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-1.6.924/doc/Deobfuscator/lib/Deobfuscator.pm -- Around line 90: '=item' outside of any '=over'

prereq_matches_use

List all used modules in META.yml requires

Error:

  • Ace
  • Algorithm::Cluster
  • Algorithm::Munkres
  • Array::Compare
  • Bio::ASN1::EntrezGene
  • Bio::Phylo::Factory
  • Bio::Phylo::Forest::Tree
  • Bio::Phylo::IO
  • Bio::Phylo::Matrices
  • Bio::Phylo::Matrices::Datum
  • Bio::Phylo::Matrices::Matrix
  • Bio::SeqFeature::Annotated
  • Bio::SeqFeature::Subseq
  • Bio::Tools::IsPcr
  • Bio::Tools::Run::Analysis
  • Bio::Tools::Run::AnalysisFactory
  • Bio::Tools::Run::Primer3
  • Bio::Tools::Run::Samtools
  • Convert::Binary::C
  • DBD::Pg
  • DBI
  • Error
  • GD
  • GD::Simple
  • Graph::Directed
  • GraphViz
  • HTML::HeadParser
  • HTML::TableExtract
  • HTTP::Request::Common
  • HTTP::Response
  • LWP
  • LWP::UserAgent
  • List::MoreUtils
  • PostScript::TextBlock
  • SVG
  • SVG::Graph
  • SVG::Graph::Data
  • SVG::Graph::Data::Node
  • SVG::Graph::Data::Tree
  • Set::Scalar
  • Spreadsheet::ParseExcel
  • Test::Builder::Module
  • Test::Most
  • Tree::DAG_Node
  • URI
  • URI::Escape
  • XML::DOM
  • XML::DOM::XPath
  • XML::LibXML
  • XML::LibXML::Reader
  • XML::Parser::PerlSAX
  • XML::SAX
  • XML::SAX::Base
  • XML::SAX::Writer
  • XML::Simple
  • XML::Twig
  • XML::Writer
  • parent
  • version

use_strict

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

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

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/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/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/SeqHound.pm, Bio/DB/SeqI.pm, Bio/DB/SeqVersion.pm, Bio/DB/SeqVersion/gi.pm, Bio/DB/SwissProt.pm, Bio/DB/TFBS.pm, Bio/DB/TFBS/transfac_pro.pm, Bio/DB/Taxonomy.pm, Bio/DB/Taxonomy/entrez.pm, Bio/DB/Taxonomy/flatfile.pm, Bio/DB/Taxonomy/greengenes.pm, Bio/DB/Taxonomy/list.pm, Bio/DB/Taxonomy/silva.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/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/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/BSMLResultWriter.pm, Bio/SearchIO/Writer/GbrowseGFF.pm, Bio/SearchIO/Writer/HSPTableWriter.pm, Bio/SearchIO/Writer/HTMLResultWriter.pm, Bio/SearchIO/Writer/HitTableWriter.pm, Bio/SearchIO/Writer/ResultTableWriter.pm, Bio/SearchIO/Writer/TextResultWriter.pm, Bio/SearchIO/XML/BlastHandler.pm, Bio/SearchIO/XML/PsiBlastHandler.pm, Bio/SearchIO/axt.pm, Bio/SearchIO/blast.pm, Bio/SearchIO/blast_pull.pm, Bio/SearchIO/blasttable.pm, Bio/SearchIO/blastxml.pm, Bio/SearchIO/cross_match.pm, Bio/SearchIO/erpin.pm, Bio/SearchIO/exonerate.pm, Bio/SearchIO/fasta.pm, Bio/SearchIO/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/Mitoprot.pm, Bio/Tools/Analysis/Protein/NetPhos.pm, Bio/Tools/Analysis/Protein/Scansite.pm, Bio/Tools/Analysis/Protein/Sopma.pm, Bio/Tools/Analysis/SimpleAnalysisBase.pm, Bio/Tools/AnalysisResult.pm, Bio/Tools/Blat.pm, Bio/Tools/CodonTable.pm, Bio/Tools/Coil.pm, Bio/Tools/ECnumber.pm, Bio/Tools/EMBOSS/Palindrome.pm, Bio/Tools/EPCR.pm, Bio/Tools/ERPIN.pm, Bio/Tools/ESTScan.pm, Bio/Tools/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/Infernal.pm, Bio/Tools/Lucy.pm, Bio/Tools/MZEF.pm, Bio/Tools/Match.pm, Bio/Tools/OddCodes.pm, Bio/Tools/Phylo/Gerp.pm, Bio/Tools/Phylo/Gumby.pm, Bio/Tools/Phylo/Molphy.pm, Bio/Tools/Phylo/Molphy/Result.pm, Bio/Tools/Phylo/PAML.pm, Bio/Tools/Phylo/PAML/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/RNAMotif.pm, Bio/Tools/RandomDistFunctions.pm, Bio/Tools/RepeatMasker.pm, Bio/Tools/Run/GenericParameters.pm, Bio/Tools/Run/ParametersI.pm, Bio/Tools/Run/RemoteBlast.pm, Bio/Tools/Run/StandAloneBlast.pm, Bio/Tools/Run/StandAloneNCBIBlast.pm, Bio/Tools/Run/StandAloneWUBlast.pm, Bio/Tools/Run/WrapperBase.pm, Bio/Tools/Seg.pm, Bio/Tools/SeqPattern.pm, Bio/Tools/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::Fasta::Subdir, 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::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::faux_dbh, Bio::DB::GFF::Adaptor::dbi::iterator, Bio::DB::GFF::Adaptor::dbi::mysql, Bio::DB::GFF::Adaptor::dbi::mysqlace, Bio::DB::GFF::Adaptor::dbi::mysqlcmap, Bio::DB::GFF::Adaptor::dbi::mysqlopt, Bio::DB::GFF::Adaptor::dbi::oracle, Bio::DB::GFF::Adaptor::dbi::oracleace, Bio::DB::GFF::Adaptor::dbi::pg, Bio::DB::GFF::Adaptor::dbi::pg_fts, Bio::DB::GFF::Adaptor::memory, Bio::DB::GFF::Adaptor::memory::feature_serializer, Bio::DB::GFF::Adaptor::memory::iterator, Bio::DB::GFF::Aggregator, Bio::DB::GFF::Aggregator::alignment, Bio::DB::GFF::Aggregator::clone, Bio::DB::GFF::Aggregator::coding, Bio::DB::GFF::Aggregator::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::ID_Iterator, Bio::DB::GFF::RelSegment, Bio::DB::GFF::Segment, Bio::DB::GFF::Typename, Bio::DB::GFF::Util::Binning, Bio::DB::GFF::Util::Rearrange, Bio::DB::GenBank, Bio::DB::GenPept, Bio::DB::HIV::HIVAnnotProcessor, Bio::DB::HIV::HIVQueryHelper, Bio::DB::InMemoryCache, Bio::DB::Indexed::Stream, Bio::DB::LocationI, Bio::DB::MeSH, Bio::DB::NCBIHelper, Bio::DB::Qual, Bio::DB::Query::GenBank, Bio::DB::Query::HIVQuery, Bio::DB::Query::WebQuery, Bio::DB::QueryI, Bio::DB::RandomAccessI, Bio::DB::RefSeq, Bio::DB::ReferenceI, Bio::DB::Registry, Bio::DB::SeqFeature, Bio::DB::SeqFeature::NormalizedFeature, Bio::DB::SeqFeature::NormalizedFeatureI, Bio::DB::SeqFeature::NormalizedTableFeatureI, Bio::DB::SeqFeature::Segment, Bio::DB::SeqFeature::Store::DBI::Iterator, Bio::DB::SeqFeature::Store::DBI::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::berkeleydb3, Bio::DB::SeqFeature::Store::memory, Bio::DB::SeqHound, Bio::DB::SeqI, Bio::DB::SeqVersion, Bio::DB::SeqVersion::gi, Bio::DB::SwissProt, Bio::DB::TFBS, Bio::DB::TFBS::transfac_pro, Bio::DB::Taxonomy, Bio::DB::Taxonomy::entrez, Bio::DB::Taxonomy::flatfile, Bio::DB::Taxonomy::greengenes, Bio::DB::Taxonomy::list, Bio::DB::Taxonomy::silva, 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::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::BSMLResultWriter, Bio::SearchIO::Writer::GbrowseGFF, Bio::SearchIO::Writer::HSPTableWriter, Bio::SearchIO::Writer::HTMLResultWriter, Bio::SearchIO::Writer::HitTableWriter, Bio::SearchIO::Writer::ResultTableWriter, Bio::SearchIO::Writer::TextResultWriter, Bio::SearchIO::XML::BlastHandler, Bio::SearchIO::XML::PsiBlastHandler, Bio::SearchIO::axt, Bio::SearchIO::blast, Bio::SearchIO::blast_pull, Bio::SearchIO::blasttable, Bio::SearchIO::blastxml, Bio::SearchIO::cross_match, Bio::SearchIO::erpin, Bio::SearchIO::exonerate, Bio::SearchIO::fasta, Bio::SearchIO::hmmer, Bio::SearchIO::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::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::Mitoprot, Bio::Tools::Analysis::Protein::NetPhos, Bio::Tools::Analysis::Protein::Scansite, Bio::Tools::Analysis::Protein::Sopma, Bio::Tools::Analysis::SimpleAnalysisBase, Bio::Tools::AnalysisResult, Bio::Tools::Blat, Bio::Tools::CodonTable, Bio::Tools::Coil, Bio::Tools::ECnumber, Bio::Tools::EMBOSS::Palindrome, Bio::Tools::EPCR, Bio::Tools::ERPIN, Bio::Tools::ESTScan, Bio::Tools::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::Infernal, Bio::Tools::Lucy, Bio::Tools::MZEF, Bio::Tools::Match, Bio::Tools::OddCodes, Bio::Tools::Phylo::Gerp, Bio::Tools::Phylo::Gumby, Bio::Tools::Phylo::Molphy, Bio::Tools::Phylo::Molphy::Result, Bio::Tools::Phylo::PAML, Bio::Tools::Phylo::PAML::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::RNAMotif, Bio::Tools::RandomDistFunctions, Bio::Tools::RepeatMasker, Bio::Tools::Run::GenericParameters, Bio::Tools::Run::ParametersI, Bio::Tools::Run::StandAloneWUBlast, Bio::Tools::Run::WrapperBase, Bio::Tools::Seg, Bio::Tools::SeqPattern, Bio::Tools::SeqStats, Bio::Tools::SeqWords, Bio::Tools::Sigcleave, Bio::Tools::Signalp, Bio::Tools::Signalp::ExtendedSignalp, Bio::Tools::Sim4::Exon, Bio::Tools::Sim4::Results, Bio::Tools::Spidey::Exon, Bio::Tools::Spidey::Results, Bio::Tools::TandemRepeatsFinder, Bio::Tools::TargetP, Bio::Tools::Tmhmm, Bio::Tools::dpAlign, Bio::Tools::ipcress, Bio::Tools::isPcr, Bio::Tools::pICalculator, Bio::Tools::pSW, Bio::Tools::tRNAscanSE, Bio::Tree::AlleleNode, Bio::Tree::AnnotatableNode, Bio::Tree::Compatible, Bio::Tree::DistanceFactory, Bio::Tree::Draw::Cladogram, Bio::Tree::Node, Bio::Tree::NodeI, Bio::Tree::NodeNHX, Bio::Tree::RandomFactory, Bio::Tree::Statistics, Bio::Tree::Tree, Bio::Tree::TreeFunctionsI, Bio::Tree::TreeI, Bio::TreeIO, Bio::TreeIO::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

build_prereq_matches_use

List all modules used in the test suite in META.yml build_requires

Error:

  • version

meta_yml_has_repository_resource

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

Modules

Name Abstract Version View
Bio::Align::AlignI An interface for describing sequence alignments. 1.006924 metacpan
Bio::Align::DNAStatistics Calculate some statistics for a DNA alignment 1.006924 metacpan
Bio::Align::Graphics Graphic Rendering of Bio::Align::AlignI Objects 1.006924 metacpan
Bio::Align::PairwiseStatistics Base statistic object for Pairwise Alignments 1.006924 metacpan
Bio::Align::ProteinStatistics Calculate Protein Alignment statistics (mostly distances) 1.006924 metacpan
Bio::Align::StatisticsI Calculate some statistics for an alignment 1.006924 metacpan
Bio::Align::Utilities A collection of utilities regarding converting and manipulating alignment objects 1.006924 metacpan
Bio::AlignIO Handler for AlignIO Formats 1.006924 metacpan
Bio::AlignIO::Handler::GenericAlignHandler Bio::HandlerI-based generic data handler class for alignment-based data 1.006924 metacpan
Bio::AlignIO::arp ARP MSA Sequence input/output stream 1.006924 metacpan
Bio::AlignIO::bl2seq bl2seq sequence input/output stream 1.006924 metacpan
Bio::AlignIO::clustalw clustalw sequence input/output stream 1.006924 metacpan
Bio::AlignIO::emboss Parse EMBOSS alignment output (from applications water and needle) 1.006924 metacpan
Bio::AlignIO::fasta fasta MSA Sequence input/output stream 1.006924 metacpan
Bio::AlignIO::largemultifasta Largemultifasta MSA Sequence input/output stream 1.006924 metacpan
Bio::AlignIO::maf Multiple Alignment Format sequence input stream 1.006924 metacpan
Bio::AlignIO::mase mase sequence input/output stream 1.006924 metacpan
Bio::AlignIO::mega Parse and Create MEGA format data files 1.006924 metacpan
Bio::AlignIO::meme meme sequence input/output stream 1.006924 metacpan
Bio::AlignIO::metafasta Metafasta MSA Sequence input/output stream 1.006924 metacpan
Bio::AlignIO::msf msf sequence input/output stream 1.006924 metacpan
Bio::AlignIO::nexml NeXML format sequence alignment input/output stream driver 1.006924 metacpan
Bio::AlignIO::nexus NEXUS format sequence input/output stream 1.006924 metacpan
Bio::AlignIO::pfam pfam sequence input/output stream 1.006924 metacpan
Bio::AlignIO::phylip PHYLIP format sequence input/output stream 1.006924 metacpan
Bio::AlignIO::po po MSA Sequence input/output stream 1.006924 metacpan
Bio::AlignIO::proda proda sequence input/output stream 1.006924 metacpan
Bio::AlignIO::prodom prodom sequence input/output stream 1.006924 metacpan
Bio::AlignIO::psi Read/Write PSI-BLAST profile alignment files 1.006924 metacpan
Bio::AlignIO::selex selex sequence input/output stream 1.006924 metacpan
Bio::AlignIO::stockholm stockholm sequence input/output stream 1.006924 metacpan
Bio::AlignIO::xmfa XMFA MSA Sequence input/output stream 1.006924 metacpan
Bio::AnalysisI An interface to any (local or remote) analysis tool 1.006924 metacpan
Bio::AnalysisI::JobI 1.006924 metacpan
Bio::AnalysisParserI Generic analysis output parser interface 1.006924 metacpan
Bio::AnalysisResultI Interface for analysis result objects 1.006924 metacpan
Bio::AnnotatableI the base interface an annotatable object must implement 1.006924 metacpan
Bio::Annotation::AnnotationFactory Instantiates a new Bio::AnnotationI (or derived class) through a factory 1.006924 metacpan
Bio::Annotation::Collection Default Perl implementation of AnnotationCollectionI 1.006924 metacpan
Bio::Annotation::Comment A comment object, holding text 1.006924 metacpan
Bio::Annotation::DBLink untyped links between databases 1.006924 metacpan
Bio::Annotation::OntologyTerm An ontology term adapted to AnnotationI 1.006924 metacpan
Bio::Annotation::Reference Specialised DBLink object for Literature References 1.006924 metacpan
Bio::Annotation::Relation Relationship (pairwise) with other objects SeqI and NodeI; 1.006924 metacpan
Bio::Annotation::SimpleValue A simple scalar 1.006924 metacpan
Bio::Annotation::StructuredValue A scalar with embedded structured information 1.006924 metacpan
Bio::Annotation::TagTree AnnotationI with tree-like hierarchal key-value relationships ('structured tags') that can be represented as simple text. 1.006924 metacpan
Bio::Annotation::Target Provides an object which represents a target (ie, a similarity hit) from one object to something in another database 1.006924 metacpan
Bio::Annotation::Tree Provide a tree as an annotation to a Bio::AnnotatableI object 1.006924 metacpan
Bio::Annotation::TypeManager Manages types for annotation collections 1.006924 metacpan
Bio::AnnotationCollectionI Interface for annotation collections 1.006924 metacpan
Bio::AnnotationI Annotation interface 1.006924 metacpan
Bio::Assembly::Contig Perl module to hold and manipulate sequence assembly contigs. 1.006924 metacpan
Bio::Assembly::ContigAnalysis 1.006924 metacpan
Bio::Assembly::IO Handler for Assembly::IO Formats 1.006924 metacpan
Bio::Assembly::IO::ace module to load ACE files from various assembly programs 1.006924 metacpan
Bio::Assembly::IO::bowtie An IO module for assemblies in Bowtie format *BETA* 1.006924 metacpan
Bio::Assembly::IO::maq Driver to read assembly files in maq format *BETA* 1.006924 metacpan
Bio::Assembly::IO::phrap driver to load phrap.out files. 1.006924 metacpan
Bio::Assembly::IO::sam An IO module for assemblies in Sam format *BETA* 1.006924 metacpan
Bio::Assembly::IO::tigr Driver to read and write assembly files in the TIGR Assembler v2 default format. 1.006924 metacpan
Bio::Assembly::Scaffold Perl module to hold and manipulate sequence assembly data. 1.006924 metacpan
Bio::Assembly::ScaffoldI Abstract Inteface of Sequence Assemblies 1.006924 metacpan
Bio::Assembly::Singlet Perl module to hold and manipulate singlets from sequence assembly contigs. 1.006924 metacpan
Bio::Assembly::Tools::ContigSpectrum create and manipulate contig spectra 1.006924 metacpan
Bio::Cluster::ClusterFactory Instantiates a new Bio::ClusterI (or derived class) through a factory 1.006924 metacpan
Bio::Cluster::FamilyI Family Interface 1.006924 metacpan
Bio::Cluster::SequenceFamily Sequence Family object 1.006924 metacpan
Bio::Cluster::UniGene UniGene object 1.006924 metacpan
Bio::Cluster::UniGeneI abstract interface of UniGene object 1.006924 metacpan
Bio::ClusterI Cluster Interface 1.006924 metacpan
Bio::ClusterIO Handler for Cluster Formats 1.006924 metacpan
Bio::ClusterIO::dbsnp dbSNP input stream 1.006924 metacpan
Bio::ClusterIO::unigene UniGene input stream 1.006924 metacpan
Bio::CodonUsage::IO for reading and writing codon usage tables to file 1.006924 metacpan
Bio::CodonUsage::Table for access to the Codon usage Database at http://www.kazusa.or.jp/codon. 1.006924 metacpan
Bio::Coordinate::Chain 1.006924 metacpan
Bio::Coordinate::Collection 1.006924 metacpan
Bio::Coordinate::ExtrapolatingPair 1.006924 metacpan
Bio::Coordinate::GeneMapper 1.006924 metacpan
Bio::Coordinate::Graph 1.006924 metacpan
Bio::Coordinate::MapperI 1.006924 metacpan
Bio::Coordinate::Pair 1.006924 metacpan
Bio::Coordinate::Result 1.006924 metacpan
Bio::Coordinate::Result::Gap 1.006924 metacpan
Bio::Coordinate::Result::Match 1.006924 metacpan
Bio::Coordinate::ResultI 1.006924 metacpan
Bio::Coordinate::Utils 1.006924 metacpan
Bio::DB::Ace Database object interface to ACeDB servers 1.006924 metacpan
Bio::DB::BioFetch Database object interface to BioFetch retrieval 1.006924 metacpan
Bio::DB::CUTG for access to the Codon usage Database at http://www.kazusa.or.jp/codon. 1.006924 metacpan
Bio::DB::DBFetch Database object for retrieving using the dbfetch script 1.006924 metacpan
Bio::DB::EMBL Database object interface for EMBL entry retrieval 1.006924 metacpan
Bio::DB::EntrezGene Database object interface to Entrez Gene 1.006924 metacpan
Bio::DB::Expression DESCRIPTION of Object 1.006924 metacpan
Bio::DB::Expression::geo *** DESCRIPTION of Class 1.006924 metacpan
Bio::DB::Failover A Bio::DB::RandomAccessI compliant class which wraps a prioritized list of DBs 1.006924 metacpan
Bio::DB::Fasta Fast indexed access to fasta files 1.006924 metacpan
Bio::DB::Fasta::Subdir 1.006924 metacpan
Bio::DB::FileCache In file cache for BioSeq objects 1.006924 metacpan
Bio::DB::Flat Interface for indexed flat files 1.006924 metacpan
Bio::DB::Flat::BDB Interface for BioHackathon standard BDB-indexed flat file 1.006924 metacpan
Bio::DB::Flat::BDB::embl embl adaptor for Open-bio standard BDB-indexed flat file 1.006924 metacpan
Bio::DB::Flat::BDB::fasta fasta adaptor for Open-bio standard BDB-indexed flat file 1.006924 metacpan
Bio::DB::Flat::BDB::genbank genbank adaptor for Open-bio standard BDB-indexed flat file 1.006924 metacpan
Bio::DB::Flat::BDB::swiss swissprot adaptor for Open-bio standard BDB-indexed flat file 1.006924 metacpan
Bio::DB::Flat::BinarySearch BinarySearch search indexing system for sequence files 1.006924 metacpan
Bio::DB::GFF Storage and retrieval of sequence annotation data 1.006924 metacpan
Bio::DB::GFF::Adaptor::ace ace interface (for multiple inheritance) 1.006924 metacpan
Bio::DB::GFF::Adaptor::berkeleydb Bio::DB::GFF database adaptor for in-memory databases 1.006924 metacpan
Bio::DB::GFF::Adaptor::berkeleydb::iterator iterator for Bio::DB::GFF::Adaptor::berkeleydb 1.006924 metacpan
Bio::DB::GFF::Adaptor::biofetch Cache BioFetch objects in a Bio::DB::GFF database 1.006924 metacpan
Bio::DB::GFF::Adaptor::biofetch_oracle Cache BioFetch objects in a Bio::DB::GFF database 1.006924 metacpan
Bio::DB::GFF::Adaptor::dbi Database adaptor for DBI (SQL) databases 1.006924 metacpan
Bio::DB::GFF::Adaptor::dbi::caching_handle Cache for database handles 1.006924 metacpan
Bio::DB::GFF::Adaptor::dbi::faux_dbh 1.006924 metacpan
Bio::DB::GFF::Adaptor::dbi::iterator iterator for Bio::DB::GFF::Adaptor::dbi 1.006924 metacpan
Bio::DB::GFF::Adaptor::dbi::mysql Database adaptor for a specific mysql schema 1.006924 metacpan
Bio::DB::GFF::Adaptor::dbi::mysqlace Unholy union between mysql GFF database and acedb database 1.006924 metacpan
Bio::DB::GFF::Adaptor::dbi::mysqlcmap Database adaptor for an integraded CMap/GBrowse mysql schema 1.006924 metacpan
Bio::DB::GFF::Adaptor::dbi::mysqlopt Deprecated database adaptor 1.006924 metacpan
Bio::DB::GFF::Adaptor::dbi::oracle Database adaptor for a specific oracle schema 1.006924 metacpan
Bio::DB::GFF::Adaptor::dbi::oracleace Unholy union between oracle GFF database and acedb database 1.006924 metacpan
Bio::DB::GFF::Adaptor::dbi::pg Database adaptor for a specific postgres schema 1.006924 metacpan
Bio::DB::GFF::Adaptor::dbi::pg_fts Database adaptor for a specific postgres schema with a TSearch2 implementation 1.006924 metacpan
Bio::DB::GFF::Adaptor::memory Bio::DB::GFF database adaptor for in-memory databases 1.006924 metacpan
Bio::DB::GFF::Adaptor::memory::feature_serializer utility methods for serializing and deserializing GFF features 1.006924 metacpan
Bio::DB::GFF::Adaptor::memory::iterator iterator for Bio::DB::GFF::Adaptor::memory 1.006924 metacpan
Bio::DB::GFF::Aggregator Aggregate GFF groups into composite features 1.006924 metacpan
Bio::DB::GFF::Aggregator::alignment Alignment aggregator 1.006924 metacpan
Bio::DB::GFF::Aggregator::clone Clone aggregator 1.006924 metacpan
Bio::DB::GFF::Aggregator::coding The Coding Region Aggregator 1.006924 metacpan
Bio::DB::GFF::Aggregator::gene Sequence Ontology Geene 1.006924 metacpan
Bio::DB::GFF::Aggregator::match Match aggregator 1.006924 metacpan
Bio::DB::GFF::Aggregator::none No aggregation 1.006924 metacpan
Bio::DB::GFF::Aggregator::orf An aggregator for orf regions 1.006924 metacpan
Bio::DB::GFF::Aggregator::processed_transcript Sequence Ontology Transcript 1.006924 metacpan
Bio::DB::GFF::Aggregator::so_transcript Sequence Ontology Transcript 1.006924 metacpan
Bio::DB::GFF::Aggregator::transcript Transcript aggregator 1.006924 metacpan
Bio::DB::GFF::Aggregator::ucsc_acembly UCSC acembly aggregator 1.006924 metacpan
Bio::DB::GFF::Aggregator::ucsc_ensgene UCSC ensGene aggregator 1.006924 metacpan
Bio::DB::GFF::Aggregator::ucsc_genscan UCSC genscan aggregator 1.006924 metacpan
Bio::DB::GFF::Aggregator::ucsc_refgene UCSC refGene aggregator 1.006924 metacpan
Bio::DB::GFF::Aggregator::ucsc_sanger22 UCSC sanger22 aggregator 1.006924 metacpan
Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo UCSC sanger22pseudo aggregator 1.006924 metacpan
Bio::DB::GFF::Aggregator::ucsc_softberry UCSC softberry aggregator 1.006924 metacpan
Bio::DB::GFF::Aggregator::ucsc_twinscan UCSC twinscan aggregator 1.006924 metacpan
Bio::DB::GFF::Aggregator::ucsc_unigene UCSC UniGene aggregator 1.006924 metacpan
Bio::DB::GFF::Featname The name of a feature 1.006924 metacpan
Bio::DB::GFF::Feature A relative segment identified by a feature type 1.006924 metacpan
Bio::DB::GFF::FeatureIterator 1.006924 metacpan
Bio::DB::GFF::Homol A segment of DNA that is homologous to another 1.006924 metacpan
Bio::DB::GFF::ID_Iterator 1.006924 metacpan
Bio::DB::GFF::RelSegment Sequence segment with relative coordinate support 1.006924 metacpan
Bio::DB::GFF::Segment Simple DNA segment object 1.006924 metacpan
Bio::DB::GFF::Typename The name of a feature type 1.006924 metacpan
Bio::DB::GFF::Util::Binning binning utility for Bio::DB::GFF index 1.006924 metacpan
Bio::DB::GFF::Util::Rearrange rearrange utility 1.006924 metacpan
Bio::DB::GenBank Database object interface to GenBank 1.006924 metacpan
Bio::DB::GenPept Database object interface to GenPept 1.006924 metacpan
Bio::DB::GenericWebAgent helper base class for parameter-based remote server access and response retrieval. 1.006924 metacpan
Bio::DB::HIV Database object interface to the Los Alamos HIV Sequence Database 1.006924 metacpan
Bio::DB::HIV::HIVAnnotProcessor 1.006924 metacpan
Bio::DB::HIV::HIVQueryHelper Routines and packages used by Bio::DB::HIV and Bio::DB::Query::HIVQuery 1.006924 metacpan
Bio::DB::InMemoryCache Abstract interface for a sequence database 1.006924 metacpan
Bio::DB::Indexed::Stream 1.006924 metacpan
Bio::DB::IndexedBase Base class for modules using indexed sequence files 1.006924 metacpan
Bio::DB::LocationI A RandomAccessI-like abstract interface for retrieving location data from a sequence database and returning Bio::LocationI objects 1.006924 metacpan
Bio::DB::MeSH Term retrieval from a Web MeSH database 1.006924 metacpan
Bio::DB::NCBIHelper A collection of routines useful for queries to NCBI databases. 1.006924 metacpan
Bio::DB::Qual Fast indexed access to quality files 1.006924 metacpan
Bio::DB::Query::GenBank Build a GenBank Entrez Query 1.006924 metacpan
Bio::DB::Query::HIVQuery Query interface to the Los Alamos HIV Sequence Database 1.006924 metacpan
Bio::DB::Query::WebQuery Helper class for web-based sequence queryies 1.006924 metacpan
Bio::DB::QueryI Object Interface to queryable sequence databases 1.006924 metacpan
Bio::DB::RandomAccessI Abstract interface for a sequence database 1.006924 metacpan
Bio::DB::RefSeq Database object interface for RefSeq retrieval 1.006924 metacpan
Bio::DB::ReferenceI A RandomAccessI-like abstract interface for retrieving Reference data from a sequence database and returning Bio::Annotation::Reference objects 1.006924 metacpan
Bio::DB::Registry Access to the Open Bio Database Access registry scheme 1.006924 metacpan
Bio::DB::SeqFeature Normalized feature for use with Bio::DB::SeqFeature::Store 1.006924 metacpan
Bio::DB::SeqFeature::NormalizedFeature Normalized feature for use with Bio::DB::SeqFeature::Store 1.006924 metacpan
Bio::DB::SeqFeature::NormalizedFeatureI Interface for normalized features 1.006924 metacpan
Bio::DB::SeqFeature::NormalizedTableFeatureI Interface for normalized features whose hierarchy is stored in a table 1.006924 metacpan
Bio::DB::SeqFeature::Segment Location-based access to genome annotation data 1.006924 metacpan
Bio::DB::SeqFeature::Store Storage and retrieval of sequence annotation data 1.006924 metacpan
Bio::DB::SeqFeature::Store::DBI::Iterator utility methods for creating and iterating over SeqFeature records 1.006924 metacpan
Bio::DB::SeqFeature::Store::DBI::Pg PostgreSQL implementation of Bio::DB::SeqFeature::Store 1.006924 metacpan
Bio::DB::SeqFeature::Store::DBI::SQLite SQLite implementation of Bio::DB::SeqFeature::Store 1.006924 metacpan
Bio::DB::SeqFeature::Store::DBI::mysql Mysql implementation of Bio::DB::SeqFeature::Store 1.006924 metacpan
Bio::DB::SeqFeature::Store::FeatureFileLoader feature file loader for Bio::DB::SeqFeature::Store 1.006924 metacpan
Bio::DB::SeqFeature::Store::FeatureIterator 1.006924 metacpan
Bio::DB::SeqFeature::Store::GFF2Loader GFF2 file loader for Bio::DB::SeqFeature::Store 1.006924 metacpan
Bio::DB::SeqFeature::Store::GFF3Loader GFF3 file loader for Bio::DB::SeqFeature::Store 1.006924 metacpan
Bio::DB::SeqFeature::Store::LoadHelper Internal utility for Bio::DB::SeqFeature::Store 1.006924 metacpan
Bio::DB::SeqFeature::Store::Loader Loader 1.006924 metacpan
Bio::DB::SeqFeature::Store::bdb fetch and store objects from a BerkeleyDB 1.006924 metacpan
Bio::DB::SeqFeature::Store::berkeleydb Storage and retrieval of sequence annotation data in Berkeleydb files 1.006924 metacpan
Bio::DB::SeqFeature::Store::berkeleydb3 Storage and retrieval of sequence annotation data in Berkeleydb files 1.006924 metacpan
Bio::DB::SeqFeature::Store::berkeleydb::Iterator 1.006924 metacpan
Bio::DB::SeqFeature::Store::memory In-memory implementation of Bio::DB::SeqFeature::Store 1.006924 metacpan
Bio::DB::SeqFeature::Store::memory::Iterator 1.006924 metacpan
Bio::DB::SeqHound Database object interface to SeqHound 1.006924 metacpan
Bio::DB::SeqI Abstract Interface for Sequence databases 1.006924 metacpan
Bio::DB::SeqVersion front end to querying databases for identifier versions 1.006924 metacpan
Bio::DB::SeqVersion::gi interface to NCBI Sequence Revision History page 1.006924 metacpan
Bio::DB::SwissProt Database object interface to SwissProt retrieval 1.006924 metacpan
Bio::DB::TFBS Access to a Transcription Factor Binding Site database 1.006924 metacpan
Bio::DB::TFBS::transfac_pro An implementation of Bio::DB::TFBS which uses local flat files for transfac pro 1.006924 metacpan
Bio::DB::Taxonomy Access to a taxonomy database 1.006924 metacpan
Bio::DB::Taxonomy::entrez Taxonomy Entrez driver 1.006924 metacpan
Bio::DB::Taxonomy::flatfile Use the NCBI taxonomy from local indexed flat files 1.006924 metacpan
Bio::DB::Taxonomy::greengenes Use the Greengenes taxonomy 1.006924 metacpan
Bio::DB::Taxonomy::list An implementation of Bio::DB::Taxonomy that accepts lists of words to build a database 1.006924 metacpan
Bio::DB::Taxonomy::silva Use the Silva taxonomy 1.006924 metacpan
Bio::DB::Universal Artificial database that delegates to specific databases 1.006924 metacpan
Bio::DB::UpdateableSeqI An interface for writing to a database of sequences. 1.006924 metacpan
Bio::DB::WebDBSeqI Object Interface to generalize Web Databases for retrieving sequences 1.006924 metacpan
Bio::DBLinkContainerI Abstract interface for any object wanting to use database cross references 1.006924 metacpan
Bio::Das::FeatureTypeI Simple interface to Sequence Ontology feature types 1.006924 metacpan
Bio::Das::SegmentI DAS-style access to a feature database 1.006924 metacpan
Bio::DasI DAS-style access to a feature database 1.006924 metacpan
Bio::DescribableI interface for objects with human readable names and descriptions 1.006924 metacpan
Bio::Draw::Pictogram generate SVG output of Pictogram display for consensus motifs 1.006924 metacpan
Bio::Event::EventGeneratorI This interface describes the basic event generator class. 1.006924 metacpan
Bio::Event::EventHandlerI An Event Handler Interface 1.006924 metacpan
Bio::Factory::AnalysisI An interface to analysis tool factory 1.006924 metacpan
Bio::Factory::ApplicationFactoryI Interface class for Application Factories 1.006924 metacpan
Bio::Factory::DriverFactory Base class for factory classes loading drivers 1.006924 metacpan
Bio::Factory::FTLocationFactory A FeatureTable Location Parser 1.006924 metacpan
Bio::Factory::LocationFactoryI A factory interface for generating locations from a string 1.006924 metacpan
Bio::Factory::MapFactoryI A Factory for getting markers 1.006924 metacpan
Bio::Factory::ObjectBuilderI Interface for an object builder 1.006924 metacpan
Bio::Factory::ObjectFactory Instantiates a new Bio::Root::RootI (or derived class) through a factory 1.006924 metacpan
Bio::Factory::ObjectFactoryI A General object creator factory 1.006924 metacpan
Bio::Factory::SeqAnalysisParserFactory class capable of creating SeqAnalysisParserI compliant parsers 1.006924 metacpan
Bio::Factory::SeqAnalysisParserFactoryI interface describing objects capable of creating SeqAnalysisParserI compliant parsers 1.006924 metacpan
Bio::Factory::SequenceFactoryI This interface allows for generic building of sequences in factories which create sequences (like SeqIO) 1.006924 metacpan
Bio::Factory::SequenceProcessorI Interface for chained sequence processing algorithms 1.006924 metacpan
Bio::Factory::SequenceStreamI Interface describing the basics of a Sequence Stream. 1.006924 metacpan
Bio::Factory::TreeFactoryI Factory Interface for getting and writing trees from/to a data stream 1.006924 metacpan
Bio::FeatureHolderI the base interface an object with features must implement 1.006924 metacpan
Bio::HandlerBaseI Interface class for handler methods which interact with any event-driven parsers (drivers). 1.006924 metacpan
Bio::IdCollectionI interface for objects with multiple identifiers 1.006924 metacpan
Bio::IdentifiableI interface for objects with identifiers 1.006924 metacpan
Bio::Index::Abstract Abstract interface for indexing a flat file 1.006924 metacpan
Bio::Index::AbstractSeq base class for AbstractSeq 1.006924 metacpan
Bio::Index::Blast Indexes Blast reports and supports retrieval based on query accession(s) 1.006924 metacpan
Bio::Index::BlastTable Indexes tabular Blast reports (-m 8 or -m 9 format) and supports retrieval based on query accession(s) 1.006924 metacpan
Bio::Index::EMBL Interface for indexing (multiple) EMBL/Swissprot .dat files (i.e. flat file EMBL/Swissprot format). 1.006924 metacpan
Bio::Index::Fasta Interface for indexing (multiple) fasta files 1.006924 metacpan
Bio::Index::Fastq Interface for indexing (multiple) fastq files 1.006924 metacpan
Bio::Index::GenBank Interface for indexing one or more GenBank files (i.e. flat file GenBank format). 1.006924 metacpan
Bio::Index::Hmmer indexes HMMER reports and supports retreival based on query 1.006924 metacpan
Bio::Index::Qual Interface for indexing (multiple) fasta qual files 1.006924 metacpan
Bio::Index::Stockholm 1.006924 metacpan
Bio::Index::SwissPfam Interface for indexing swisspfam files 1.006924 metacpan
Bio::Index::Swissprot Interface for indexing one or more Swissprot files. 1.006924 metacpan
Bio::LiveSeq::AARange AARange abstract class for LiveSeq 1.006924 metacpan
Bio::LiveSeq::Chain DoubleChain DataStructure for Perl 1.006924 metacpan
Bio::LiveSeq::ChainI Double linked chain data structure 1.006924 metacpan
Bio::LiveSeq::DNA DNA object for LiveSeq 1.006924 metacpan
Bio::LiveSeq::Exon Range abstract class for LiveSeq 1.006924 metacpan
Bio::LiveSeq::Gene Range abstract class for LiveSeq 1.006924 metacpan
Bio::LiveSeq::IO::BioPerl Loader for LiveSeq from EMBL entries with BioPerl 1.006924 metacpan
Bio::LiveSeq::IO::Loader Parent Loader for LiveSeq 1.006924 metacpan
Bio::LiveSeq::Intron Range abstract class for LiveSeq 1.006924 metacpan
Bio::LiveSeq::Mutation Mutation event descriptor class 1.006924 metacpan
Bio::LiveSeq::Mutator Package mutating LiveSequences 1.006924 metacpan
Bio::LiveSeq::Prim_Transcript Prim_Transcript class for LiveSeq 1.006924 metacpan
Bio::LiveSeq::Range Range abstract class for LiveSeq 1.006924 metacpan
Bio::LiveSeq::Repeat_Region Repeat_Region class for LiveSeq 1.006924 metacpan
Bio::LiveSeq::Repeat_Unit Repeat_Unit class for LiveSeq 1.006924 metacpan
Bio::LiveSeq::SeqI Abstract sequence interface class for LiveSeq 1.006924 metacpan
Bio::LiveSeq::Transcript Transcript class for LiveSeq 1.006924 metacpan
Bio::LiveSeq::Translation Translation class for LiveSeq 1.006924 metacpan
Bio::LocatableSeq 1.006924 metacpan
Bio::Location::Atomic Implementation of a Atomic Location on a Sequence 1.006924 metacpan
Bio::Location::AvWithinCoordPolicy class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise 1.006924 metacpan
Bio::Location::CoordinatePolicyI Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location 1.006924 metacpan
Bio::Location::Fuzzy Implementation of a Location on a Sequence which has unclear start and/or end locations 1.006924 metacpan
Bio::Location::FuzzyLocationI Abstract interface of a Location on a Sequence which has unclear start/end location 1.006924 metacpan
Bio::Location::NarrowestCoordPolicy class implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range 1.006924 metacpan
Bio::Location::Simple Implementation of a Simple Location on a Sequence 1.006924 metacpan
Bio::Location::Split Implementation of a Location on a Sequence which has multiple locations (start/end points) 1.006924 metacpan
Bio::Location::SplitLocationI Abstract interface of a Location on a Sequence which has multiple locations (start/end points) 1.006924 metacpan
Bio::Location::WidestCoordPolicy class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable range 1.006924 metacpan
Bio::LocationI Abstract interface of a Location on a Sequence 1.006924 metacpan
Bio::Map::Clone An central map object representing a clone 1.006924 metacpan
Bio::Map::Contig A MapI implementation handling the contigs of a Physical Map (such as FPC) 1.006924 metacpan
Bio::Map::CytoMap A Bio::MapI compliant map implementation handling cytogenic bands 1.006924 metacpan
Bio::Map::CytoMarker An object representing a marker. 1.006924 metacpan
Bio::Map::CytoPosition Marker class with cytogenetic band storing attributes 1.006924 metacpan
Bio::Map::EntityI An Entity Interface 1.006924 metacpan
Bio::Map::FPCMarker An central map object representing a marker 1.006924 metacpan
Bio::Map::Gene An gene modelled as a mappable element. 1.006924 metacpan
Bio::Map::GeneMap A MapI implementation to represent the area around a gene 1.006924 metacpan
Bio::Map::GenePosition A typed position, suitable for modelling the various regions of a gene. 1.006924 metacpan
Bio::Map::GeneRelative Represents being relative to named sub-regions of a gene. 1.006924 metacpan
Bio::Map::LinkageMap A representation of a genetic linkage map. 1.006924 metacpan
Bio::Map::LinkagePosition Create a Position for a Marker that will be placed on a Bio::Map::LinkageMap 1.006924 metacpan
Bio::Map::MapI Interface for describing Map objects in bioperl 1.006924 metacpan
Bio::Map::Mappable An object representing a generic map element that can have multiple locations in several maps. 1.006924 metacpan
Bio::Map::MappableI An object that can be placed in a map 1.006924 metacpan
Bio::Map::Marker An central map object representing a generic marker that can have multiple location in several maps. 1.006924 metacpan
Bio::Map::MarkerI Interface for basic marker functionality 1.006924 metacpan
Bio::Map::Microsatellite An object representing a Microsatellite marker. 1.006924 metacpan
Bio::Map::OrderedPosition Abstracts the notion of a member of an ordered list of markers. Each marker is a certain distance from the one in the ordered list before it. 1.006924 metacpan
Bio::Map::OrderedPositionWithDistance Abstracts the notion of a member of an ordered list of markers. Each marker is a certain distance from the one in the ordered list before it. 1.006924 metacpan
Bio::Map::Physical A class for handling a Physical Map (such as FPC) 1.006924 metacpan
Bio::Map::Position A single position of a Marker, or the range over which that marker lies, in a Map 1.006924 metacpan
Bio::Map::PositionHandler A Position Handler Implementation 1.006924 metacpan
Bio::Map::PositionHandlerI A Position Handler Interface 1.006924 metacpan
Bio::Map::PositionI Abstracts the notion of a position having a value in the context of a marker and a Map 1.006924 metacpan
Bio::Map::PositionWithSequence A position with a sequence. 1.006924 metacpan
Bio::Map::Prediction An object representing the predictions of something that can have multiple locations in several maps. 1.006924 metacpan
Bio::Map::Relative Represents what a Position's coordiantes are relative to. 1.006924 metacpan
Bio::Map::RelativeI Interface for describing what a Position's coordiantes are relative to. 1.006924 metacpan
Bio::Map::SimpleMap A MapI implementation handling the basics of a Map 1.006924 metacpan
Bio::Map::TranscriptionFactor A transcription factor modelled as a mappable element 1.006924 metacpan
Bio::MapIO A Map Factory object 1.006924 metacpan
Bio::MapIO::fpc A FPC Map reader 1.006924 metacpan
Bio::MapIO::mapmaker A Mapmaker Map reader 1.006924 metacpan
Bio::Matrix::Generic A generic matrix implementation 1.006924 metacpan
Bio::Matrix::IO A factory for Matrix parsing 1.006924 metacpan
Bio::Matrix::IO::mlagan A parser for the mlagan substitution matrix 1.006924 metacpan
Bio::Matrix::IO::phylip A parser for PHYLIP distance matricies 1.006924 metacpan
Bio::Matrix::IO::scoring A parser for PAM/BLOSUM matricies 1.006924 metacpan
Bio::Matrix::MatrixI An interface for describing a Matrix 1.006924 metacpan
Bio::Matrix::Mlagan A generic matrix with mlagan fields 1.006924 metacpan
Bio::Matrix::PSM::IO PSM parser 1.006924 metacpan
Bio::Matrix::PSM::IO::mast PSM mast parser implementation 1.006924 metacpan
Bio::Matrix::PSM::IO::masta motif fasta format parser 1.006924 metacpan
Bio::Matrix::PSM::IO::meme PSM meme parser implementation 1.006924 metacpan
Bio::Matrix::PSM::IO::psiblast PSM psiblast parser 1.006924 metacpan
Bio::Matrix::PSM::IO::transfac PSM transfac parser 1.006924 metacpan
Bio::Matrix::PSM::InstanceSite A PSM site occurance 1.006924 metacpan
Bio::Matrix::PSM::InstanceSiteI InstanceSite interface, holds an instance of a PSM 1.006924 metacpan
Bio::Matrix::PSM::ProtMatrix SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) with log-odds scoring information. 1.006924 metacpan
Bio::Matrix::PSM::ProtPsm handle combination of site matricies 1.006924 metacpan
Bio::Matrix::PSM::Psm handle combination of site matricies 1.006924 metacpan
Bio::Matrix::PSM::PsmHeader PSM mast parser implementation 1.006924 metacpan
Bio::Matrix::PSM::PsmHeaderI handles the header data from a PSM file 1.006924 metacpan
Bio::Matrix::PSM::PsmI abstract interface to handler of site matricies 1.006924 metacpan
Bio::Matrix::PSM::SiteMatrix SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds 1.006924 metacpan
Bio::Matrix::PSM::SiteMatrixI SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds 1.006924 metacpan
Bio::Matrix::PhylipDist A Phylip Distance Matrix object 1.006924 metacpan
Bio::Matrix::Scoring Object which can hold scoring matrix information 1.006924 metacpan
Bio::MolEvol::CodonModel Codon Evolution Models 1.006924 metacpan
Bio::Nexml::Factory A factory module for creating BioPerl and Bio::Phylo objects from/to nexml documents 1.006924 metacpan
Bio::NexmlIO stream handler for NeXML documents 1.006924 metacpan
Bio::Ontology::DocumentRegistry Keep track of where to find ontologies. Allows lookups by name. 1.006924 metacpan
Bio::Ontology::GOterm representation of GO terms 1.006924 metacpan
Bio::Ontology::InterProTerm Implementation of InterProI term interface 1.006924 metacpan
Bio::Ontology::OBOEngine An Ontology Engine for OBO style flat file format from the Gene Ontology Consortium 1.006924 metacpan
Bio::Ontology::OBOterm representation of OBO terms 1.006924 metacpan
Bio::Ontology::Ontology standard implementation of an Ontology 1.006924 metacpan
Bio::Ontology::OntologyEngineI Interface a minimal Ontology implementation should satisfy 1.006924 metacpan
Bio::Ontology::OntologyI Interface for an ontology implementation 1.006924 metacpan
Bio::Ontology::OntologyStore A repository of ontologies 1.006924 metacpan
Bio::Ontology::Path a path for an ontology term graph 1.006924 metacpan
Bio::Ontology::PathI Interface for a path between ontology terms 1.006924 metacpan
Bio::Ontology::Relationship a relationship for an ontology 1.006924 metacpan
Bio::Ontology::RelationshipFactory Instantiates a new Bio::Ontology::RelationshipI (or derived class) through a factory 1.006924 metacpan
Bio::Ontology::RelationshipI Interface for a relationship between ontology terms 1.006924 metacpan
Bio::Ontology::RelationshipType a relationship type for an ontology 1.006924 metacpan
Bio::Ontology::SimpleGOEngine::GraphAdaptor Graph adaptor for Bio::Ontology::SimpleGOEngine 1.006924 metacpan
Bio::Ontology::SimpleOntologyEngine Implementation of OntologyEngineI interface 1.006924 metacpan
Bio::Ontology::Term implementation of the interface for ontology terms 1.006924 metacpan
Bio::Ontology::TermFactory Instantiates a new Bio::Ontology::TermI (or derived class) through a factory 1.006924 metacpan
Bio::Ontology::TermI interface for ontology terms 1.006924 metacpan
Bio::OntologyIO Parser factory for Ontology formats 1.006924 metacpan
Bio::OntologyIO::Handlers::BaseSAXHandler 1.006924 metacpan
Bio::OntologyIO::Handlers::InterProHandler XML handler class for InterProParser 1.006924 metacpan
Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler parse an InterPro XML file and persist the resulting terms to a Biosql database 1.006924 metacpan
Bio::OntologyIO::InterProParser Parser for InterPro xml files. 1.006924 metacpan
Bio::OntologyIO::dagflat a base class parser for GO flat-file type formats 1.006924 metacpan
Bio::OntologyIO::goflat a parser for the Gene Ontology flat-file format 1.006924 metacpan
Bio::OntologyIO::obo a parser for OBO flat-file format from Gene Ontology Consortium 1.006924 metacpan
Bio::OntologyIO::simplehierarchy a base class parser for simple hierarchy-by-indentation type formats 1.006924 metacpan
Bio::OntologyIO::soflat a parser for the Sequence Ontology flat-file format 1.006924 metacpan
Bio::ParameterBaseI Simple interface class for any parameter-related data such as IDs, database name, program arguments, and other odds and ends. 1.006924 metacpan
Bio::Perl Functional access to BioPerl for people who don't know objects 1.006924 metacpan
Bio::Phenotype::Correlate Representation of a correlating phenotype in a given species 1.006924 metacpan
Bio::Phenotype::MeSH::Term A MeSH term 1.006924 metacpan
Bio::Phenotype::MeSH::Twig Context for a MeSH term 1.006924 metacpan
Bio::Phenotype::Measure Representation of context/value(-range)/unit triplets 1.006924 metacpan
Bio::Phenotype::OMIM::MiniMIMentry Representation of a Mini MIM entry 1.006924 metacpan
Bio::Phenotype::OMIM::OMIMentry represents OMIM (Online Mendelian Inheritance in Man) database entries 1.006924 metacpan
Bio::Phenotype::OMIM::OMIMentryAllelicVariant Representation of a allelic variant of the OMIM database 1.006924 metacpan
Bio::Phenotype::OMIM::OMIMparser parser for the OMIM database 1.006924 metacpan
Bio::Phenotype::Phenotype A class for modeling phenotypes 1.006924 metacpan
Bio::Phenotype::PhenotypeI An interface for classes modeling phenotypes 1.006924 metacpan
Bio::PhyloNetwork Module to compute with Phylogenetic Networks 1.006924 metacpan
Bio::PhyloNetwork::Factory Module to sequentially generate Phylogenetic Networks 1.006924 metacpan
Bio::PhyloNetwork::FactoryX Module to sequentially generate Phylogenetic Networks 1.006924 metacpan
Bio::PhyloNetwork::GraphViz Interface between PhyloNetwork and GraphViz 1.006924 metacpan
Bio::PhyloNetwork::RandomFactory Module to generate random Phylogenetic Networks 1.006924 metacpan
Bio::PhyloNetwork::TreeFactory Module to sequentially generate Phylogenetic Trees 1.006924 metacpan
Bio::PhyloNetwork::TreeFactoryMulti Module to sequentially generate Phylogenetic Trees 1.006924 metacpan
Bio::PhyloNetwork::TreeFactoryX Module to sequentially generate Phylogenetic Trees 1.006924 metacpan
Bio::PhyloNetwork::muVector Module to compute with vectors of arbitrary dimension 1.006924 metacpan
Bio::PopGen::Genotype An implementation of GenotypeI which is just an allele container 1.006924 metacpan
Bio::PopGen::GenotypeI A marker and alleles for a specific individual 1.006924 metacpan
Bio::PopGen::HtSNP 1.006924 metacpan
Bio::PopGen::IO Input individual,marker,allele information 1.006924 metacpan
Bio::PopGen::IO::csv 1.006924 metacpan
Bio::PopGen::IO::hapmap A parser for HapMap output data 1.006924 metacpan
Bio::PopGen::IO::phase A parser for Phase format data 1.006924 metacpan
Bio::PopGen::IO::prettybase Extract individual allele data from PrettyBase format 1.006924 metacpan
Bio::PopGen::Individual An implementation of an Individual who has Genotype or Sequence Results 1.006924 metacpan
Bio::PopGen::IndividualI An individual who has Genotype or Sequence Results 1.006924 metacpan
Bio::PopGen::Marker A genetic marker which one uses to generate genotypes 1.006924 metacpan
Bio::PopGen::MarkerI A Population Genetic conceptual marker 1.006924 metacpan
Bio::PopGen::PopStats A collection of methods for calculating statistics about a population or sets of populations 1.006924 metacpan
Bio::PopGen::Population A population of individuals 1.006924 metacpan
Bio::PopGen::PopulationI Interface for Populations 1.006924 metacpan
Bio::PopGen::Simulation::Coalescent A Coalescent simulation factory 1.006924 metacpan
Bio::PopGen::Simulation::GeneticDrift A simple genetic drift simulation 1.006924 metacpan
Bio::PopGen::Statistics Population Genetics statistical tests 1.006924 metacpan
Bio::PopGen::TagHaplotype 1.006924 metacpan
Bio::PopGen::Utilities Utilities for working with PopGen data and objects 1.006924 metacpan
Bio::PrimarySeq Bioperl lightweight sequence object 1.006924 metacpan
Bio::PrimarySeq::Fasta 1.006924 metacpan
Bio::PrimarySeqI Interface definition for a Bio::PrimarySeq 1.006924 metacpan
Bio::PullParserI A base module for fast 'pull' parsing 1.006924 metacpan
Bio::Range Pure perl RangeI implementation 1.006924 metacpan
Bio::RangeI Range interface 1.006924 metacpan
Bio::Restriction::Analysis cutting sequences with restriction enzymes 1.006924 metacpan
Bio::Restriction::Enzyme A single restriction endonuclease (cuts DNA at specific locations) 1.006924 metacpan
Bio::Restriction::Enzyme::MultiCut A single restriction endonuclease 1.006924 metacpan
Bio::Restriction::Enzyme::MultiSite A single restriction endonuclease 1.006924 metacpan
Bio::Restriction::EnzymeCollection Set of restriction endonucleases 1.006924 metacpan
Bio::Restriction::EnzymeI Interface class for restriction endonuclease 1.006924 metacpan
Bio::Restriction::IO Handler for sequence variation IO Formats 1.006924 metacpan
Bio::Restriction::IO::bairoch bairoch enzyme set 1.006924 metacpan
Bio::Restriction::IO::base base enzyme set 1.006924 metacpan
Bio::Restriction::IO::itype2 itype2 enzyme set 1.006924 metacpan
Bio::Restriction::IO::prototype prototype enzyme set 1.006924 metacpan
Bio::Restriction::IO::withrefm withrefm enzyme set 1.006924 metacpan
Bio::Root::Build 1.006924 metacpan
Bio::Root::Exception 1.006924 metacpan
Bio::Root::HTTPget module for fallback HTTP get operations when LWP:: is unavailable 1.006924 metacpan
Bio::Root::IO 1.006924 metacpan
Bio::Root::Root 1.006924 metacpan
Bio::Root::RootI 1.006924 metacpan
Bio::Root::Storable 1.006924 metacpan
Bio::Root::Test 1.006924 metacpan
Bio::Root::Utilities 1.006924 metacpan
Bio::Root::Version 1.006924 metacpan
Bio::Search::BlastStatistics An object for Blast statistics 1.006924 metacpan
Bio::Search::BlastUtils Utility functions for Bio::Search:: BLAST objects 1.006924 metacpan
Bio::Search::DatabaseI Interface for a database used in a sequence search 1.006924 metacpan
Bio::Search::GenericDatabase Generic implementation of Bio::Search::DatabaseI 1.006924 metacpan
Bio::Search::GenericStatistics An object for statistics 1.006924 metacpan
Bio::Search::HSP::BlastHSP Bioperl BLAST High-Scoring Pair object 1.006924 metacpan
Bio::Search::HSP::BlastPullHSP A parser and HSP object for BlastN hsps 1.006924 metacpan
Bio::Search::HSP::FastaHSP HSP object for FASTA specific data 1.006924 metacpan
Bio::Search::HSP::GenericHSP A "Generic" implementation of a High Scoring Pair 1.006924 metacpan
Bio::Search::HSP::HMMERHSP A HSP object for HMMER results 1.006924 metacpan
Bio::Search::HSP::HSPFactory A factory to create Bio::Search::HSP::HSPI objects 1.006924 metacpan
Bio::Search::HSP::HSPI 1.006924 metacpan
Bio::Search::HSP::HmmpfamHSP A parser and HSP object for hmmpfam hsps 1.006924 metacpan
Bio::Search::HSP::ModelHSP A HSP object for model-based searches 1.006924 metacpan
Bio::Search::HSP::PSLHSP A HSP for PSL output 1.006924 metacpan
Bio::Search::HSP::PsiBlastHSP Bioperl BLAST High-Scoring Pair object 1.006924 metacpan
Bio::Search::HSP::PullHSPI Bio::Search::HSP::HSPI interface for pull parsers. 1.006924 metacpan
Bio::Search::HSP::WABAHSP HSP object suitable for describing WABA alignments 1.006924 metacpan
Bio::Search::Hit::BlastHit Blast-specific subclass of Bio::Search::Hit::GenericHit 1.006924 metacpan
Bio::Search::Hit::BlastPullHit A parser and hit object for BLASTN hits 1.006924 metacpan
Bio::Search::Hit::Fasta Hit object specific for Fasta-generated hits 1.006924 metacpan
Bio::Search::Hit::GenericHit A generic implementation of the Bio::Search::Hit::HitI interface 1.006924 metacpan
Bio::Search::Hit::HMMERHit A Hit module for HMMER hits 1.006924 metacpan
Bio::Search::Hit::HitFactory A factory to create Bio::Search::Hit::HitI objects 1.006924 metacpan
Bio::Search::Hit::HitI Interface for a hit in a similarity search result 1.006924 metacpan
Bio::Search::Hit::HmmpfamHit A parser and hit object for hmmpfam hits 1.006924 metacpan
Bio::Search::Hit::ModelHit A model-based implementation of the Bio::Search::Hit::HitI interface 1.006924 metacpan
Bio::Search::Hit::PsiBlastHit Bioperl BLAST Hit object 1.006924 metacpan
Bio::Search::Hit::PullHitI Bio::Search::Hit::HitI interface for pull parsers. 1.006924 metacpan
Bio::Search::Hit::hmmer3Hit DESCRIPTION of Object 1.006924 metacpan
Bio::Search::Iteration::GenericIteration A generic implementation of the Bio::Search::Iteration::IterationI interface. 1.006924 metacpan
Bio::Search::Iteration::IterationI Abstract interface to an iteration from an iterated search result, such as PSI-BLAST. 1.006924 metacpan
Bio::Search::Processor DESCRIPTION of Object 1.006924 metacpan
Bio::Search::Result::BlastPullResult A parser and result object for BLASTN results 1.006924 metacpan
Bio::Search::Result::BlastResult Blast-specific subclass of Bio::Search::Result::GenericResult 1.006924 metacpan
Bio::Search::Result::CrossMatchResult CrossMatch-specific subclass of Bio::Search::Result::GenericResult 1.006924 metacpan
Bio::Search::Result::GenericResult Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results. 1.006924 metacpan
Bio::Search::Result::HMMERResult A Result object for HMMER results 1.006924 metacpan
Bio::Search::Result::HmmpfamResult A parser and result object for hmmpfam results 1.006924 metacpan
Bio::Search::Result::PullResultI Bio::Search::Result::ResultI interface for 'pull' parsers 1.006924 metacpan
Bio::Search::Result::ResultFactory A factory to create Bio::Search::Result::ResultI objects 1.006924 metacpan
Bio::Search::Result::ResultI Abstract interface to Search Result objects 1.006924 metacpan
Bio::Search::Result::WABAResult Result object for WABA alignment output 1.006924 metacpan
Bio::Search::Result::hmmer3Result DESCRIPTION of Object 1.006924 metacpan
Bio::Search::SearchUtils Utility functions for Bio::Search:: objects 1.006924 metacpan
Bio::Search::StatisticsI A Base object for statistics 1.006924 metacpan
Bio::Search::Tiling::MapTileUtils utilities for manipulating closed intervals for an HSP tiling algorithm 1.006924 metacpan
Bio::Search::Tiling::MapTiling An implementation of an HSP tiling algorithm, with methods to obtain frequently-requested statistics 1.006924 metacpan
Bio::Search::Tiling::TilingI Abstract interface for an HSP tiling module 1.006924 metacpan
Bio::SearchDist A perl wrapper around Sean Eddy's histogram object 1.006924 metacpan
Bio::SearchIO Driver for parsing Sequence Database Searches (BLAST, FASTA, ...) 1.006924 metacpan
Bio::SearchIO::EventHandlerI An abstract Event Handler for Search Result parsing 1.006924 metacpan
Bio::SearchIO::FastHitEventBuilder Event Handler for SearchIO events. 1.006924 metacpan
Bio::SearchIO::IteratedSearchResultEventBuilder Event Handler for SearchIO events. 1.006924 metacpan
Bio::SearchIO::SearchResultEventBuilder Event Handler for SearchIO events. 1.006924 metacpan
Bio::SearchIO::SearchWriterI Interface for outputting parsed Search results 1.006924 metacpan
Bio::SearchIO::Writer::BSMLResultWriter BSML output writer 1.006924 metacpan
Bio::SearchIO::Writer::GbrowseGFF Interface for outputting parsed search results in Gbrowse GFF format 1.006924 metacpan
Bio::SearchIO::Writer::HSPTableWriter Tab-delimited data for Bio::Search::HSP::HSPI objects 1.006924 metacpan
Bio::SearchIO::Writer::HTMLResultWriter write a Bio::Search::ResultI in HTML 1.006924 metacpan
Bio::SearchIO::Writer::HitTableWriter Tab-delimited data for Bio::Search::Hit::HitI objects 1.006924 metacpan
Bio::SearchIO::Writer::ResultTableWriter Outputs tab-delimited data for each Bio::Search::Result::ResultI object. 1.006924 metacpan
Bio::SearchIO::Writer::TextResultWriter Object to implement writing a Bio::Search::ResultI in Text. 1.006924 metacpan
Bio::SearchIO::XML::BlastHandler XML Handler for NCBI Blast XML parsing. 1.006924 metacpan
Bio::SearchIO::XML::PsiBlastHandler XML Handler for NCBI Blast PSIBLAST XML parsing. 1.006924 metacpan
Bio::SearchIO::axt a parser for axt format reports 1.006924 metacpan
Bio::SearchIO::blast Event generator for event based parsing of blast reports 1.006924 metacpan
Bio::SearchIO::blast_pull A parser for BLAST output 1.006924 metacpan
Bio::SearchIO::blasttable Driver module for SearchIO for parsing NCBI -m 8/9 format 1.006924 metacpan
Bio::SearchIO::blastxml A SearchIO implementation of NCBI Blast XML parsing. 1.006924 metacpan
Bio::SearchIO::cross_match CrossMatch-specific subclass of Bio::SearchIO 1.006924 metacpan
Bio::SearchIO::erpin SearchIO-based ERPIN parser 1.006924 metacpan
Bio::SearchIO::exonerate parser for Exonerate 1.006924 metacpan
Bio::SearchIO::fasta A SearchIO parser for FASTA results 1.006924 metacpan
Bio::SearchIO::gmap_f9 Event generator for parsing gmap reports (Z format) 1.006924 metacpan
Bio::SearchIO::hmmer A parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam) 1.006924 metacpan
Bio::SearchIO::hmmer2 A parser for HMMER output (hmmpfam, hmmsearch) 1.006924 metacpan
Bio::SearchIO::hmmer3 1.006924 metacpan
Bio::SearchIO::hmmer_pull A parser for HMMER output 1.006924 metacpan
Bio::SearchIO::infernal SearchIO-based Infernal parser 1.006924 metacpan
Bio::SearchIO::megablast a driver module for Bio::SearchIO to parse megablast reports (format 0) 1.006924 metacpan
Bio::SearchIO::psl A parser for PSL output (UCSC) 1.006924 metacpan
Bio::SearchIO::rnamotif SearchIO-based RNAMotif parser 1.006924 metacpan
Bio::SearchIO::sim4 parser for Sim4 alignments 1.006924 metacpan
Bio::SearchIO::waba SearchIO parser for Jim Kent WABA program alignment output 1.006924 metacpan
Bio::SearchIO::wise Parsing of wise output as alignments 1.006924 metacpan
Bio::Seq Sequence object, with features 1.006924 metacpan
Bio::Seq::BaseSeqProcessor Base implementation for a SequenceProcessor 1.006924 metacpan
Bio::Seq::EncodedSeq subtype of L<Bio::LocatableSeq|Bio::LocatableSeq> to store DNA that encodes a protein 1.006924 metacpan
Bio::Seq::LargeLocatableSeq LocatableSeq object that stores sequence as files in the tempdir 1.006924 metacpan
Bio::Seq::LargePrimarySeq PrimarySeq object that stores sequence as files in the tempdir (as found by File::Temp) or the default method in Bio::Root::Root 1.006924 metacpan
Bio::Seq::LargeSeq SeqI compliant object that stores sequence as files in /tmp 1.006924 metacpan
Bio::Seq::LargeSeqI Interface class for sequences that cache their residues in a temporary file 1.006924 metacpan
Bio::Seq::Meta Generic superclass for sequence objects with residue-based meta information 1.006924 metacpan
Bio::Seq::Meta::Array array-based generic implementation of a sequence class with residue-based meta information 1.006924 metacpan
Bio::Seq::MetaI Interface for sequence objects with residue-based meta information 1.006924 metacpan
Bio::Seq::PrimaryQual Bioperl lightweight Quality Object 1.006924 metacpan
Bio::Seq::PrimaryQual::Qual 1.006924 metacpan
Bio::Seq::PrimedSeq A sequence and a pair of primers matching on it 1.006924 metacpan
Bio::Seq::QualI Interface definition for a Bio::Seq::Qual 1.006924 metacpan
Bio::Seq::Quality Implementation of sequence with residue quality and trace values 1.006924 metacpan
Bio::Seq::RichSeq Module implementing a sequence created from a rich sequence database entry 1.006924 metacpan
Bio::Seq::RichSeqI interface for sequences from rich data sources, mostly databases 1.006924 metacpan
Bio::Seq::SeqBuilder Configurable object builder for sequence stream parsers 1.006924 metacpan
Bio::Seq::SeqFactory Instantiation of generic Bio::PrimarySeqI (or derived) objects through a factory 1.006924 metacpan
Bio::Seq::SeqFastaSpeedFactory Rapid creation of Bio::Seq objects through a factory 1.006924 metacpan
Bio::Seq::SeqWithQuality Bioperl object packaging a sequence with its quality. Deprecated class, use Bio::Seq::Quality instead! 1.006924 metacpan
Bio::Seq::SequenceTrace Bioperl object packaging a sequence with its trace 1.006924 metacpan
Bio::Seq::SimulatedRead Read with sequencing errors taken from a reference sequence 1.006924 metacpan
Bio::Seq::TraceI Interface definition for a Bio::Seq::Trace 1.006924 metacpan
Bio::SeqAnalysisParserI Sequence analysis output parser interface 1.006924 metacpan
Bio::SeqEvolution::DNAPoint evolve a sequence by point mutations 1.006924 metacpan
Bio::SeqEvolution::EvolutionI the interface for evolving sequences 1.006924 metacpan
Bio::SeqEvolution::Factory Factory object to instantiate sequence evolving classes 1.006924 metacpan
Bio::SeqFeature::Amplicon Amplicon feature 1.006924 metacpan
Bio::SeqFeature::AnnotationAdaptor integrates SeqFeatureIs annotation 1.006924 metacpan
Bio::SeqFeature::Collection A container class for SeqFeatures suitable for performing operations such as finding features within a range, that match a certain feature type, etc. 1.006924 metacpan
Bio::SeqFeature::CollectionI An interface for a collection of SeqFeatureI objects. 1.006924 metacpan
Bio::SeqFeature::Computation Computation SeqFeature 1.006924 metacpan
Bio::SeqFeature::FeaturePair hold pair feature information e.g. blast hits 1.006924 metacpan
Bio::SeqFeature::Gene::Exon a feature representing an exon 1.006924 metacpan
Bio::SeqFeature::Gene::ExonI Interface for a feature representing an exon 1.006924 metacpan
Bio::SeqFeature::Gene::GeneStructure A feature representing an arbitrarily complex structure of a gene 1.006924 metacpan
Bio::SeqFeature::Gene::GeneStructureI A feature representing an arbitrarily complex structure of a gene 1.006924 metacpan
Bio::SeqFeature::Gene::Intron An intron feature 1.006924 metacpan
Bio::SeqFeature::Gene::NC_Feature 1.006924 metacpan
Bio::SeqFeature::Gene::Poly_A_site poly A feature 1.006924 metacpan
Bio::SeqFeature::Gene::Promoter Describes a promoter 1.006924 metacpan
Bio::SeqFeature::Gene::Transcript A feature representing a transcript 1.006924 metacpan
Bio::SeqFeature::Gene::TranscriptI Interface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site. 1.006924 metacpan
Bio::SeqFeature::Gene::UTR A feature representing an untranslated region that is part of a transcriptional unit 1.006924 metacpan
Bio::SeqFeature::Generic Generic SeqFeature 1.006924 metacpan
Bio::SeqFeature::Lite Lightweight Bio::SeqFeatureI class 1.006924 metacpan
Bio::SeqFeature::PositionProxy handle features when truncation/revcom sequences span a feature 1.006924 metacpan
Bio::SeqFeature::Primer Primer Generic SeqFeature 1.006924 metacpan
Bio::SeqFeature::SiRNA::Oligo Perl object for small inhibitory RNAs. 1.006924 metacpan
Bio::SeqFeature::SiRNA::Pair Perl object for small inhibitory RNA (SiRNA) oligo pairs 1.006924 metacpan
Bio::SeqFeature::Similarity A sequence feature based on similarity 1.006924 metacpan
Bio::SeqFeature::SimilarityPair Sequence feature based on the similarity of two sequences. 1.006924 metacpan
Bio::SeqFeature::SubSeq Feature representing a subsequence 1.006924 metacpan
Bio::SeqFeature::Tools::FeatureNamer generates unique persistent names for features 1.006924 metacpan
Bio::SeqFeature::Tools::IDHandler maps $seq_feature-E<gt>primary_tag 1.006924 metacpan
Bio::SeqFeature::Tools::TypeMapper maps $seq_feature-E<gt>primary_tag 1.006924 metacpan
Bio::SeqFeature::Tools::Unflattener turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy 1.006924 metacpan
Bio::SeqFeature::TypedSeqFeatureI a strongly typed SeqFeature 1.006924 metacpan
Bio::SeqFeatureI Abstract interface of a Sequence Feature 1.006924 metacpan
Bio::SeqI [Developers] Abstract Interface of Sequence (with features) 1.006924 metacpan
Bio::SeqIO Handler for SeqIO Formats 1.006924 metacpan
Bio::SeqIO::FTHelper Helper class for EMBL/Genbank feature tables 1.006924 metacpan
Bio::SeqIO::Handler::GenericRichSeqHandler Bio::HandlerI-based data handler for GenBank/EMBL/UniProt (and other) sequence data 1.006924 metacpan
Bio::SeqIO::MultiFile Treating a set of files as a single input stream 1.006924 metacpan
Bio::SeqIO::abi abi trace sequence input/output stream 1.006924 metacpan
Bio::SeqIO::ace ace sequence input/output stream 1.006924 metacpan
Bio::SeqIO::agave AGAVE sequence output stream. 1.006924 metacpan
Bio::SeqIO::alf alf trace sequence input/output stream 1.006924 metacpan
Bio::SeqIO::asciitree asciitree sequence input/output stream 1.006924 metacpan
Bio::SeqIO::bsml BSML sequence input/output stream 1.006924 metacpan
Bio::SeqIO::bsml_sax BSML sequence input/output stream using SAX 1.006924 metacpan
Bio::SeqIO::chadoxml chadoxml sequence output stream 1.006924 metacpan
Bio::SeqIO::chaos chaos sequence input/output stream 1.006924 metacpan
Bio::SeqIO::chaosxml chaosxml sequence input/output stream 1.006924 metacpan
Bio::SeqIO::ctf ctf trace sequence input/output stream 1.006924 metacpan
Bio::SeqIO::embl EMBL sequence input/output stream 1.006924 metacpan
Bio::SeqIO::embldriver EMBL sequence input/output stream 1.006924 metacpan
Bio::SeqIO::entrezgene Entrez Gene ASN1 parser 1.006924 metacpan
Bio::SeqIO::excel sequence input/output stream from a MSExcel-formatted table 1.006924 metacpan
Bio::SeqIO::exp exp trace sequence input/output stream 1.006924 metacpan
Bio::SeqIO::fasta fasta sequence input/output stream 1.006924 metacpan
Bio::SeqIO::fastq fastq sequence input/output stream 1.006924 metacpan
Bio::SeqIO::flybase_chadoxml FlyBase variant of chadoxml with sequence output stream 1.006924 metacpan
Bio::SeqIO::game a class for parsing and writing game-XML 1.006924 metacpan
Bio::SeqIO::game::featHandler a class for handling feature elements 1.006924 metacpan
Bio::SeqIO::game::gameHandler PerlSAX handler for game-XML 1.006924 metacpan
Bio::SeqIO::game::gameSubs a base class for game-XML parsing 1.006924 metacpan
Bio::SeqIO::game::gameWriter a class for writing game-XML 1.006924 metacpan
Bio::SeqIO::game::seqHandler a class for handling game-XML sequences 1.006924 metacpan
Bio::SeqIO::gbdriver GenBank handler-based push parser 1.006924 metacpan
Bio::SeqIO::gbxml GenBank sequence input/output stream using SAX 1.006924 metacpan
Bio::SeqIO::gcg GCG sequence input/output stream 1.006924 metacpan
Bio::SeqIO::genbank GenBank sequence input/output stream 1.006924 metacpan
Bio::SeqIO::interpro InterProScan XML input/output stream 1.006924 metacpan
Bio::SeqIO::kegg KEGG sequence input/output stream 1.006924 metacpan
Bio::SeqIO::largefasta method i/o on very large fasta sequence files 1.006924 metacpan
Bio::SeqIO::lasergene Lasergene sequence file input/output stream 1.006924 metacpan
Bio::SeqIO::locuslink LocusLink input/output stream 1.006924 metacpan
Bio::SeqIO::mbsout input stream for output by Teshima et al.'s mbs. 1.006924 metacpan
Bio::SeqIO::metafasta metafasta sequence input/output stream 1.006924 metacpan
Bio::SeqIO::msout input stream for output by Hudson's ms 1.006924 metacpan
Bio::SeqIO::nexml NeXML sequence input/output stream 1.006924 metacpan
Bio::SeqIO::phd phd file input/output stream 1.006924 metacpan
Bio::SeqIO::pir PIR sequence input/output stream 1.006924 metacpan
Bio::SeqIO::pln pln trace sequence input/output stream 1.006924 metacpan
Bio::SeqIO::qual .qual file input/output stream 1.006924 metacpan
Bio::SeqIO::raw raw sequence file input/output stream 1.006924 metacpan
Bio::SeqIO::scf .scf file input/output stream 1.006924 metacpan
Bio::SeqIO::seqxml SeqXML sequence input/output stream 1.006924 metacpan
Bio::SeqIO::strider DNA strider sequence input/output stream 1.006924 metacpan
Bio::SeqIO::swiss Swissprot sequence input/output stream 1.006924 metacpan
Bio::SeqIO::swissdriver SwissProt/UniProt handler-based push parser 1.006924 metacpan
Bio::SeqIO::tab nearly raw sequence file input/output stream. Reads/writes id"\t"sequence"\n" 1.006924 metacpan
Bio::SeqIO::table sequence input/output stream from a delimited table 1.006924 metacpan
Bio::SeqIO::tigr TIGR XML sequence input/output stream 1.006924 metacpan
Bio::SeqIO::tigrxml Parse TIGR (new) XML 1.006924 metacpan
Bio::SeqIO::tinyseq reading/writing sequences in NCBI TinySeq format 1.006924 metacpan
Bio::SeqIO::tinyseq::tinyseqHandler XML event handlers to support NCBI TinySeq XML parsing 1.006924 metacpan
Bio::SeqIO::ztr ztr trace sequence input/output stream 1.006924 metacpan
Bio::SeqUtils Additional methods for PrimarySeq objects 1.006924 metacpan
Bio::SimpleAlign Multiple alignments held as a set of sequences 1.006924 metacpan
Bio::SimpleAnalysisI A simple interface to any (local or remote) analysis tool 1.006924 metacpan
Bio::Species Generic species object. 1.006924 metacpan
Bio::Structure::Atom Bioperl structure Object, describes an Atom 1.006924 metacpan
Bio::Structure::Chain Bioperl structure Object, describes a chain 1.006924 metacpan
Bio::Structure::Entry Bioperl structure Object, describes the whole entry 1.006924 metacpan
Bio::Structure::IO Handler for Structure Formats 1.006924 metacpan
Bio::Structure::IO::pdb PDB input/output stream 1.006924 metacpan
Bio::Structure::Model Bioperl structure Object, describes a Model 1.006924 metacpan
Bio::Structure::Residue Bioperl structure Object, describes a Residue 1.006924 metacpan
Bio::Structure::SecStr::DSSP::Res Module for parsing/accessing dssp output 1.006924 metacpan
Bio::Structure::SecStr::STRIDE::Res Module for parsing/accessing stride output 1.006924 metacpan
Bio::Structure::StructureI Abstract Interface for a Structure objects 1.006924 metacpan
Bio::Symbol::Alphabet BSANE/BioCORBA compliant symbol list alphabet 1.006924 metacpan
Bio::Symbol::AlphabetI A Symbol Alphabet 1.006924 metacpan
Bio::Symbol::DNAAlphabet A ready made DNA alphabet 1.006924 metacpan
Bio::Symbol::ProteinAlphabet A ready made Protein alphabet 1.006924 metacpan
Bio::Symbol::Symbol A biological symbol 1.006924 metacpan
Bio::Symbol::SymbolI Interface for a Symbol 1.006924 metacpan
Bio::Taxon A node in a represented taxonomy 1.006924 metacpan
Bio::Taxonomy representing Taxonomy. 1.006924 metacpan
Bio::Taxonomy::FactoryI interface to define how to access NCBI Taxonoy 1.006924 metacpan
Bio::Taxonomy::Node A node in a represented taxonomy 1.006924 metacpan
Bio::Taxonomy::Taxon Generic Taxonomic Entity object 1.006924 metacpan
Bio::Taxonomy::Tree An Organism Level Implementation of TreeI interface. 1.006924 metacpan
Bio::Tools::AlignFactory Base object for alignment factories 1.006924 metacpan
Bio::Tools::Alignment::Consed A module to work with objects from consed .ace files 1.006924 metacpan
Bio::Tools::Alignment::Trim A kludge to do specialized trimming of sequence based on quality. 1.006924 metacpan
Bio::Tools::AmpliconSearch Find amplicons in a template using degenerate PCR primers 1.006924 metacpan
Bio::Tools::Analysis::DNA::ESEfinder a wrapper around ESEfinder server 1.006924 metacpan
Bio::Tools::Analysis::Protein::Domcut a wrapper around Domcut server 1.006924 metacpan
Bio::Tools::Analysis::Protein::ELM a wrapper around the ELM server which predicts short functional motifs on amino acid sequences 1.006924 metacpan
Bio::Tools::Analysis::Protein::GOR4 a wrapper around GOR4 protein secondary structure prediction server 1.006924 metacpan
Bio::Tools::Analysis::Protein::HNN a wrapper around the HNN protein secondary structure prediction server 1.006924 metacpan
Bio::Tools::Analysis::Protein::Mitoprot a wrapper around Mitoprot server 1.006924 metacpan
Bio::Tools::Analysis::Protein::NetPhos a wrapper around NetPhos server 1.006924 metacpan
Bio::Tools::Analysis::Protein::Scansite a wrapper around the Scansite server 1.006924 metacpan
Bio::Tools::Analysis::Protein::Sopma a wrapper around the Sopma protein secondary structure prediction server 1.006924 metacpan
Bio::Tools::Analysis::SimpleAnalysisBase abstract superclass for SimpleAnalysis implementations 1.006924 metacpan
Bio::Tools::AnalysisResult Base class for analysis result objects and parsers 1.006924 metacpan
Bio::Tools::Blat parser for Blat program 1.006924 metacpan
Bio::Tools::CodonTable Codon table object 1.006924 metacpan
Bio::Tools::Coil parser for Coil output 1.006924 metacpan
Bio::Tools::ECnumber representation of EC numbers (Enzyme Classification) 1.006924 metacpan
Bio::Tools::EMBOSS::Palindrome parse EMBOSS palindrome output 1.006924 metacpan
Bio::Tools::EPCR Parse ePCR output and make features 1.006924 metacpan
Bio::Tools::ERPIN a parser for ERPIN output 1.006924 metacpan
Bio::Tools::ESTScan Results of one ESTScan run 1.006924 metacpan
Bio::Tools::Eponine Results of one Eponine run 1.006924 metacpan
Bio::Tools::Est2Genome Parse est2genome output, makes simple Bio::SeqFeature::Generic objects 1.006924 metacpan
Bio::Tools::Fgenesh parse results of one Fgenesh run 1.006924 metacpan
Bio::Tools::FootPrinter write sequence features in FootPrinter format 1.006924 metacpan
Bio::Tools::GFF A Bio::SeqAnalysisParserI compliant GFF format parser 1.006924 metacpan
Bio::Tools::Gel Calculates relative electrophoretic migration distances 1.006924 metacpan
Bio::Tools::Geneid Results of one geneid run 1.006924 metacpan
Bio::Tools::Genemark Results of one Genemark run 1.006924 metacpan
Bio::Tools::Genewise Results of one Genewise run 1.006924 metacpan
Bio::Tools::Genomewise Results of one Genomewise run 1.006924 metacpan
Bio::Tools::Genscan Results of one Genscan run 1.006924 metacpan
Bio::Tools::Glimmer parser for Glimmer 2.X/3.X prokaryotic and GlimmerM/GlimmerHMM eukaryotic gene predictions 1.006924 metacpan
Bio::Tools::Grail Results of one Grail run 1.006924 metacpan
Bio::Tools::GuessSeqFormat Module for determining the sequence format of the contents of a file, a string, or through a filehandle. 1.006924 metacpan
Bio::Tools::HMMER::Domain One particular domain hit from HMMER 1.006924 metacpan
Bio::Tools::HMMER::Results Object representing HMMER output results 1.006924 metacpan
Bio::Tools::HMMER::Set Set of identical domains from HMMER matches 1.006924 metacpan
Bio::Tools::Hmmpfam Parser for Hmmpfam program 1.006924 metacpan
Bio::Tools::IUPAC Generates unique sequence objects or regular expressions from an ambiguous IUPAC sequence 1.006924 metacpan
Bio::Tools::Infernal A parser for Infernal output 1.006924 metacpan
Bio::Tools::Lucy Object for analyzing the output from Lucy, a vector and quality trimming program from TIGR 1.006924 metacpan
Bio::Tools::MZEF Results of one MZEF run 1.006924 metacpan
Bio::Tools::Match Parses output from Transfac's match(TM) 1.006924 metacpan
Bio::Tools::OddCodes Object holding alternative alphabet coding for one protein sequence 1.006924 metacpan
Bio::Tools::Phylo::Gerp Parses output from GERP 1.006924 metacpan
Bio::Tools::Phylo::Gumby Parses output from gumby 1.006924 metacpan
Bio::Tools::Phylo::Molphy parser for Molphy output 1.006924 metacpan
Bio::Tools::Phylo::Molphy::Result container for data parsed from a ProtML run 1.006924 metacpan
Bio::Tools::Phylo::PAML Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00 1.006924 metacpan
Bio::Tools::Phylo::PAML::Codeml Parses output from the PAML program codeml. 1.006924 metacpan
Bio::Tools::Phylo::PAML::ModelResult A container for NSSite Model Result from PAML 1.006924 metacpan
Bio::Tools::Phylo::PAML::Result A PAML result set object 1.006924 metacpan
Bio::Tools::Phylo::Phylip::ProtDist parser for ProtDist output 1.006924 metacpan
Bio::Tools::Prediction::Exon A predicted exon feature 1.006924 metacpan
Bio::Tools::Prediction::Gene a predicted gene structure feature 1.006924 metacpan
Bio::Tools::Primer3 Create input for and work with the output from the program primer3 1.006924 metacpan
Bio::Tools::Primer::Assessor::Base base class for common assessor things 1.006924 metacpan
Bio::Tools::Primer::AssessorI interface for assessing primer pairs 1.006924 metacpan
Bio::Tools::Primer::Feature position of a single primer 1.006924 metacpan
Bio::Tools::Primer::Pair two primers on left and right side 1.006924 metacpan
Bio::Tools::Prints Parser for FingerPRINTScanII program 1.006924 metacpan
Bio::Tools::Profile parse Profile output 1.006924 metacpan
Bio::Tools::Promoterwise parser for Promoterwise tab format output 1.006924 metacpan
Bio::Tools::PrositeScan Parser for ps_scan result 1.006924 metacpan
Bio::Tools::Protparam submit to and parse output from protparam ; 1.006924 metacpan
Bio::Tools::Pseudowise Results of one Pseudowise run 1.006924 metacpan
Bio::Tools::QRNA A Parser for qrna output 1.006924 metacpan
Bio::Tools::RNAMotif A parser for RNAMotif output 1.006924 metacpan
Bio::Tools::RandomDistFunctions A set of routines useful for generating random data in different distributions 1.006924 metacpan
Bio::Tools::RepeatMasker a parser for RepeatMasker output 1.006924 metacpan
Bio::Tools::Run::GenericParameters An object for the parameters used to run programs 1.006924 metacpan
Bio::Tools::Run::ParametersI A Base object for the parameters used to run programs 1.006924 metacpan
Bio::Tools::Run::RemoteBlast Object for remote execution of the NCBI Blast via HTTP 1.006924 metacpan
Bio::Tools::Run::StandAloneBlast Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). There is experimental support for WU-Blast and NCBI rpsblast. 1.006924 metacpan
Bio::Tools::Run::StandAloneNCBIBlast Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). With experimental support for NCBI rpsblast. 1.006924 metacpan
Bio::Tools::Run::StandAloneWUBlast Object for the local execution of WU-Blast. 1.006924 metacpan
Bio::Tools::Run::WrapperBase A Base object for wrappers around executables 1.006924 metacpan
Bio::Tools::Seg parse C<seg> output 1.006924 metacpan
Bio::Tools::SeqPattern represent a sequence pattern or motif 1.006924 metacpan
Bio::Tools::SeqPattern::Backtranslate 1.006924 metacpan
Bio::Tools::SeqStats Object holding statistics for one particular sequence 1.006924 metacpan
Bio::Tools::SeqWords Object holding n-mer statistics for a sequence 1.006924 metacpan
Bio::Tools::SiRNA 1.006924 metacpan
Bio::Tools::SiRNA::Ruleset::saigo Perl object implementing the Saigo group's rules for designing small inhibitory RNAs 1.006924 metacpan
Bio::Tools::SiRNA::Ruleset::tuschl Perl object implementing the tuschl group's rules for designing small inhibitory RNAs 1.006924 metacpan
Bio::Tools::Sigcleave Bioperl object for sigcleave analysis 1.006924 metacpan
Bio::Tools::Signalp parser for Signalp output 1.006924 metacpan
Bio::Tools::Signalp::ExtendedSignalp enhanced parser for Signalp output 1.006924 metacpan
Bio::Tools::Sim4::Exon A single exon determined by an alignment 1.006924 metacpan
Bio::Tools::Sim4::Results Results of one Sim4 run 1.006924 metacpan
Bio::Tools::Spidey::Exon A single exon determined by an alignment 1.006924 metacpan
Bio::Tools::Spidey::Results Results of a Spidey run 1.006924 metacpan
Bio::Tools::TandemRepeatsFinder a parser for Tandem Repeats Finder output 1.006924 metacpan
Bio::Tools::TargetP Results of one TargetP run 1.006924 metacpan
Bio::Tools::Tmhmm parse TMHMM output (TransMembrane HMM) 1.006924 metacpan
Bio::Tools::dpAlign Perl extension to do pairwise dynamic programming sequence alignment 1.006924 metacpan
Bio::Tools::ipcress Parse ipcress output and make features 1.006924 metacpan
Bio::Tools::isPcr Parse isPcr output and make features 1.006924 metacpan
Bio::Tools::pICalculator calculate the isoelectric point of a protein 1.006924 metacpan
Bio::Tools::pSW pairwise Smith Waterman object 1.006924 metacpan
Bio::Tools::tRNAscanSE A parser for tRNAscan-SE output 1.006924 metacpan
Bio::Tree::AlleleNode A Node with Alleles attached 1.006924 metacpan
Bio::Tree::AnnotatableNode A Tree Node with support for annotation 1.006924 metacpan
Bio::Tree::Compatible Testing compatibility of phylogenetic trees with nested taxa. 1.006924 metacpan
Bio::Tree::DistanceFactory Construct a tree using distance based methods 1.006924 metacpan
Bio::Tree::Draw::Cladogram Drawing phylogenetic trees in Encapsulated PostScript (EPS) format. 1.006924 metacpan
Bio::Tree::Node A Simple Tree Node 1.006924 metacpan
Bio::Tree::NodeI Interface describing a Tree Node 1.006924 metacpan
Bio::Tree::NodeNHX A Simple Tree Node with support for NHX tags 1.006924 metacpan
Bio::Tree::RandomFactory TreeFactory for generating Random Trees 1.006924 metacpan
Bio::Tree::Statistics Calculate certain statistics for a Tree 1.006924 metacpan
Bio::Tree::Tree An implementation of the TreeI interface. 1.006924 metacpan
Bio::Tree::TreeFunctionsI Decorated Interface implementing basic Tree exploration methods 1.006924 metacpan
Bio::Tree::TreeI A Tree object suitable for lots of things, designed originally for Phylogenetic Trees. 1.006924 metacpan
Bio::TreeIO Parser for Tree files 1.006924 metacpan
Bio::TreeIO::NewickParser 1.006924 metacpan
Bio::TreeIO::TreeEventBuilder Build Bio::Tree::Tree's and Bio::Tree::Node's from Events 1.006924 metacpan
Bio::TreeIO::cluster A TreeIO driver module for parsing Algorithm::Cluster::treecluster() output 1.006924 metacpan
Bio::TreeIO::lintree Parser for lintree output trees 1.006924 metacpan
Bio::TreeIO::newick 1.006924 metacpan
Bio::TreeIO::nexml A TreeIO driver module for parsing NeXML tree files 1.006924 metacpan
Bio::TreeIO::nexus A TreeIO driver module for parsing Nexus tree output from PAUP 1.006924 metacpan
Bio::TreeIO::nhx TreeIO implementation for parsing Newick/New Hampshire eXtendend (NHX) format. 1.006924 metacpan
Bio::TreeIO::pag Bio::TreeIO driver for Pagel format 1.006924 metacpan
Bio::TreeIO::phyloxml TreeIO implementation for parsing PhyloXML format. 1.006924 metacpan
Bio::TreeIO::svggraph A simple output format that converts a Tree object to an SVG output 1.006924 metacpan
Bio::TreeIO::tabtree A simple output format which displays a tree as an ASCII drawing 1.006924 metacpan
Bio::UpdateableSeqI Descendant of Bio::SeqI that allows updates 1.006924 metacpan
Bio::Variation::AAChange Sequence change class for polypeptides 1.006924 metacpan
Bio::Variation::AAReverseMutate point mutation and codon information from single amino acid changes 1.006924 metacpan
Bio::Variation::Allele Sequence object with allele-specific attributes 1.006924 metacpan
Bio::Variation::DNAMutation DNA level mutation class 1.006924 metacpan
Bio::Variation::IO Handler for sequence variation IO Formats 1.006924 metacpan
Bio::Variation::IO::flat flat file sequence variation input/output stream 1.006924 metacpan
Bio::Variation::IO::xml XML sequence variation input/output stream 1.006924 metacpan
Bio::Variation::RNAChange Sequence change class for RNA level 1.006924 metacpan
Bio::Variation::SNP submitted SNP 1.006924 metacpan
Bio::Variation::SeqDiff Container class for mutation/variant descriptions 1.006924 metacpan
Bio::Variation::VariantI Sequence Change SeqFeature abstract class 1.006924 metacpan
Bio::WebAgent A base class for Web (any protocol) access 1.006924 metacpan
FeatureStore 1.006924 metacpan

Other Files

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