BioPerl 1.7.8
- Released by
- CJFIELDS
- Version
- Release Date
- 2021-02-03
- Kwalitee
- 150
- Core Kwalitee
- 96.88
- LINKS
BioPerl 1.7.8 Latest
Kwalitee Issues
- 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::Flat, Bio::Location::Split, Bio::Matrix::PSM::SiteMatrixI, Bio::Search::BlastUtils, Bio::SearchIO::SearchWriterI, Bio::SearchIO::cross_match, Bio::SeqIO::game, Bio::Tools::Primer::Assessor::Base, Bio::Tools::Primer::AssessorI, Bio::Tools::Primer::Feature, Bio::Tools::Primer::Pair
- meta_yml_declares_perl_version
-
If you are using Build.PL define the {requires}{perl} = VERSION field. If you are using MakeMaker (Makefile.PL) you should upgrade ExtUtils::MakeMaker to 6.48 and use MIN_PERL_VERSION parameter. Perl::MinimumVersion can help you determine which version of Perl your module needs.
- use_warnings
-
Add 'use warnings' (or its equivalents) to all modules, 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::nexus, Bio::AlignIO::pfam, Bio::AlignIO::phylip, Bio::AlignIO::po, Bio::AlignIO::proda, Bio::AlignIO::prodom, Bio::AlignIO::psi, Bio::AlignIO::selex, 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::CodonUsage::IO, Bio::CodonUsage::Table, Bio::DB::DBFetch, Bio::DB::Failover, Bio::DB::Fasta, 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::Util::Binning, Bio::DB::GFF::Util::Rearrange, Bio::DB::InMemoryCache, Bio::DB::LocationI, Bio::DB::Qual, Bio::DB::Query::WebQuery, Bio::DB::QueryI, Bio::DB::RandomAccessI, Bio::DB::ReferenceI, Bio::DB::Registry, Bio::DB::SeqI, Bio::DB::Taxonomy, Bio::DB::Taxonomy::flatfile, Bio::DB::Taxonomy::greengenes, Bio::DB::Taxonomy::list, Bio::DB::Taxonomy::silva, Bio::DB::UpdateableSeqI, Bio::DB::WebDBSeqI, Bio::DBLinkContainerI, Bio::Das::FeatureTypeI, Bio::Das::SegmentI, Bio::DasI, Bio::DescribableI, Bio::Event::EventGeneratorI, Bio::Event::EventHandlerI, Bio::Factory::AnalysisI, Bio::Factory::ApplicationFactoryI, Bio::Factory::DriverFactory, Bio::Factory::FTLocationFactory, Bio::Factory::LocationFactoryI, 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::Qual, Bio::Index::SwissPfam, Bio::Index::Swissprot, Bio::LocatableSeq, Bio::Location::Atomic, Bio::Location::AvWithinCoordPolicy, Bio::Location::CoordinatePolicyI, Bio::Location::Fuzzy, Bio::Location::FuzzyLocationI, Bio::Location::NarrowestCoordPolicy, Bio::Location::Simple, Bio::Location::Split, Bio::Location::SplitLocationI, Bio::Location::WidestCoordPolicy, Bio::LocationI, Bio::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::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::PrimarySeq, Bio::PrimarySeqI, Bio::PullParserI, Bio::Range, Bio::RangeI, Bio::Root::Exception, Bio::Root::IO, Bio::Root::Root, Bio::Root::RootI, Bio::Root::Storable, Bio::Root::TestObject, Bio::Root::Utilities, Bio::Root::Version, Bio::Search::BlastStatistics, Bio::Search::BlastUtils, Bio::Search::DatabaseI, Bio::Search::GenericDatabase, Bio::Search::GenericStatistics, Bio::Search::HSP::BlastHSP, Bio::Search::HSP::BlastPullHSP, Bio::Search::HSP::FastaHSP, Bio::Search::HSP::GenericHSP, Bio::Search::HSP::HSPFactory, Bio::Search::HSP::HSPI, 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::HitFactory, Bio::Search::Hit::HitI, Bio::Search::Hit::ModelHit, Bio::Search::Hit::PsiBlastHit, Bio::Search::Hit::PullHitI, 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::PullResultI, Bio::Search::Result::ResultFactory, Bio::Search::Result::ResultI, Bio::Search::Result::WABAResult, Bio::Search::SearchUtils, Bio::Search::StatisticsI, Bio::SearchIO::EventHandlerI, Bio::SearchIO::FastHitEventBuilder, Bio::SearchIO::IteratedSearchResultEventBuilder, Bio::SearchIO::SearchResultEventBuilder, Bio::SearchIO::SearchWriterI, Bio::SearchIO::Writer::GbrowseGFF, Bio::SearchIO::Writer::HSPTableWriter, Bio::SearchIO::Writer::HTMLResultWriter, Bio::SearchIO::Writer::HitTableWriter, Bio::SearchIO::Writer::ResultTableWriter, Bio::SearchIO::Writer::TextResultWriter, Bio::SearchIO::axt, Bio::SearchIO::blast, Bio::SearchIO::blast_pull, Bio::SearchIO::blasttable, Bio::SearchIO::cross_match, Bio::SearchIO::erpin, Bio::SearchIO::exonerate, Bio::SearchIO::fasta, Bio::SearchIO::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::SequenceTrace, Bio::Seq::TraceI, Bio::SeqAnalysisParserI, 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::ace, Bio::SeqIO::asciitree, Bio::SeqIO::bsml, Bio::SeqIO::bsml_sax, Bio::SeqIO::embl, Bio::SeqIO::embldriver, Bio::SeqIO::fastq, Bio::SeqIO::game, Bio::SeqIO::game::featHandler, Bio::SeqIO::game::gameHandler, Bio::SeqIO::game::gameSubs, Bio::SeqIO::game::gameWriter, Bio::SeqIO::game::seqHandler, Bio::SeqIO::gbxml, Bio::SeqIO::gcg, Bio::SeqIO::genbank, Bio::SeqIO::kegg, Bio::SeqIO::largefasta, Bio::SeqIO::locuslink, Bio::SeqIO::mbsout, Bio::SeqIO::metafasta, Bio::SeqIO::msout, Bio::SeqIO::phd, Bio::SeqIO::pir, 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::SimpleAnalysisI, Bio::Taxon, Bio::Tools::Alignment::Consed, Bio::Tools::Alignment::Trim, Bio::Tools::Analysis::SimpleAnalysisBase, Bio::Tools::AnalysisResult, Bio::Tools::Blat, Bio::Tools::CodonTable, Bio::Tools::Coil, Bio::Tools::ECnumber, Bio::Tools::EMBOSS::Palindrome, Bio::Tools::EPCR, Bio::Tools::ESTScan, Bio::Tools::Eponine, Bio::Tools::Est2Genome, Bio::Tools::Fgenesh, Bio::Tools::FootPrinter, Bio::Tools::GFF, Bio::Tools::Geneid, Bio::Tools::Genemark, Bio::Tools::Genewise, Bio::Tools::Genomewise, Bio::Tools::Genscan, Bio::Tools::Glimmer, Bio::Tools::Grail, Bio::Tools::IUPAC, Bio::Tools::Lucy, Bio::Tools::MZEF, Bio::Tools::Match, Bio::Tools::OddCodes, Bio::Tools::Phylo::Gerp, Bio::Tools::Phylo::Molphy, Bio::Tools::Phylo::Molphy::Result, Bio::Tools::Phylo::Phylip::ProtDist, Bio::Tools::Prediction::Exon, Bio::Tools::Prediction::Gene, Bio::Tools::Primer3, Bio::Tools::Primer::Assessor::Base, Bio::Tools::Primer::AssessorI, Bio::Tools::Primer::Feature, Bio::Tools::Primer::Pair, Bio::Tools::Prints, Bio::Tools::Profile, Bio::Tools::Promoterwise, Bio::Tools::PrositeScan, Bio::Tools::Pseudowise, Bio::Tools::QRNA, Bio::Tools::RandomDistFunctions, Bio::Tools::RepeatMasker, Bio::Tools::Run::Analysis, Bio::Tools::Run::AnalysisFactory, Bio::Tools::Run::GenericParameters, Bio::Tools::Run::ParametersI, Bio::Tools::Run::Phylo::PhyloBase, 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::ipcress, Bio::Tools::isPcr, Bio::Tools::pICalculator, Bio::Tools::tRNAscanSE, Bio::Tree::AnnotatableNode, Bio::Tree::Compatible, Bio::Tree::DistanceFactory, 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::nexus, Bio::TreeIO::nhx, Bio::TreeIO::pag, Bio::TreeIO::phyloxml, Bio::TreeIO::tabtree, Bio::UpdateableSeqI, Bio::WebAgent
- meta_yml_has_provides
-
Add all modules contained in this distribution to the META.yml field 'provides'. Module::Build or Dist::Zilla::Plugin::MetaProvides do this automatically for you.
Modules
| Name | Abstract | Version | View |
|---|---|---|---|
| Bio::Align::AlignI | An interface for describing sequence alignments. | 1.007008 | metacpan |
| Bio::Align::DNAStatistics | Calculate some statistics for a DNA alignment | 1.007008 | metacpan |
| Bio::Align::PairwiseStatistics | Base statistic object for Pairwise Alignments | 1.007008 | metacpan |
| Bio::Align::ProteinStatistics | Calculate Protein Alignment statistics (mostly distances) | 1.007008 | metacpan |
| Bio::Align::StatisticsI | Calculate some statistics for an alignment | 1.007008 | metacpan |
| Bio::Align::Utilities | A collection of utilities regarding converting and manipulating alignment objects | 1.007008 | metacpan |
| Bio::AlignIO | Handler for AlignIO Formats | 1.007008 | metacpan |
| Bio::AlignIO::Handler::GenericAlignHandler | Bio::HandlerI-based generic data handler class for alignment-based data | 1.007008 | metacpan |
| Bio::AlignIO::arp | ARP MSA Sequence input/output stream | 1.007008 | metacpan |
| Bio::AlignIO::bl2seq | bl2seq sequence input/output stream | 1.007008 | metacpan |
| Bio::AlignIO::clustalw | clustalw sequence input/output stream | 1.007008 | metacpan |
| Bio::AlignIO::emboss | Parse EMBOSS alignment output (from applications water and needle) | 1.007008 | metacpan |
| Bio::AlignIO::fasta | fasta MSA Sequence input/output stream | 1.007008 | metacpan |
| Bio::AlignIO::largemultifasta | Largemultifasta MSA Sequence input/output stream | 1.007008 | metacpan |
| Bio::AlignIO::maf | Multiple Alignment Format sequence input stream | 1.007008 | metacpan |
| Bio::AlignIO::mase | mase sequence input/output stream | 1.007008 | metacpan |
| Bio::AlignIO::mega | Parse and Create MEGA format data files | 1.007008 | metacpan |
| Bio::AlignIO::meme | meme sequence input/output stream | 1.007008 | metacpan |
| Bio::AlignIO::metafasta | Metafasta MSA Sequence input/output stream | 1.007008 | metacpan |
| Bio::AlignIO::msf | msf sequence input/output stream | 1.007008 | metacpan |
| Bio::AlignIO::nexus | NEXUS format sequence input/output stream | 1.007008 | metacpan |
| Bio::AlignIO::pfam | pfam sequence input/output stream | 1.007008 | metacpan |
| Bio::AlignIO::phylip | PHYLIP format sequence input/output stream | 1.007008 | metacpan |
| Bio::AlignIO::po | po MSA Sequence input/output stream | 1.007008 | metacpan |
| Bio::AlignIO::proda | proda sequence input/output stream | 1.007008 | metacpan |
| Bio::AlignIO::prodom | prodom sequence input/output stream | 1.007008 | metacpan |
| Bio::AlignIO::psi | Read/Write PSI-BLAST profile alignment files | 1.007008 | metacpan |
| Bio::AlignIO::selex | selex sequence input/output stream | 1.007008 | metacpan |
| Bio::AlignIO::xmfa | XMFA MSA Sequence input/output stream | 1.007008 | metacpan |
| Bio::AnalysisI | An interface to any (local or remote) analysis tool | 1.007008 | metacpan |
| Bio::AnalysisParserI | Generic analysis output parser interface | 1.007008 | metacpan |
| Bio::AnalysisResultI | Interface for analysis result objects | 1.007008 | metacpan |
| Bio::AnnotatableI | the base interface an annotatable object must implement | 1.007008 | metacpan |
| Bio::Annotation::AnnotationFactory | Instantiates a new Bio::AnnotationI (or derived class) through a factory | 1.007008 | metacpan |
| Bio::Annotation::Collection | Default Perl implementation of AnnotationCollectionI | 1.007008 | metacpan |
| Bio::Annotation::Comment | A comment object, holding text | 1.007008 | metacpan |
| Bio::Annotation::DBLink | untyped links between databases | 1.007008 | metacpan |
| Bio::Annotation::OntologyTerm | An ontology term adapted to AnnotationI | 1.007008 | metacpan |
| Bio::Annotation::Reference | Specialised DBLink object for Literature References | 1.007008 | metacpan |
| Bio::Annotation::Relation | Relationship (pairwise) with other objects SeqI and NodeI; | 1.007008 | metacpan |
| Bio::Annotation::SimpleValue | A simple scalar | 1.007008 | metacpan |
| Bio::Annotation::StructuredValue | A scalar with embedded structured information | 1.007008 | metacpan |
| Bio::Annotation::TagTree | AnnotationI with tree-like hierarchal key-value relationships ('structured tags') that can be represented as simple text. | 1.007008 | metacpan |
| Bio::Annotation::Target | Provides an object which represents a target (ie, a similarity hit) from one object to something in another database | 1.007008 | metacpan |
| Bio::Annotation::Tree | Provide a tree as an annotation to a Bio::AnnotatableI object | 1.007008 | metacpan |
| Bio::Annotation::TypeManager | Manages types for annotation collections | 1.007008 | metacpan |
| Bio::AnnotationCollectionI | Interface for annotation collections | 1.007008 | metacpan |
| Bio::AnnotationI | Annotation interface | 1.007008 | metacpan |
| Bio::CodonUsage::IO | for reading and writing codon usage tables to file | 1.007008 | metacpan |
| Bio::CodonUsage::Table | for access to the Codon usage Database at http://www.kazusa.or.jp/codon. | 1.007008 | metacpan |
| Bio::DB::DBFetch | Database object for retrieving using the dbfetch script | 1.007008 | metacpan |
| Bio::DB::Failover | A Bio::DB::RandomAccessI compliant class which wraps a prioritized list of DBs | 1.007008 | metacpan |
| Bio::DB::Fasta | Fast indexed access to fasta files | 1.007008 | metacpan |
| Bio::DB::FileCache | In file cache for BioSeq objects | 1.007008 | metacpan |
| Bio::DB::Flat | Interface for indexed flat files | 1.007008 | metacpan |
| Bio::DB::Flat::BDB | Interface for BioHackathon standard BDB-indexed flat file | 1.007008 | metacpan |
| Bio::DB::Flat::BDB::embl | embl adaptor for Open-bio standard BDB-indexed flat file | 1.007008 | metacpan |
| Bio::DB::Flat::BDB::fasta | fasta adaptor for Open-bio standard BDB-indexed flat file | 1.007008 | metacpan |
| Bio::DB::Flat::BDB::genbank | genbank adaptor for Open-bio standard BDB-indexed flat file | 1.007008 | metacpan |
| Bio::DB::Flat::BDB::swiss | swissprot adaptor for Open-bio standard BDB-indexed flat file | 1.007008 | metacpan |
| Bio::DB::Flat::BinarySearch | BinarySearch search indexing system for sequence files | 1.007008 | metacpan |
| Bio::DB::GFF::Util::Binning | binning utility for Bio::DB::GFF index | 1.007008 | metacpan |
| Bio::DB::GFF::Util::Rearrange | rearrange utility | 1.007008 | metacpan |
| Bio::DB::GenericWebAgent | helper base class for parameter-based remote server access and response retrieval. | 1.007008 | metacpan |
| Bio::DB::InMemoryCache | Abstract interface for a sequence database | 1.007008 | metacpan |
| Bio::DB::IndexedBase | Base class for modules using indexed sequence files | 1.007008 | metacpan |
| Bio::DB::LocationI | A RandomAccessI-like abstract interface for retrieving location data from a sequence database and returning Bio::LocationI objects | 1.007008 | metacpan |
| Bio::DB::Qual | Fast indexed access to quality files | 1.007008 | metacpan |
| Bio::DB::Query::WebQuery | Helper class for web-based sequence queryies | 1.007008 | metacpan |
| Bio::DB::QueryI | Object Interface to queryable sequence databases | 1.007008 | metacpan |
| Bio::DB::RandomAccessI | Abstract interface for a sequence database | 1.007008 | metacpan |
| Bio::DB::ReferenceI | A RandomAccessI-like abstract interface for retrieving Reference data from a sequence database and returning Bio::Annotation::Reference objects | 1.007008 | metacpan |
| Bio::DB::Registry | Access to the Open Bio Database Access registry scheme | 1.007008 | metacpan |
| Bio::DB::SeqI | Abstract Interface for Sequence databases | 1.007008 | metacpan |
| Bio::DB::Taxonomy | Access to a taxonomy database | 1.007008 | metacpan |
| Bio::DB::Taxonomy::flatfile | Use the NCBI taxonomy from local indexed flat files | 1.007008 | metacpan |
| Bio::DB::Taxonomy::greengenes | Use the Greengenes taxonomy | 1.007008 | metacpan |
| Bio::DB::Taxonomy::list | An implementation of Bio::DB::Taxonomy that accepts lists of words to build a database | 1.007008 | metacpan |
| Bio::DB::Taxonomy::silva | Use the Silva taxonomy | 1.007008 | metacpan |
| Bio::DB::UpdateableSeqI | An interface for writing to a database of sequences. | 1.007008 | metacpan |
| Bio::DB::WebDBSeqI | Object Interface to generalize Web Databases for retrieving sequences | 1.007008 | metacpan |
| Bio::DBLinkContainerI | Abstract interface for any object wanting to use database cross references | 1.007008 | metacpan |
| Bio::Das::FeatureTypeI | Simple interface to Sequence Ontology feature types | 1.007008 | metacpan |
| Bio::Das::SegmentI | DAS-style access to a feature database | 1.007008 | metacpan |
| Bio::DasI | DAS-style access to a feature database | 1.007008 | metacpan |
| Bio::DescribableI | interface for objects with human readable names and descriptions | 1.007008 | metacpan |
| Bio::Event::EventGeneratorI | This interface describes the basic event generator class. | 1.007008 | metacpan |
| Bio::Event::EventHandlerI | An Event Handler Interface | 1.007008 | metacpan |
| Bio::Factory::AnalysisI | An interface to analysis tool factory | 1.007008 | metacpan |
| Bio::Factory::ApplicationFactoryI | Interface class for Application Factories | 1.007008 | metacpan |
| Bio::Factory::DriverFactory | Base class for factory classes loading drivers | 1.007008 | metacpan |
| Bio::Factory::FTLocationFactory | A FeatureTable Location Parser | 1.007008 | metacpan |
| Bio::Factory::LocationFactoryI | A factory interface for generating locations from a string | 1.007008 | metacpan |
| Bio::Factory::ObjectBuilderI | Interface for an object builder | 1.007008 | metacpan |
| Bio::Factory::ObjectFactory | Instantiates a new Bio::Root::RootI (or derived class) through a factory | 1.007008 | metacpan |
| Bio::Factory::ObjectFactoryI | A General object creator factory | 1.007008 | metacpan |
| Bio::Factory::SeqAnalysisParserFactory | class capable of creating SeqAnalysisParserI compliant parsers | 1.007008 | metacpan |
| Bio::Factory::SeqAnalysisParserFactoryI | interface describing objects capable of creating SeqAnalysisParserI compliant parsers | 1.007008 | metacpan |
| Bio::Factory::SequenceFactoryI | This interface allows for generic building of sequences in factories which create sequences (like SeqIO) | 1.007008 | metacpan |
| Bio::Factory::SequenceProcessorI | Interface for chained sequence processing algorithms | 1.007008 | metacpan |
| Bio::Factory::SequenceStreamI | Interface describing the basics of a Sequence Stream. | 1.007008 | metacpan |
| Bio::Factory::TreeFactoryI | Factory Interface for getting and writing trees from/to a data stream | 1.007008 | metacpan |
| Bio::FeatureHolderI | the base interface an object with features must implement | 1.007008 | metacpan |
| Bio::HandlerBaseI | Interface class for handler methods which interact with any event-driven parsers (drivers). | 1.007008 | metacpan |
| Bio::IdCollectionI | interface for objects with multiple identifiers | 1.007008 | metacpan |
| Bio::IdentifiableI | interface for objects with identifiers | 1.007008 | metacpan |
| Bio::Index::Abstract | Abstract interface for indexing a flat file | 1.007008 | metacpan |
| Bio::Index::AbstractSeq | base class for AbstractSeq | 1.007008 | metacpan |
| Bio::Index::Blast | Indexes Blast reports and supports retrieval based on query accession(s) | 1.007008 | metacpan |
| Bio::Index::BlastTable | Indexes tabular Blast reports (-m 8 or -m 9 format) and supports retrieval based on query accession(s) | 1.007008 | metacpan |
| Bio::Index::EMBL | Interface for indexing (multiple) EMBL/Swissprot .dat files (i.e. flat file EMBL/Swissprot format). | 1.007008 | metacpan |
| Bio::Index::Fasta | Interface for indexing (multiple) fasta files | 1.007008 | metacpan |
| Bio::Index::Fastq | Interface for indexing (multiple) fastq files | 1.007008 | metacpan |
| Bio::Index::GenBank | Interface for indexing one or more GenBank files (i.e. flat file GenBank format). | 1.007008 | metacpan |
| Bio::Index::Qual | Interface for indexing (multiple) fasta qual files | 1.007008 | metacpan |
| Bio::Index::SwissPfam | Interface for indexing swisspfam files | 1.007008 | metacpan |
| Bio::Index::Swissprot | Interface for indexing one or more Swissprot files. | 1.007008 | metacpan |
| Bio::LocatableSeq | A Bio::PrimarySeq object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq. | 1.007008 | metacpan |
| Bio::Location::Atomic | Implementation of a Atomic Location on a Sequence | 1.007008 | metacpan |
| Bio::Location::AvWithinCoordPolicy | class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise | 1.007008 | metacpan |
| Bio::Location::CoordinatePolicyI | Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location | 1.007008 | metacpan |
| Bio::Location::Fuzzy | Implementation of a Location on a Sequence which has unclear start and/or end locations | 1.007008 | metacpan |
| Bio::Location::FuzzyLocationI | Abstract interface of a Location on a Sequence which has unclear start/end location | 1.007008 | metacpan |
| Bio::Location::NarrowestCoordPolicy | class implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range | 1.007008 | metacpan |
| Bio::Location::Simple | Implementation of a Simple Location on a Sequence | 1.007008 | metacpan |
| Bio::Location::Split | Implementation of a Location on a Sequence which has multiple locations (start/end points) | 1.007008 | metacpan |
| Bio::Location::SplitLocationI | Abstract interface of a Location on a Sequence which has multiple locations (start/end points) | 1.007008 | metacpan |
| Bio::Location::WidestCoordPolicy | class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable range | 1.007008 | metacpan |
| Bio::LocationI | Abstract interface of a Location on a Sequence | 1.007008 | metacpan |
| Bio::Matrix::Generic | A generic matrix implementation | 1.007008 | metacpan |
| Bio::Matrix::IO | A factory for Matrix parsing | 1.007008 | metacpan |
| Bio::Matrix::IO::mlagan | A parser for the mlagan substitution matrix | 1.007008 | metacpan |
| Bio::Matrix::IO::phylip | A parser for PHYLIP distance matricies | 1.007008 | metacpan |
| Bio::Matrix::IO::scoring | A parser for PAM/BLOSUM matricies | 1.007008 | metacpan |
| Bio::Matrix::MatrixI | An interface for describing a Matrix | 1.007008 | metacpan |
| Bio::Matrix::Mlagan | A generic matrix with mlagan fields | 1.007008 | metacpan |
| Bio::Matrix::PSM::IO | PSM parser | 1.007008 | metacpan |
| Bio::Matrix::PSM::IO::mast | PSM mast parser implementation | 1.007008 | metacpan |
| Bio::Matrix::PSM::IO::masta | motif fasta format parser | 1.007008 | metacpan |
| Bio::Matrix::PSM::IO::meme | PSM meme parser implementation | 1.007008 | metacpan |
| Bio::Matrix::PSM::IO::psiblast | PSM psiblast parser | 1.007008 | metacpan |
| Bio::Matrix::PSM::IO::transfac | PSM transfac parser | 1.007008 | metacpan |
| Bio::Matrix::PSM::InstanceSite | A PSM site occurrence | 1.007008 | metacpan |
| Bio::Matrix::PSM::InstanceSiteI | InstanceSite interface, holds an instance of a PSM | 1.007008 | metacpan |
| Bio::Matrix::PSM::ProtMatrix | SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) with log-odds scoring information. | 1.007008 | metacpan |
| Bio::Matrix::PSM::ProtPsm | handle combination of site matricies | 1.007008 | metacpan |
| Bio::Matrix::PSM::Psm | handle combination of site matricies | 1.007008 | metacpan |
| Bio::Matrix::PSM::PsmHeader | PSM mast parser implementation | 1.007008 | metacpan |
| Bio::Matrix::PSM::PsmHeaderI | handles the header data from a PSM file | 1.007008 | metacpan |
| Bio::Matrix::PSM::PsmI | abstract interface to handler of site matricies | 1.007008 | metacpan |
| Bio::Matrix::PSM::SiteMatrix | SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds | 1.007008 | metacpan |
| Bio::Matrix::PSM::SiteMatrixI | SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds | 1.007008 | metacpan |
| Bio::Matrix::PhylipDist | A Phylip Distance Matrix object | 1.007008 | metacpan |
| Bio::Matrix::Scoring | Object which can hold scoring matrix information | 1.007008 | metacpan |
| Bio::Ontology::DocumentRegistry | Keep track of where to find ontologies. Allows lookups by name. | 1.007008 | metacpan |
| Bio::Ontology::GOterm | representation of GO terms | 1.007008 | metacpan |
| Bio::Ontology::InterProTerm | Implementation of InterProI term interface | 1.007008 | metacpan |
| Bio::Ontology::OBOEngine | An Ontology Engine for OBO style flat file format from the Gene Ontology Consortium | 1.007008 | metacpan |
| Bio::Ontology::OBOterm | representation of OBO terms | 1.007008 | metacpan |
| Bio::Ontology::Ontology | standard implementation of an Ontology | 1.007008 | metacpan |
| Bio::Ontology::OntologyEngineI | Interface a minimal Ontology implementation should satisfy | 1.007008 | metacpan |
| Bio::Ontology::OntologyI | Interface for an ontology implementation | 1.007008 | metacpan |
| Bio::Ontology::OntologyStore | A repository of ontologies | 1.007008 | metacpan |
| Bio::Ontology::Path | a path for an ontology term graph | 1.007008 | metacpan |
| Bio::Ontology::PathI | Interface for a path between ontology terms | 1.007008 | metacpan |
| Bio::Ontology::Relationship | a relationship for an ontology | 1.007008 | metacpan |
| Bio::Ontology::RelationshipFactory | Instantiates a new Bio::Ontology::RelationshipI (or derived class) through a factory | 1.007008 | metacpan |
| Bio::Ontology::RelationshipI | Interface for a relationship between ontology terms | 1.007008 | metacpan |
| Bio::Ontology::RelationshipType | a relationship type for an ontology | 1.007008 | metacpan |
| Bio::Ontology::SimpleGOEngine::GraphAdaptor | Graph adaptor for Bio::Ontology::SimpleGOEngine | 1.007008 | metacpan |
| Bio::Ontology::SimpleOntologyEngine | Implementation of OntologyEngineI interface | 1.007008 | metacpan |
| Bio::Ontology::Term | implementation of the interface for ontology terms | 1.007008 | metacpan |
| Bio::Ontology::TermFactory | Instantiates a new Bio::Ontology::TermI (or derived class) through a factory | 1.007008 | metacpan |
| Bio::Ontology::TermI | interface for ontology terms | 1.007008 | metacpan |
| Bio::OntologyIO | Parser factory for Ontology formats | 1.007008 | metacpan |
| Bio::OntologyIO::Handlers::BaseSAXHandler | base class for SAX Handlers | 1.007008 | metacpan |
| Bio::OntologyIO::Handlers::InterProHandler | XML handler class for InterProParser | 1.007008 | metacpan |
| Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler | parse an InterPro XML file and persist the resulting terms to a Biosql database | 1.007008 | metacpan |
| Bio::OntologyIO::InterProParser | Parser for InterPro xml files. | 1.007008 | metacpan |
| Bio::OntologyIO::dagflat | a base class parser for GO flat-file type formats | 1.007008 | metacpan |
| Bio::OntologyIO::goflat | a parser for the Gene Ontology flat-file format | 1.007008 | metacpan |
| Bio::OntologyIO::obo | parser for OBO flat-file format | 1.007008 | metacpan |
| Bio::OntologyIO::simplehierarchy | a base class parser for simple hierarchy-by-indentation type formats | 1.007008 | metacpan |
| Bio::OntologyIO::soflat | a parser for the Sequence Ontology flat-file format | 1.007008 | metacpan |
| Bio::ParameterBaseI | Simple interface class for any parameter-related data such as IDs, database name, program arguments, and other odds and ends. | 1.007008 | metacpan |
| Bio::PrimarySeq | Bioperl lightweight sequence object | 1.007008 | metacpan |
| Bio::PrimarySeqI | Interface definition for a Bio::PrimarySeq | 1.007008 | metacpan |
| Bio::PullParserI | A base module for fast 'pull' parsing | 1.007008 | metacpan |
| Bio::Range | Pure perl RangeI implementation | 1.007008 | metacpan |
| Bio::RangeI | Range interface | 1.007008 | metacpan |
| Bio::Root::Exception | BioPerl exceptions | 1.007008 | metacpan |
| Bio::Root::HTTPget | module for fallback HTTP get operations when LWP:: is unavailable | 1.007008 | metacpan |
| Bio::Root::IO | BioPerl base IO handling class | 1.007008 | metacpan |
| Bio::Root::Root | implementation of Bio::Root::RootI interface | 1.007008 | metacpan |
| Bio::Root::RootI | base interface for all BioPerl classes | 1.007008 | metacpan |
| Bio::Root::Storable | Safely store/retrieve objects from disk | 1.007008 | metacpan |
| Bio::Root::Test | common base for all BioPerl test scripts | 1.007008 | metacpan |
| Bio::Root::TestObject | 1.007008 | metacpan | |
| Bio::Root::Utilities | general-purpose utilities | 1.007008 | metacpan |
| Bio::Root::Version | don't use, get version from each module | 1.007008 | metacpan |
| Bio::Search::BlastStatistics | An object for Blast statistics | 1.007008 | metacpan |
| Bio::Search::BlastUtils | Utility functions for Bio::Search:: BLAST objects | 1.007008 | metacpan |
| Bio::Search::DatabaseI | Interface for a database used in a sequence search | 1.007008 | metacpan |
| Bio::Search::GenericDatabase | Generic implementation of Bio::Search::DatabaseI | 1.007008 | metacpan |
| Bio::Search::GenericStatistics | An object for statistics | 1.007008 | metacpan |
| Bio::Search::HSP::BlastHSP | Bioperl BLAST High-Scoring Pair object | 1.007008 | metacpan |
| Bio::Search::HSP::BlastPullHSP | A parser and HSP object for BlastN hsps | 1.007008 | metacpan |
| Bio::Search::HSP::FastaHSP | HSP object for FASTA specific data | 1.007008 | metacpan |
| Bio::Search::HSP::GenericHSP | A "Generic" implementation of a High Scoring Pair | 1.007008 | metacpan |
| Bio::Search::HSP::HSPFactory | A factory to create Bio::Search::HSP::HSPI objects | 1.007008 | metacpan |
| Bio::Search::HSP::HSPI | Interface for a High Scoring Pair in a similarity search result | 1.007008 | metacpan |
| Bio::Search::HSP::ModelHSP | A HSP object for model-based searches | 1.007008 | metacpan |
| Bio::Search::HSP::PSLHSP | A HSP for PSL output | 1.007008 | metacpan |
| Bio::Search::HSP::PsiBlastHSP | Bioperl BLAST High-Scoring Pair object | 1.007008 | metacpan |
| Bio::Search::HSP::PullHSPI | Bio::Search::HSP::HSPI interface for pull parsers. | 1.007008 | metacpan |
| Bio::Search::HSP::WABAHSP | HSP object suitable for describing WABA alignments | 1.007008 | metacpan |
| Bio::Search::Hit::BlastHit | Blast-specific subclass of Bio::Search::Hit::GenericHit | 1.007008 | metacpan |
| Bio::Search::Hit::BlastPullHit | A parser and hit object for BLASTN hits | 1.007008 | metacpan |
| Bio::Search::Hit::Fasta | Hit object specific for Fasta-generated hits | 1.007008 | metacpan |
| Bio::Search::Hit::GenericHit | A generic implementation of the Bio::Search::Hit::HitI interface | 1.007008 | metacpan |
| Bio::Search::Hit::HitFactory | A factory to create Bio::Search::Hit::HitI objects | 1.007008 | metacpan |
| Bio::Search::Hit::HitI | Interface for a hit in a similarity search result | 1.007008 | metacpan |
| Bio::Search::Hit::ModelHit | A model-based implementation of the Bio::Search::Hit::HitI interface | 1.007008 | metacpan |
| Bio::Search::Hit::PsiBlastHit | Bioperl BLAST Hit object | 1.007008 | metacpan |
| Bio::Search::Hit::PullHitI | Bio::Search::Hit::HitI interface for pull parsers. | 1.007008 | metacpan |
| Bio::Search::Iteration::GenericIteration | A generic implementation of the Bio::Search::Iteration::IterationI interface. | 1.007008 | metacpan |
| Bio::Search::Iteration::IterationI | Abstract interface to an iteration from an iterated search result, such as PSI-BLAST. | 1.007008 | metacpan |
| Bio::Search::Processor | DESCRIPTION of Object | 1.007008 | metacpan |
| Bio::Search::Result::BlastPullResult | A parser and result object for BLASTN results | 1.007008 | metacpan |
| Bio::Search::Result::BlastResult | Blast-specific subclass of Bio::Search::Result::GenericResult | 1.007008 | metacpan |
| Bio::Search::Result::CrossMatchResult | CrossMatch-specific subclass of Bio::Search::Result::GenericResult | 1.007008 | metacpan |
| Bio::Search::Result::GenericResult | Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results. | 1.007008 | metacpan |
| Bio::Search::Result::INFERNALResult | A Result object for INFERNAL results | 1.007008 | metacpan |
| Bio::Search::Result::PullResultI | Bio::Search::Result::ResultI interface for 'pull' parsers | 1.007008 | metacpan |
| Bio::Search::Result::ResultFactory | A factory to create Bio::Search::Result::ResultI objects | 1.007008 | metacpan |
| Bio::Search::Result::ResultI | Abstract interface to Search Result objects | 1.007008 | metacpan |
| Bio::Search::Result::WABAResult | Result object for WABA alignment output | 1.007008 | metacpan |
| Bio::Search::SearchUtils | Utility functions for Bio::Search:: objects | 1.007008 | metacpan |
| Bio::Search::StatisticsI | A Base object for statistics | 1.007008 | metacpan |
| Bio::Search::Tiling::MapTileUtils | utilities for manipulating closed intervals for an HSP tiling algorithm | 1.007008 | metacpan |
| Bio::Search::Tiling::MapTiling | An implementation of an HSP tiling algorithm, with methods to obtain frequently-requested statistics | 1.007008 | metacpan |
| Bio::Search::Tiling::TilingI | Abstract interface for an HSP tiling module | 1.007008 | metacpan |
| Bio::SearchIO | Driver for parsing Sequence Database Searches (BLAST, FASTA, ...) | 1.007008 | metacpan |
| Bio::SearchIO::EventHandlerI | An abstract Event Handler for Search Result parsing | 1.007008 | metacpan |
| Bio::SearchIO::FastHitEventBuilder | Event Handler for SearchIO events. | 1.007008 | metacpan |
| Bio::SearchIO::IteratedSearchResultEventBuilder | Event Handler for SearchIO events. | 1.007008 | metacpan |
| Bio::SearchIO::SearchResultEventBuilder | Event Handler for SearchIO events. | 1.007008 | metacpan |
| Bio::SearchIO::SearchWriterI | Interface for outputting parsed Search results | 1.007008 | metacpan |
| Bio::SearchIO::Writer::GbrowseGFF | Interface for outputting parsed search results in Gbrowse GFF format | 1.007008 | metacpan |
| Bio::SearchIO::Writer::HSPTableWriter | Tab-delimited data for Bio::Search::HSP::HSPI objects | 1.007008 | metacpan |
| Bio::SearchIO::Writer::HTMLResultWriter | write a Bio::Search::ResultI in HTML | 1.007008 | metacpan |
| Bio::SearchIO::Writer::HitTableWriter | Tab-delimited data for Bio::Search::Hit::HitI objects | 1.007008 | metacpan |
| Bio::SearchIO::Writer::ResultTableWriter | Outputs tab-delimited data for each Bio::Search::Result::ResultI object. | 1.007008 | metacpan |
| Bio::SearchIO::Writer::TextResultWriter | Object to implement writing a Bio::Search::ResultI in Text. | 1.007008 | metacpan |
| Bio::SearchIO::axt | a parser for axt format reports | 1.007008 | metacpan |
| Bio::SearchIO::blast | Event generator for event based parsing of blast reports | 1.007008 | metacpan |
| Bio::SearchIO::blast_pull | A parser for BLAST output | 1.007008 | metacpan |
| Bio::SearchIO::blasttable | Driver module for SearchIO for parsing NCBI -m 8/9 format | 1.007008 | metacpan |
| Bio::SearchIO::cross_match | CrossMatch-specific subclass of Bio::SearchIO | 1.007008 | metacpan |
| Bio::SearchIO::erpin | SearchIO-based ERPIN parser | 1.007008 | metacpan |
| Bio::SearchIO::exonerate | parser for Exonerate | 1.007008 | metacpan |
| Bio::SearchIO::fasta | A SearchIO parser for FASTA results | 1.007008 | metacpan |
| Bio::SearchIO::gmap_f9 | Event generator for parsing gmap reports (Z format) | 1.007008 | metacpan |
| Bio::SearchIO::infernal | SearchIO-based Infernal parser | 1.007008 | metacpan |
| Bio::SearchIO::megablast | a driver module for Bio::SearchIO to parse megablast reports (format 0) | 1.007008 | metacpan |
| Bio::SearchIO::psl | A parser for PSL output (UCSC) | 1.007008 | metacpan |
| Bio::SearchIO::rnamotif | SearchIO-based RNAMotif parser | 1.007008 | metacpan |
| Bio::SearchIO::sim4 | parser for Sim4 alignments | 1.007008 | metacpan |
| Bio::SearchIO::waba | SearchIO parser for Jim Kent WABA program alignment output | 1.007008 | metacpan |
| Bio::SearchIO::wise | Parsing of wise output as alignments | 1.007008 | metacpan |
| Bio::Seq | Sequence object, with features | 1.007008 | metacpan |
| Bio::Seq::BaseSeqProcessor | Base implementation for a SequenceProcessor | 1.007008 | metacpan |
| Bio::Seq::EncodedSeq | subtype of L<Bio::LocatableSeq|Bio::LocatableSeq> to store DNA that encodes a protein | 1.007008 | metacpan |
| Bio::Seq::LargeLocatableSeq | LocatableSeq object that stores sequence as files in the tempdir | 1.007008 | 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 | 1.007008 | metacpan |
| Bio::Seq::LargeSeq | SeqI compliant object that stores sequence as files in /tmp | 1.007008 | metacpan |
| Bio::Seq::LargeSeqI | Interface class for sequences that cache their residues in a temporary file | 1.007008 | metacpan |
| Bio::Seq::Meta | Generic superclass for sequence objects with residue-based meta information | 1.007008 | metacpan |
| Bio::Seq::Meta::Array | array-based generic implementation of a sequence class with residue-based meta information | 1.007008 | metacpan |
| Bio::Seq::MetaI | Interface for sequence objects with residue-based meta information | 1.007008 | metacpan |
| Bio::Seq::PrimaryQual | Bioperl lightweight Quality Object | 1.007008 | metacpan |
| Bio::Seq::PrimedSeq | A sequence and a pair of primers matching on it | 1.007008 | metacpan |
| Bio::Seq::QualI | Interface definition for a Bio::Seq::Qual | 1.007008 | metacpan |
| Bio::Seq::Quality | Implementation of sequence with residue quality and trace values | 1.007008 | metacpan |
| Bio::Seq::RichSeq | Module implementing a sequence created from a rich sequence database entry | 1.007008 | metacpan |
| Bio::Seq::RichSeqI | interface for sequences from rich data sources, mostly databases | 1.007008 | metacpan |
| Bio::Seq::SeqBuilder | Configurable object builder for sequence stream parsers | 1.007008 | metacpan |
| Bio::Seq::SeqFactory | Instantiation of generic Bio::PrimarySeqI (or derived) objects through a factory | 1.007008 | metacpan |
| Bio::Seq::SeqFastaSpeedFactory | Rapid creation of Bio::Seq objects through a factory | 1.007008 | metacpan |
| Bio::Seq::SequenceTrace | Bioperl object packaging a sequence with its trace | 1.007008 | metacpan |
| Bio::Seq::SimulatedRead | Read with sequencing errors taken from a reference sequence | 1.007008 | metacpan |
| Bio::Seq::TraceI | Interface definition for a Bio::Seq::Trace | 1.007008 | metacpan |
| Bio::SeqAnalysisParserI | Sequence analysis output parser interface | 1.007008 | metacpan |
| Bio::SeqFeature::Amplicon | Amplicon feature | 1.007008 | metacpan |
| Bio::SeqFeature::AnnotationAdaptor | integrates SeqFeatureIs annotation | 1.007008 | 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. | 1.007008 | metacpan |
| Bio::SeqFeature::CollectionI | An interface for a collection of SeqFeatureI objects. | 1.007008 | metacpan |
| Bio::SeqFeature::Computation | Computation SeqFeature | 1.007008 | metacpan |
| Bio::SeqFeature::FeaturePair | hold pair feature information e.g. blast hits | 1.007008 | metacpan |
| Bio::SeqFeature::Gene::Exon | a feature representing an exon | 1.007008 | metacpan |
| Bio::SeqFeature::Gene::ExonI | Interface for a feature representing an exon | 1.007008 | metacpan |
| Bio::SeqFeature::Gene::GeneStructure | A feature representing an arbitrarily complex structure of a gene | 1.007008 | metacpan |
| Bio::SeqFeature::Gene::GeneStructureI | A feature representing an arbitrarily complex structure of a gene | 1.007008 | metacpan |
| Bio::SeqFeature::Gene::Intron | An intron feature | 1.007008 | metacpan |
| Bio::SeqFeature::Gene::NC_Feature | 1.007008 | metacpan | |
| Bio::SeqFeature::Gene::Poly_A_site | poly A feature | 1.007008 | metacpan |
| Bio::SeqFeature::Gene::Promoter | Describes a promoter | 1.007008 | metacpan |
| Bio::SeqFeature::Gene::Transcript | A feature representing a transcript | 1.007008 | metacpan |
| Bio::SeqFeature::Gene::TranscriptI | Interface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site. | 1.007008 | metacpan |
| Bio::SeqFeature::Gene::UTR | A feature representing an untranslated region that is part of a transcriptional unit | 1.007008 | metacpan |
| Bio::SeqFeature::Generic | Generic SeqFeature | 1.007008 | metacpan |
| Bio::SeqFeature::Lite | Lightweight Bio::SeqFeatureI class | 1.007008 | metacpan |
| Bio::SeqFeature::PositionProxy | handle features when truncation/revcom sequences span a feature | 1.007008 | metacpan |
| Bio::SeqFeature::Primer | Primer Generic SeqFeature | 1.007008 | metacpan |
| Bio::SeqFeature::Similarity | A sequence feature based on similarity | 1.007008 | metacpan |
| Bio::SeqFeature::SimilarityPair | Sequence feature based on the similarity of two sequences. | 1.007008 | metacpan |
| Bio::SeqFeature::SubSeq | Feature representing a subsequence | 1.007008 | metacpan |
| Bio::SeqFeature::Tools::FeatureNamer | generates unique persistent names for features | 1.007008 | metacpan |
| Bio::SeqFeature::Tools::IDHandler | maps $seq_feature->primary_tag | 1.007008 | metacpan |
| Bio::SeqFeature::Tools::TypeMapper | maps $seq_feature->primary_tag | 1.007008 | metacpan |
| Bio::SeqFeature::Tools::Unflattener | turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy | 1.007008 | metacpan |
| Bio::SeqFeature::TypedSeqFeatureI | a strongly typed SeqFeature | 1.007008 | metacpan |
| Bio::SeqFeatureI | Abstract interface of a Sequence Feature | 1.007008 | metacpan |
| Bio::SeqI | [Developers] Abstract Interface of Sequence (with features) | 1.007008 | metacpan |
| Bio::SeqIO | Handler for SeqIO Formats | 1.007008 | metacpan |
| Bio::SeqIO::FTHelper | Helper class for EMBL/Genbank feature tables | 1.007008 | metacpan |
| Bio::SeqIO::Handler::GenericRichSeqHandler | Bio::HandlerI-based data handler for GenBank/EMBL/UniProt (and other) sequence data | 1.007008 | metacpan |
| Bio::SeqIO::MultiFile | Treating a set of files as a single input stream | 1.007008 | metacpan |
| Bio::SeqIO::ace | ace sequence input/output stream | 1.007008 | metacpan |
| Bio::SeqIO::asciitree | asciitree sequence input/output stream | 1.007008 | metacpan |
| Bio::SeqIO::bsml | BSML sequence input/output stream | 1.007008 | metacpan |
| Bio::SeqIO::bsml_sax | BSML sequence input/output stream using SAX | 1.007008 | metacpan |
| Bio::SeqIO::embl | EMBL sequence input/output stream | 1.007008 | metacpan |
| Bio::SeqIO::embldriver | EMBL sequence input/output stream | 1.007008 | metacpan |
| Bio::SeqIO::fasta | fasta sequence input/output stream | 1.007008 | metacpan |
| Bio::SeqIO::fastq | fastq sequence input/output stream | 1.007008 | metacpan |
| Bio::SeqIO::game | a class for parsing and writing game-XML | 1.007008 | metacpan |
| Bio::SeqIO::game::featHandler | a class for handling feature elements | 1.007008 | metacpan |
| Bio::SeqIO::game::gameHandler | PerlSAX handler for game-XML | 1.007008 | metacpan |
| Bio::SeqIO::game::gameSubs | a base class for game-XML parsing | 1.007008 | metacpan |
| Bio::SeqIO::game::gameWriter | a class for writing game-XML | 1.007008 | metacpan |
| Bio::SeqIO::game::seqHandler | a class for handling game-XML sequences | 1.007008 | metacpan |
| Bio::SeqIO::gbdriver | GenBank handler-based push parser | 1.007008 | metacpan |
| Bio::SeqIO::gbxml | GenBank sequence input/output stream using SAX | 1.007008 | metacpan |
| Bio::SeqIO::gcg | GCG sequence input/output stream | 1.007008 | metacpan |
| Bio::SeqIO::genbank | GenBank sequence input/output stream | 1.007008 | metacpan |
| Bio::SeqIO::kegg | KEGG sequence input/output stream | 1.007008 | metacpan |
| Bio::SeqIO::largefasta | method i/o on very large fasta sequence files | 1.007008 | metacpan |
| Bio::SeqIO::locuslink | LocusLink input/output stream | 1.007008 | metacpan |
| Bio::SeqIO::mbsout | input stream for output by Teshima et al.'s mbs. | 1.007008 | metacpan |
| Bio::SeqIO::metafasta | metafasta sequence input/output stream | 1.007008 | metacpan |
| Bio::SeqIO::msout | input stream for output by Hudson's ms | 1.007008 | metacpan |
| Bio::SeqIO::phd | phd file input/output stream | 1.007008 | metacpan |
| Bio::SeqIO::pir | PIR sequence input/output stream | 1.007008 | metacpan |
| Bio::SeqIO::qual | .qual file input/output stream | 1.007008 | metacpan |
| Bio::SeqIO::raw | raw sequence file input/output stream | 1.007008 | metacpan |
| Bio::SeqIO::scf | .scf file input/output stream | 1.007008 | metacpan |
| Bio::SeqIO::seqxml | SeqXML sequence input/output stream | 1.007008 | metacpan |
| Bio::SeqIO::swiss | Swissprot sequence input/output stream | 1.007008 | metacpan |
| Bio::SeqIO::swissdriver | SwissProt/UniProt handler-based push parser | 1.007008 | metacpan |
| Bio::SeqIO::tab | nearly raw sequence file input/output stream. Reads/writes id"\t"sequence"\n" | 1.007008 | metacpan |
| Bio::SeqIO::table | sequence input/output stream from a delimited table | 1.007008 | metacpan |
| Bio::SeqIO::tigr | TIGR XML sequence input/output stream | 1.007008 | metacpan |
| Bio::SeqIO::tigrxml | Parse TIGR (new) XML | 1.007008 | metacpan |
| Bio::SeqIO::tinyseq | reading/writing sequences in NCBI TinySeq format | 1.007008 | metacpan |
| Bio::SeqIO::tinyseq::tinyseqHandler | XML event handlers to support NCBI TinySeq XML parsing | 1.007008 | metacpan |
| Bio::SeqUtils | Additional methods for PrimarySeq objects | 1.007008 | metacpan |
| Bio::SimpleAlign | Multiple alignments held as a set of sequences | 1.007008 | metacpan |
| Bio::SimpleAnalysisI | A simple interface to any (local or remote) analysis tool | 1.007008 | metacpan |
| Bio::Species | Generic species object. | 1.007008 | metacpan |
| Bio::Taxon | A node in a represented taxonomy | 1.007008 | metacpan |
| Bio::Tools::Alignment::Consed | A module to work with objects from consed .ace files | 1.007008 | metacpan |
| Bio::Tools::Alignment::Trim | A kludge to do specialized trimming of sequence based on quality. | 1.007008 | metacpan |
| Bio::Tools::AmpliconSearch | Find amplicons in a template using degenerate PCR primers | 1.007008 | metacpan |
| Bio::Tools::Analysis::SimpleAnalysisBase | abstract superclass for SimpleAnalysis implementations | 1.007008 | metacpan |
| Bio::Tools::AnalysisResult | Base class for analysis result objects and parsers | 1.007008 | metacpan |
| Bio::Tools::Blat | parser for Blat program | 1.007008 | metacpan |
| Bio::Tools::CodonTable | Codon table object | 1.007008 | metacpan |
| Bio::Tools::Coil | parser for Coil output | 1.007008 | metacpan |
| Bio::Tools::ECnumber | representation of EC numbers (Enzyme Classification) | 1.007008 | metacpan |
| Bio::Tools::EMBOSS::Palindrome | parse EMBOSS palindrome output | 1.007008 | metacpan |
| Bio::Tools::EPCR | Parse ePCR output and make features | 1.007008 | metacpan |
| Bio::Tools::ESTScan | Results of one ESTScan run | 1.007008 | metacpan |
| Bio::Tools::Eponine | Results of one Eponine run | 1.007008 | metacpan |
| Bio::Tools::Est2Genome | Parse est2genome output, makes simple Bio::SeqFeature::Generic objects | 1.007008 | metacpan |
| Bio::Tools::Fgenesh | parse results of one Fgenesh run | 1.007008 | metacpan |
| Bio::Tools::FootPrinter | write sequence features in FootPrinter format | 1.007008 | metacpan |
| Bio::Tools::GFF | A Bio::SeqAnalysisParserI compliant GFF format parser | 1.007008 | metacpan |
| Bio::Tools::Geneid | Results of one geneid run | 1.007008 | metacpan |
| Bio::Tools::Genemark | Results of one Genemark run | 1.007008 | metacpan |
| Bio::Tools::Genewise | Results of one Genewise run | 1.007008 | metacpan |
| Bio::Tools::Genomewise | Results of one Genomewise run | 1.007008 | metacpan |
| Bio::Tools::Genscan | Results of one Genscan run | 1.007008 | metacpan |
| Bio::Tools::Glimmer | parser for Glimmer 2.X/3.X prokaryotic and GlimmerM/GlimmerHMM eukaryotic gene predictions | 1.007008 | metacpan |
| Bio::Tools::Grail | Results of one Grail run | 1.007008 | metacpan |
| Bio::Tools::GuessSeqFormat | Module for determining the sequence format of the contents of a file, a string, or through a filehandle. | 1.007008 | metacpan |
| Bio::Tools::IUPAC | Generates unique sequence objects or regular expressions from an ambiguous IUPAC sequence | 1.007008 | metacpan |
| Bio::Tools::Lucy | Object for analyzing the output from Lucy, a vector and quality trimming program from TIGR | 1.007008 | metacpan |
| Bio::Tools::MZEF | Results of one MZEF run | 1.007008 | metacpan |
| Bio::Tools::Match | Parses output from Transfac's match(TM) | 1.007008 | metacpan |
| Bio::Tools::OddCodes | Object holding alternative alphabet coding for one protein sequence | 1.007008 | metacpan |
| Bio::Tools::Phylo::Gerp | Parses output from GERP | 1.007008 | metacpan |
| Bio::Tools::Phylo::Molphy | parser for Molphy output | 1.007008 | metacpan |
| Bio::Tools::Phylo::Molphy::Result | container for data parsed from a ProtML run | 1.007008 | metacpan |
| Bio::Tools::Phylo::Phylip::ProtDist | parser for ProtDist output | 1.007008 | metacpan |
| Bio::Tools::Prediction::Exon | A predicted exon feature | 1.007008 | metacpan |
| Bio::Tools::Prediction::Gene | a predicted gene structure feature | 1.007008 | metacpan |
| Bio::Tools::Primer3 | Create input for and work with the output from the program primer3 | 1.007008 | metacpan |
| Bio::Tools::Primer::Assessor::Base | base class for common assessor things | 1.007008 | metacpan |
| Bio::Tools::Primer::AssessorI | interface for assessing primer pairs | 1.007008 | metacpan |
| Bio::Tools::Primer::Feature | position of a single primer | 1.007008 | metacpan |
| Bio::Tools::Primer::Pair | two primers on left and right side | 1.007008 | metacpan |
| Bio::Tools::Prints | Parser for FingerPRINTScanII program | 1.007008 | metacpan |
| Bio::Tools::Profile | parse Profile output | 1.007008 | metacpan |
| Bio::Tools::Promoterwise | parser for Promoterwise tab format output | 1.007008 | metacpan |
| Bio::Tools::PrositeScan | Parser for ps_scan result | 1.007008 | metacpan |
| Bio::Tools::Pseudowise | Results of one Pseudowise run | 1.007008 | metacpan |
| Bio::Tools::QRNA | A Parser for qrna output | 1.007008 | metacpan |
| Bio::Tools::RandomDistFunctions | A set of routines useful for generating random data in different distributions | 1.007008 | metacpan |
| Bio::Tools::RepeatMasker | a parser for RepeatMasker output | 1.007008 | metacpan |
| Bio::Tools::Run::Analysis | Module representing any (remote or local) analysis tool | 1.007008 | metacpan |
| Bio::Tools::Run::AnalysisFactory | A directory of analysis tools | 1.007008 | metacpan |
| Bio::Tools::Run::GenericParameters | An object for the parameters used to run programs | 1.007008 | metacpan |
| Bio::Tools::Run::ParametersI | A Base object for the parameters used to run programs | 1.007008 | metacpan |
| Bio::Tools::Run::Phylo::PhyloBase | 1.007008 | metacpan | |
| Bio::Tools::Run::WrapperBase | A Base object for wrappers around executables | 1.007008 | metacpan |
| Bio::Tools::Seg | parse C<seg> output | 1.007008 | metacpan |
| Bio::Tools::SeqPattern | represent a sequence pattern or motif | 1.007008 | metacpan |
| Bio::Tools::SeqPattern::Backtranslate | reverse translate protein patterns | 1.007008 | metacpan |
| Bio::Tools::SeqStats | Object holding statistics for one particular sequence | 1.007008 | metacpan |
| Bio::Tools::SeqWords | Object holding n-mer statistics for a sequence | 1.007008 | metacpan |
| Bio::Tools::Sigcleave | Bioperl object for sigcleave analysis | 1.007008 | metacpan |
| Bio::Tools::Signalp | parser for Signalp output | 1.007008 | metacpan |
| Bio::Tools::Signalp::ExtendedSignalp | enhanced parser for Signalp output | 1.007008 | metacpan |
| Bio::Tools::Sim4::Exon | A single exon determined by an alignment | 1.007008 | metacpan |
| Bio::Tools::Sim4::Results | Results of one Sim4 run | 1.007008 | metacpan |
| Bio::Tools::Spidey::Exon | A single exon determined by an alignment | 1.007008 | metacpan |
| Bio::Tools::Spidey::Results | Results of a Spidey run | 1.007008 | metacpan |
| Bio::Tools::TandemRepeatsFinder | a parser for Tandem Repeats Finder output | 1.007008 | metacpan |
| Bio::Tools::TargetP | Results of one TargetP run | 1.007008 | metacpan |
| Bio::Tools::Tmhmm | parse TMHMM output (TransMembrane HMM) | 1.007008 | metacpan |
| Bio::Tools::ipcress | Parse ipcress output and make features | 1.007008 | metacpan |
| Bio::Tools::isPcr | Parse isPcr output and make features | 1.007008 | metacpan |
| Bio::Tools::pICalculator | calculate the isoelectric point of a protein | 1.007008 | metacpan |
| Bio::Tools::tRNAscanSE | A parser for tRNAscan-SE output | 1.007008 | metacpan |
| Bio::Tree::AnnotatableNode | A Tree Node with support for annotation | 1.007008 | metacpan |
| Bio::Tree::Compatible | Testing compatibility of phylogenetic trees with nested taxa. | 1.007008 | metacpan |
| Bio::Tree::DistanceFactory | Construct a tree using distance based methods | 1.007008 | metacpan |
| Bio::Tree::Node | A Simple Tree Node | 1.007008 | metacpan |
| Bio::Tree::NodeI | Interface describing a Tree Node | 1.007008 | metacpan |
| Bio::Tree::NodeNHX | A Simple Tree Node with support for NHX tags | 1.007008 | metacpan |
| Bio::Tree::RandomFactory | TreeFactory for generating Random Trees | 1.007008 | metacpan |
| Bio::Tree::Statistics | Calculate certain statistics for a Tree | 1.007008 | metacpan |
| Bio::Tree::Tree | An implementation of the TreeI interface. | 1.007008 | metacpan |
| Bio::Tree::TreeFunctionsI | Decorated Interface implementing basic Tree exploration methods | 1.007008 | metacpan |
| Bio::Tree::TreeI | A Tree object suitable for lots of things, designed originally for Phylogenetic Trees. | 1.007008 | metacpan |
| Bio::TreeIO | Parser for Tree files | 1.007008 | metacpan |
| Bio::TreeIO::NewickParser | newick string parser | 1.007008 | metacpan |
| Bio::TreeIO::TreeEventBuilder | Build Bio::Tree::Tree's and Bio::Tree::Node's from Events | 1.007008 | metacpan |
| Bio::TreeIO::cluster | A TreeIO driver module for parsing Algorithm::Cluster::treecluster() output | 1.007008 | metacpan |
| Bio::TreeIO::lintree | Parser for lintree output trees | 1.007008 | metacpan |
| Bio::TreeIO::newick | parsing and writing of Newick/PHYLIP/New Hampshire format | 1.007008 | metacpan |
| Bio::TreeIO::nexus | A TreeIO driver module for parsing Nexus tree output from PAUP | 1.007008 | metacpan |
| Bio::TreeIO::nhx | TreeIO implementation for parsing Newick/New Hampshire eXtendend (NHX) format. | 1.007008 | metacpan |
| Bio::TreeIO::pag | Bio::TreeIO driver for Pagel format | 1.007008 | metacpan |
| Bio::TreeIO::phyloxml | TreeIO implementation for parsing PhyloXML format. | 1.007008 | metacpan |
| Bio::TreeIO::tabtree | A simple output format which displays a tree as an ASCII drawing | 1.007008 | metacpan |
| Bio::UpdateableSeqI | Descendant of Bio::SeqI that allows updates | 1.007008 | metacpan |
| Bio::WebAgent | A base class for Web (any protocol) access | 1.007008 | metacpan |
| BioPerl | Perl modules for biology | 1.007008 | metacpan |
Provides
| Name | File | View |
|---|---|---|
| Bio::AnalysisI::JobI | lib/Bio/AnalysisI.pm | metacpan |
| Bio::DB::Indexed::Stream | lib/Bio/DB/IndexedBase.pm | metacpan |
| Bio::PrimarySeq::Fasta | lib/Bio/DB/Fasta.pm | metacpan |
| Bio::Seq::PrimaryQual::Qual | lib/Bio/DB/Qual.pm | metacpan |
| Bio::Tools::Run::Analysis::Job | lib/Bio/Tools/Run/Analysis.pm | metacpan |
| Bio::Tools::Run::Analysis::Utils | lib/Bio/Tools/Run/Analysis.pm | metacpan |