/WABAHSP.pm
- Bio/Search/Hit/BlastHit.pm
- Bio/Search/Hit/Fasta.pm
- Bio/Search/Hit/GenericHit.pm
- Bio/Search/Hit/HMMERHit.pm
- Bio/Search/Hit/HitFactory.pm
- Bio/Search/Hit/HitI.pm
- Bio/Search/Hit/HmmpfamHit.pm
- Bio/Search/Hit/PsiBlastHit.pm
- Bio/Search/Hit/PullHitI.pm
- Bio/Search/Iteration/GenericIteration.pm
- Bio/Search/Iteration/IterationI.pm
- Bio/Search/Processor.pm
- Bio/Search/Result/BlastResult.pm
- Bio/Search/Result/GenericResult.pm
- Bio/Search/Result/HMMERResult.pm
- Bio/Search/Result/HmmpfamResult.pm
- Bio/Search/Result/PullResultI.pm
- Bio/Search/Result/ResultFactory.pm
- Bio/Search/Result/ResultI.pm
- Bio/Search/Result/WABAResult.pm
- Bio/Search/SearchUtils.pm
- Bio/Search/StatisticsI.pm
- Bio/SearchDist.pm
- Bio/SearchIO.pm
- Bio/SearchIO/EventHandlerI.pm
- Bio/SearchIO/FastHitEventBuilder.pm
- Bio/SearchIO/IteratedSearchResultEventBuilder.pm
- Bio/SearchIO/SearchResultEventBuilder.pm
- Bio/SearchIO/SearchWriterI.pm
- Bio/SearchIO/Writer/BSMLResultWriter.pm
- Bio/SearchIO/Writer/GbrowseGFF.pm
- Bio/SearchIO/Writer/HSPTableWriter.pm
- Bio/SearchIO/Writer/HTMLResultWriter.pm
- Bio/SearchIO/Writer/HitTableWriter.pm
- Bio/SearchIO/Writer/ResultTableWriter.pm
- Bio/SearchIO/Writer/TextResultWriter.pm
- Bio/SearchIO/axt.pm
- Bio/SearchIO/blast.pm
- Bio/SearchIO/blasttable.pm
- Bio/SearchIO/blastxml.pm
- Bio/SearchIO/exonerate.pm
- Bio/SearchIO/fasta.pm
- Bio/SearchIO/hmmer.pm
- Bio/SearchIO/hmmer_pull.pm
- Bio/SearchIO/megablast.pm
- Bio/SearchIO/psl.pm
- Bio/SearchIO/sim4.pm
- Bio/SearchIO/waba.pm
- Bio/SearchIO/wise.pm
- Bio/Seq.pm
- Bio/Seq/BaseSeqProcessor.pm
- Bio/Seq/EncodedSeq.pm
- Bio/Seq/LargeLocatableSeq.pm
- Bio/Seq/LargePrimarySeq.pm
- Bio/Seq/LargeSeq.pm
- Bio/Seq/LargeSeqI.pm
- Bio/Seq/Meta.pm
- Bio/Seq/Meta/Array.pm
- Bio/Seq/MetaI.pm
- Bio/Seq/PrimaryQual.pm
- Bio/Seq/PrimedSeq.pm
- Bio/Seq/QualI.pm
- Bio/Seq/Quality.pm
- Bio/Seq/RichSeq.pm
- Bio/Seq/RichSeqI.pm
- Bio/Seq/SeqBuilder.pm
- Bio/Seq/SeqFactory.pm
- Bio/Seq/SeqFastaSpeedFactory.pm
- Bio/Seq/SeqWithQuality.pm
- Bio/Seq/SequenceTrace.pm
- Bio/Seq/TraceI.pm
- Bio/SeqAnalysisParserI.pm
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- Bio/SeqFeature/Computation.pm
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- Bio/SeqFeature/Gene/Exon.pm
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- Bio/SeqFeature/Gene/Poly_A_site.pm
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- Bio/SeqFeature/Similarity.pm
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- Bio/SeqFeature/Tools/FeatureNamer.pm
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- Bio/SeqFeature/TypedSeqFeatureI.pm
- Bio/SeqFeatureI.pm
- Bio/SeqI.pm
- Bio/SeqIO.pm
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- Bio/SeqIO/chaos.pm
- Bio/SeqIO/chaosxml.pm
- Bio/SeqIO/ctf.pm
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- 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
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- Bio/Tools/ERPIN.pm
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- Bio/Tools/Phylo/Phylip/ProtDist.pm
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- Bio/Tools/Prints.pm
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- Bio/Tools/PrositeScan.pm
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- Bio/Tools/RNAMotif.pm
- Bio/Tools/RandomDistFunctions.pm
- Bio/Tools/RepeatMasker.pm
- Bio/Tools/RestrictionEnzyme.pm
- Bio/Tools/Run/GenericParameters.pm
- Bio/Tools/Run/ParametersI.pm
- Bio/Tools/Run/README
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- Bio/Tools/Run/StandAloneBlast.pm
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- Bio/Tools/SeqWords.pm
- Bio/Tools/SiRNA.pm
- Bio/Tools/SiRNA/Ruleset/saigo.pm
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- Bio/Tools/Sigcleave.pm
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- Bio/Tools/Tmhmm.pm
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- Bio/Tools/ipcress.pm
- Bio/Tools/isPcr.pm
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- Bio/Tools/pSW.pm
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- Bio/Tree/AlleleNode.pm
- Bio/Tree/Compatible.pm
- Bio/Tree/DistanceFactory.pm
- Bio/Tree/Draw/Cladogram.pm
- Bio/Tree/Node.pm
- Bio/Tree/NodeI.pm
- Bio/Tree/NodeNHX.pm
- Bio/Tree/RandomFactory.pm
- Bio/Tree/Statistics.pm
- Bio/Tree/Tree.pm
- Bio/Tree/TreeFunctionsI.pm
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- Bio/TreeIO.pm
- Bio/TreeIO/TreeEventBuilder.pm
- Bio/TreeIO/cluster.pm
- Bio/TreeIO/lintree.pm
- Bio/TreeIO/newick.pm
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- Bio/UpdateableSeqI.pm
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- Bio/Variation/AAReverseMutate.pm
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- Bio/Variation/DNAMutation.pm
- Bio/Variation/IO.pm
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- Bio/Variation/IO/xml.pm
- Bio/Variation/README
- Bio/Variation/RNAChange.pm
- Bio/Variation/SNP.pm
- Bio/Variation/SeqDiff.pm
- Bio/Variation/VariantI.pm
- Bio/WebAgent.pm
- Build.PL
- Changes
- DEPENDENCIES
- DEPRECATED
- INSTALL
- INSTALL.WIN
- LICENSE
- MANIFEST
- META.yml
- Makefile.PL
- ModuleBuildBioperl.pm
- PLATFORMS
- README
- doc/Deobfuscator/Build.PL
- doc/Deobfuscator/Changes
- doc/Deobfuscator/LICENSE
- doc/Deobfuscator/MANIFEST
- doc/Deobfuscator/META.yml
- doc/Deobfuscator/Makefile.PL
- doc/Deobfuscator/README
- doc/Deobfuscator/bin/deob_index.pl
- doc/Deobfuscator/cgi-bin/deob_detail.cgi
- doc/Deobfuscator/cgi-bin/deob_flowchart.png
- doc/Deobfuscator/cgi-bin/deob_help.html
- doc/Deobfuscator/cgi-bin/deob_interface.cgi
- doc/Deobfuscator/lib/Deobfuscator.pm
- doc/Deobfuscator/t/00.load.t
- doc/Deobfuscator/t/pod.t
- doc/README
- doc/makedoc.PL
- examples/Bio-DB-GFF/load_ucsc.pl
- examples/align/align_on_codons.pl
- examples/align/aligntutorial.pl
- examples/align/clustalw.pl
- examples/align/simplealign.pl
- examples/biblio/biblio-eutils-example.pl
- examples/biblio/biblio-soap-example.pl
- examples/biblio/biblio_soap.pl
- examples/biographics/all_glyphs.pl
- examples/biographics/dynamic_glyphs.pl
- examples/biographics/feature_data.gff
- examples/biographics/feature_data.txt
- examples/biographics/lots_of_glyphs.pl
- examples/biographics/render_sequence.pl
- 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/rev_and_trans.pl
- examples/revcom_dir.pl
- examples/root/README
- examples/root/exceptions1.pl
- examples/root/exceptions2.pl
- examples/root/exceptions3.pl
- examples/root/exceptions4.pl
- examples/root/lib/Bio/PrimarySeq.pm
- examples/root/lib/Bio/PrimarySeqI.pm
- examples/root/lib/Bio/Seq.pm
- examples/root/lib/Bio/SeqI.pm
- examples/root/lib/TestInterface.pm
- examples/root/lib/TestObject.pm
- 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/run_genscan.pl
- examples/tools/run_primer3.pl
- examples/tools/seq_pattern.pl
- examples/tools/standaloneblast.pl
- examples/tree/paup2phylip.pl
- maintenance/README
- maintenance/authors.pl
- maintenance/check_NAME.pl
- maintenance/check_URLs.pl
- maintenance/modules.pl
- maintenance/ncbi_blast_switches.pl
- maintenance/pod.pl
- maintenance/symlink_script.pl
- maintenance/symlink_scripts.PLS
- 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/TAG
- scripts/Bio-DB-GFF/bp_genbank2gff.PLS
- scripts/Bio-DB-GFF/bulk_load_gff.PLS
- scripts/Bio-DB-GFF/fast_load_gff.PLS
- scripts/Bio-DB-GFF/genbank2gff3.PLS
- scripts/Bio-DB-GFF/generate_histogram.PLS
- scripts/Bio-DB-GFF/load_gff.PLS
- scripts/Bio-DB-GFF/meta_gff.PLS
- scripts/Bio-DB-GFF/process_gadfly.PLS
- scripts/Bio-DB-GFF/process_sgd.PLS
- scripts/Bio-DB-GFF/process_wormbase.PLS
- scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS
- scripts/DB/TAG
- scripts/DB/biofetch_genbank_proxy.PLS
- scripts/DB/bioflat_index.PLS
- scripts/DB/biogetseq.PLS
- scripts/DB/flanks.PLS
- scripts/README
- scripts/biblio/TAG
- scripts/biblio/biblio.PLS
- scripts/biographics/bp_embl2picture.PLS
- scripts/biographics/bp_glyphs1-demo.PLS
- scripts/biographics/bp_glyphs2-demo.PLS
- scripts/das/README
- scripts/das/TAG
- scripts/graphics/README
- scripts/graphics/TAG
- scripts/graphics/contig_draw.PLS
- scripts/graphics/feature_draw.PLS
- scripts/graphics/frend.PLS
- scripts/graphics/search_overview.PLS
- scripts/index/TAG
- scripts/index/bp_fetch.PLS
- scripts/index/bp_index.PLS
- scripts/index/bp_seqret.PLS
- scripts/popgen/composite_LD.PLS
- scripts/popgen/heterogeneity_test.PLS
- scripts/searchio/README
- scripts/searchio/TAG
- scripts/searchio/fastam9_to_table.PLS
- scripts/searchio/filter_search.PLS
- scripts/searchio/hmmer_to_table.PLS
- scripts/searchio/parse_hmmsearch.PLS
- scripts/searchio/search2table.PLS
- scripts/seq/TAG
- scripts/seq/extract_feature_seq.PLS
- scripts/seq/make_mrna_protein.PLS
- scripts/seq/seqconvert.PLS
- scripts/seq/split_seq.PLS
- scripts/seq/translate_seq.PLS
- scripts/seq/unflatten_seq.PLS
- scripts/seqstats/TAG
- scripts/seqstats/aacomp.PLS
- scripts/seqstats/chaos_plot.PLS
- scripts/seqstats/gccalc.PLS
- scripts/seqstats/oligo_count.PLS
- scripts/taxa/TAG
- scripts/taxa/classify_hits_kingdom.PLS
- scripts/taxa/local_taxonomydb_query.PLS
- scripts/taxa/query_entrez_taxa.PLS
- scripts/taxa/taxid4species.PLS
- scripts/taxa/taxonomy2tree.PLS
- scripts/tree/TAG
- scripts/tree/blast2tree.PLS
- scripts/tree/nexus2nh.PLS
- scripts/tree/tree2pag.PLS
- scripts/utilities/README
- scripts/utilities/TAG
- scripts/utilities/bp_mrtrans.PLS
- scripts/utilities/bp_nrdb.PLS
- scripts/utilities/bp_sreformat.PLS
- scripts/utilities/dbsplit.PLS
- scripts/utilities/mask_by_search.PLS
- scripts/utilities/mutate.PLS
- scripts/utilities/pairwise_kaks.PLS
- scripts/utilities/remote_blast.PLS
- scripts/utilities/search2BSML.PLS
- scripts/utilities/search2alnblocks.PLS
- scripts/utilities/search2gff.PLS
- scripts/utilities/search2tribe.PLS
- scripts/utilities/seq_length.PLS
- t/AAChange.t
- t/AAReverseMutate.t
- t/AlignIO.t
- t/AlignStats.t
- t/AlignUtil.t
- t/Allele.t
- t/Alphabet.t
- t/Annotation.t
- t/AnnotationAdaptor.t
- t/Assembly.t
- t/Biblio.t
- t/BiblioReferences.t
- t/Biblio_biofetch.t
- t/Biblio_eutils.t
- t/BioDBGFF.t
- t/BioDBSeqFeature.t
- t/BioFetch_DB.t
- t/BioGraphics.t
- t/BlastIndex.t
- t/Chain.t
- t/ClusterIO.t
- t/Coalescent.t
- t/CodonTable.t
- t/Compatible.t
- t/CoordinateGraph.t
- t/CoordinateMapper.t
- t/Correlate.t
- t/CytoMap.t
- t/DB.t
- t/DBCUTG.t
- t/DBFasta.t
- t/DNAMutation.t
- t/Domcut.t
- t/ECnumber.t
- t/ELM.t
- t/EMBL_DB.t
- t/EMBOSS_Tools.t
- t/ESEfinder.t
- t/EUtilities.t
- t/EncodedSeq.t
- t/Exception.t
- t/Exonerate.t
- t/FeatureHolder.x
- t/FeatureIO.t
- t/FootPrinter.t
- t/GDB.t
- t/GFF.t
- t/GOR4.t
- t/GOterm.t
- t/GbrowseGFF.t
- t/Gel.t
- t/GeneCoordinateMapper.t
- t/Geneid.t
- t/Genewise.t
- t/Genomewise.t
- t/Genpred.t
- t/GraphAdaptor.t
- t/GuessSeqFormat.t
- t/HNN.t
- t/HtSNP.t
- t/IUPAC.t
- t/Index.t
- t/InstanceSite.t
- t/InterProParser.t
- t/LargeLocatableSeq.t
- t/LinkageMap.t
- t/LiveSeq.t
- t/LocatableSeq.t
- t/Location.t
- t/LocationFactory.t
- t/LocusLink.t
- t/Map.t
- t/MapIO.t
- t/Matrix.t
- t/MeSH.t
- t/Measure.t
- t/MetaSeq.t
- t/MicrosatelliteMarker.t
- t/MiniMIMentry.t
- t/MitoProt.t
- t/Molphy.t
- t/MultiFile.t
- t/Mutation.t
- t/Mutator.t
- t/NetPhos.t
- t/Node.t
- t/OMIMentry.t
- t/OMIMentryAllelicVariant.t
- t/OMIMparser.t
- t/OddCodes.t
- t/Ontology.t
- t/OntologyEngine.t
- t/OntologyStore.t
- t/PAML.t
- t/Perl.t
- t/Phenotype.t
- t/PhylipDist.t
- t/PhysicalMap.t
- t/Pictogram.t
- t/PopGen.t
- t/PopGenSims.t
- t/PrimarySeq.t
- t/Primer.t
- t/Promoterwise.t
- t/ProtDist.t
- t/ProtMatrix.t
- t/ProtPsm.t
- t/Pseudowise.t
- t/QRNA.t
- t/RNAChange.t
- t/RandDistFunctions.t
- t/RandomTreeFactory.t
- t/Range.t
- t/RangeI.t
- t/RefSeq.t
- t/Registry.t
- t/Relationship.t
- t/RelationshipType.t
- t/RemoteBlast.t
- t/RepeatMasker.t
- t/RestrictionAnalysis.t
- t/RestrictionIO.t
- t/RootI.t
- t/RootIO.t
- t/RootStorable.t
- t/SNP.t
- t/Scansite.t
- t/SearchDist.t
- t/SearchIO.t
- t/Seg.t
- t/Seq.t
- t/SeqAnalysisParser.t
- t/SeqBuilder.t
- t/SeqDiff.t
- t/SeqFeatCollection.t
- t/SeqFeature.t
- t/SeqHound_DB.t
- t/SeqIO.t
- t/SeqPattern.t
- t/SeqStats.t
- t/SeqUtils.t
- t/SeqVersion.t
- t/SeqWords.t
- t/SequenceFamily.t
- t/Sigcleave.t
- t/Signalp.t
- t/Sim4.t
- t/SimilarityPair.t
- t/SimpleAlign.t
- t/SiteMatrix.t
- t/Sopma.t
- t/Species.t
- t/Spidey.t
- t/StandAloneBlast.t
- t/StructIO.t
- t/Structure.t
- t/Symbol.t
- t/TagHaplotype.t
- t/TaxonTree.t
- t/Taxonomy.t
- t/Tempfile.t
- t/Term.t
- t/Test.pm
- t/Tmhmm.t
- t/Tools.t
- t/Tree.t
- t/TreeBuild.t
- t/TreeIO.t
- t/UCSCParsers.t
- t/Unflattener.t
- t/Unflattener2.t
- t/UniGene.t
- t/Variation_IO.t
- t/WABA.t
- t/XEMBL_DB.t
- t/abi.t
- t/ace.t
- t/alignUtilities.t
- t/asciitree.t
- t/bsml_sax.t
- t/chaosxml.t
- t/cigarstring.t
- t/consed.t
- t/ctf.t
- t/data/1A11.pdb
- t/data/1A3I.pdb
- t/data/1BPT.pdb
- t/data/503384.MEGABLAST.0
- t/data/503384.MEGABLAST.2
- t/data/5X_1895.FASTXY
- t/data/8HVP.pdb
- t/data/AAC12660.fa
- t/data/AB077698.gb
- t/data/AE003528_ecoli.bls
- t/data/AE003644_Adh-genomic.gb
- t/data/AF032047.gbk
- t/data/AF165282.gb
- t/data/AHCYL1.kegg
- t/data/ATF14F8.gbk
- t/data/AY095303S1.gbk
- t/data/AY763288.gb
- t/data/AnnIX-v003.gbk
- t/data/BAB68554.gb
- t/data/BC000007.gbk
- t/data/BEL16-LTR_AG.embl
- t/data/BK000016-tpa.gbk
- t/data/BLOSUM50
- t/data/BN000066-tpa.embl
- t/data/Bird_Ovomucoids.nex
- t/data/D10483.gbk
- t/data/D12555.gbk
- t/data/DQ018368.gb
- t/data/ECAPAH02.embl
- t/data/GO.defs.test
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- t/data/Genscan.FastA
- t/data/Glimmer2.out
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- t/data/HUMBETGLOA.FASTA
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- t/data/Kingdoms_DNA.nex
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