BioPerl 1.6.923 Deleted
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::CUTG, Bio::DB::Flat, Bio::DB::SeqFeature::NormalizedFeatureI, Bio::DB::SeqFeature::NormalizedTableFeatureI, Bio::DB::SeqFeature::Store::DBI::Iterator, Bio::Location::Split, Bio::Matrix::PSM::SiteMatrixI, Bio::MolEvol::CodonModel, Bio::Phenotype::PhenotypeI, Bio::Search::BlastUtils, Bio::SearchIO::SearchWriterI, Bio::SearchIO::XML::BlastHandler, Bio::SearchIO::XML::PsiBlastHandler, Bio::SearchIO::cross_match, Bio::SeqIO::game, Bio::Tools::Primer::Assessor::Base, Bio::Tools::Primer::AssessorI, Bio::Tools::Primer::Feature, Bio::Tools::Primer::Pair, Bio::Tools::Run::hmmer3, Bio::Tools::dpAlign
- main_module_version_matches_dist_version
-
Make sure that the main module name and version are the same of the distribution.
- no_pod_errors
-
Remove the POD errors. You can check for POD errors automatically by including Test::Pod to your test suite.
Error: BioPerl-1.6.923/doc/Deobfuscator/lib/Deobfuscator.pm -- Around line 90: '=item' outside of any '=over'
- 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::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::Coordinate::Chain, Bio::Coordinate::Collection, Bio::Coordinate::ExtrapolatingPair, Bio::Coordinate::GeneMapper, Bio::Coordinate::Graph, Bio::Coordinate::MapperI, Bio::Coordinate::Pair, Bio::Coordinate::Result, Bio::Coordinate::Result::Gap, Bio::Coordinate::Result::Match, Bio::Coordinate::ResultI, Bio::Coordinate::Utils, 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, Bio::DB::FileCache, Bio::DB::Flat, Bio::DB::Flat::BDB, Bio::DB::Flat::BDB::embl, Bio::DB::Flat::BDB::fasta, Bio::DB::Flat::BDB::genbank, Bio::DB::Flat::BDB::swiss, Bio::DB::Flat::BinarySearch, Bio::DB::GFF, Bio::DB::GFF::Adaptor::ace, Bio::DB::GFF::Adaptor::berkeleydb, Bio::DB::GFF::Adaptor::berkeleydb::iterator, Bio::DB::GFF::Adaptor::biofetch, Bio::DB::GFF::Adaptor::biofetch_oracle, Bio::DB::GFF::Adaptor::dbi, Bio::DB::GFF::Adaptor::dbi::caching_handle, Bio::DB::GFF::Adaptor::dbi::iterator, Bio::DB::GFF::Adaptor::dbi::mysql, Bio::DB::GFF::Adaptor::dbi::mysqlace, Bio::DB::GFF::Adaptor::dbi::mysqlcmap, Bio::DB::GFF::Adaptor::dbi::mysqlopt, Bio::DB::GFF::Adaptor::dbi::oracle, Bio::DB::GFF::Adaptor::dbi::oracleace, Bio::DB::GFF::Adaptor::dbi::pg, Bio::DB::GFF::Adaptor::dbi::pg_fts, Bio::DB::GFF::Adaptor::memory, Bio::DB::GFF::Adaptor::memory::feature_serializer, Bio::DB::GFF::Adaptor::memory::iterator, Bio::DB::GFF::Aggregator, Bio::DB::GFF::Aggregator::alignment, Bio::DB::GFF::Aggregator::clone, Bio::DB::GFF::Aggregator::coding, Bio::DB::GFF::Aggregator::gene, Bio::DB::GFF::Aggregator::match, Bio::DB::GFF::Aggregator::none, Bio::DB::GFF::Aggregator::orf, Bio::DB::GFF::Aggregator::processed_transcript, Bio::DB::GFF::Aggregator::so_transcript, Bio::DB::GFF::Aggregator::transcript, Bio::DB::GFF::Aggregator::ucsc_acembly, Bio::DB::GFF::Aggregator::ucsc_ensgene, Bio::DB::GFF::Aggregator::ucsc_genscan, Bio::DB::GFF::Aggregator::ucsc_refgene, Bio::DB::GFF::Aggregator::ucsc_sanger22, Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo, Bio::DB::GFF::Aggregator::ucsc_softberry, Bio::DB::GFF::Aggregator::ucsc_twinscan, Bio::DB::GFF::Aggregator::ucsc_unigene, Bio::DB::GFF::Featname, Bio::DB::GFF::Feature, Bio::DB::GFF::Homol, Bio::DB::GFF::RelSegment, Bio::DB::GFF::Segment, Bio::DB::GFF::Typename, Bio::DB::GFF::Util::Binning, Bio::DB::GFF::Util::Rearrange, Bio::DB::GenBank, Bio::DB::GenPept, Bio::DB::HIV::HIVAnnotProcessor, Bio::DB::HIV::HIVQueryHelper, Bio::DB::InMemoryCache, Bio::DB::IndexedBase, 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::berkeleydb, 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::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::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::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::HSPI, 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::Run::hmmer3, 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, BioPerl
- no_invalid_versions
-
Fix the version numbers so that version::is_lax($version) returns true.
Error:
- BioPerl.pm: HASH(0x55607e6fed90)
- consistent_version
-
Split the distribution, or fix the version numbers to make them consistent (use the highest version number to avoid version downgrade).
Error: 0.000003,1.006923,1.10
- 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.
- meta_yml_has_repository_resource
-
Add a 'repository' resource to the META.yml via 'meta_add' accessor (for Module::Build) or META_ADD parameter (for ExtUtils::MakeMaker).
Modules
Name | Abstract | Version | View |
---|---|---|---|
Bio::Align::AlignI | An interface for describing sequence alignments. | metacpan | |
Bio::Align::DNAStatistics | Calculate some statistics for a DNA alignment | metacpan | |
Bio::Align::Graphics | Graphic Rendering of Bio::Align::AlignI Objects | metacpan | |
Bio::Align::PairwiseStatistics | Base statistic object for Pairwise Alignments | metacpan | |
Bio::Align::ProteinStatistics | Calculate Protein Alignment statistics (mostly distances) | metacpan | |
Bio::Align::StatisticsI | Calculate some statistics for an alignment | metacpan | |
Bio::Align::Utilities | A collection of utilities regarding converting and manipulating alignment objects | metacpan | |
Bio::AlignIO | Handler for AlignIO Formats | metacpan | |
Bio::AlignIO::Handler::GenericAlignHandler | Bio::HandlerI-based generic data handler class for alignment-based data | metacpan | |
Bio::AlignIO::arp | ARP MSA Sequence input/output stream | metacpan | |
Bio::AlignIO::bl2seq | bl2seq sequence input/output stream | metacpan | |
Bio::AlignIO::clustalw | clustalw sequence input/output stream | metacpan | |
Bio::AlignIO::emboss | Parse EMBOSS alignment output (from applications water and needle) | metacpan | |
Bio::AlignIO::fasta | fasta MSA Sequence input/output stream | metacpan | |
Bio::AlignIO::largemultifasta | Largemultifasta MSA Sequence input/output stream | metacpan | |
Bio::AlignIO::maf | Multiple Alignment Format sequence input stream | metacpan | |
Bio::AlignIO::mase | mase sequence input/output stream | metacpan | |
Bio::AlignIO::mega | Parse and Create MEGA format data files | metacpan | |
Bio::AlignIO::meme | meme sequence input/output stream | metacpan | |
Bio::AlignIO::metafasta | Metafasta MSA Sequence input/output stream | metacpan | |
Bio::AlignIO::msf | msf sequence input/output stream | metacpan | |
Bio::AlignIO::nexml | NeXML format sequence alignment input/output stream driver | metacpan | |
Bio::AlignIO::nexus | NEXUS format sequence input/output stream | metacpan | |
Bio::AlignIO::pfam | pfam sequence input/output stream | metacpan | |
Bio::AlignIO::phylip | PHYLIP format sequence input/output stream | metacpan | |
Bio::AlignIO::po | po MSA Sequence input/output stream | metacpan | |
Bio::AlignIO::proda | proda sequence input/output stream | metacpan | |
Bio::AlignIO::prodom | prodom sequence input/output stream | metacpan | |
Bio::AlignIO::psi | Read/Write PSI-BLAST profile alignment files | metacpan | |
Bio::AlignIO::selex | selex sequence input/output stream | metacpan | |
Bio::AlignIO::stockholm | stockholm sequence input/output stream | metacpan | |
Bio::AlignIO::xmfa | XMFA MSA Sequence input/output stream | metacpan | |
Bio::AnalysisI | An interface to any (local or remote) analysis tool | metacpan | |
Bio::AnalysisParserI | Generic analysis output parser interface | metacpan | |
Bio::AnalysisResultI | Interface for analysis result objects | metacpan | |
Bio::AnnotatableI | the base interface an annotatable object must implement | metacpan | |
Bio::Annotation::AnnotationFactory | Instantiates a new Bio::AnnotationI (or derived class) through a factory | metacpan | |
Bio::Annotation::Collection | Default Perl implementation of AnnotationCollectionI | metacpan | |
Bio::Annotation::Comment | A comment object, holding text | metacpan | |
Bio::Annotation::DBLink | untyped links between databases | metacpan | |
Bio::Annotation::OntologyTerm | An ontology term adapted to AnnotationI | metacpan | |
Bio::Annotation::Reference | Specialised DBLink object for Literature References | metacpan | |
Bio::Annotation::Relation | Relationship (pairwise) with other objects SeqI and NodeI; | metacpan | |
Bio::Annotation::SimpleValue | A simple scalar | metacpan | |
Bio::Annotation::StructuredValue | A scalar with embedded structured information | metacpan | |
Bio::Annotation::TagTree | AnnotationI with tree-like hierarchal key-value relationships ('structured tags') that can be represented as simple text. | metacpan | |
Bio::Annotation::Target | Provides an object which represents a target (ie, a similarity hit) from one object to something in another database | metacpan | |
Bio::Annotation::Tree | Provide a tree as an annotation to a Bio::AnnotatableI object | metacpan | |
Bio::Annotation::TypeManager | Manages types for annotation collections | metacpan | |
Bio::AnnotationCollectionI | Interface for annotation collections | metacpan | |
Bio::AnnotationI | Annotation interface | metacpan | |
Bio::Assembly::Contig | Perl module to hold and manipulate sequence assembly contigs. | metacpan | |
Bio::Assembly::ContigAnalysis | metacpan | ||
Bio::Assembly::IO | Handler for Assembly::IO Formats | metacpan | |
Bio::Assembly::IO::ace | module to load ACE files from various assembly programs | metacpan | |
Bio::Assembly::IO::bowtie | An IO module for assemblies in Bowtie format *BETA* | metacpan | |
Bio::Assembly::IO::maq | Driver to read assembly files in maq format *BETA* | metacpan | |
Bio::Assembly::IO::phrap | driver to load phrap.out files. | metacpan | |
Bio::Assembly::IO::sam | An IO module for assemblies in Sam format *BETA* | metacpan | |
Bio::Assembly::IO::tigr | Driver to read and write assembly files in the TIGR Assembler v2 default format. | metacpan | |
Bio::Assembly::Scaffold | Perl module to hold and manipulate sequence assembly data. | metacpan | |
Bio::Assembly::ScaffoldI | Abstract Inteface of Sequence Assemblies | metacpan | |
Bio::Assembly::Singlet | Perl module to hold and manipulate singlets from sequence assembly contigs. | metacpan | |
Bio::Assembly::Tools::ContigSpectrum | create and manipulate contig spectra | metacpan | |
Bio::Cluster::ClusterFactory | Instantiates a new Bio::ClusterI (or derived class) through a factory | metacpan | |
Bio::Cluster::FamilyI | Family Interface | metacpan | |
Bio::Cluster::SequenceFamily | Sequence Family object | metacpan | |
Bio::Cluster::UniGene | UniGene object | metacpan | |
Bio::Cluster::UniGeneI | abstract interface of UniGene object | metacpan | |
Bio::ClusterI | Cluster Interface | metacpan | |
Bio::ClusterIO | Handler for Cluster Formats | metacpan | |
Bio::ClusterIO::dbsnp | dbSNP input stream | metacpan | |
Bio::ClusterIO::unigene | UniGene input stream | metacpan | |
Bio::CodonUsage::IO | for reading and writing codon usage tables to file | metacpan | |
Bio::CodonUsage::Table | for access to the Codon usage Database at http://www.kazusa.or.jp/codon. | metacpan | |
Bio::Coordinate::Chain | Mapping locations through a chain of coordinate mappers | metacpan | |
Bio::Coordinate::Collection | Noncontinuous match between two coordinate sets | metacpan | |
Bio::Coordinate::ExtrapolatingPair | Continuous match between two coordinate sets | metacpan | |
Bio::Coordinate::GeneMapper | transformations between gene related coordinate systems | metacpan | |
Bio::Coordinate::Graph | Finds shortest path between nodes in a graph | metacpan | |
Bio::Coordinate::MapperI | Interface describing coordinate mappers | metacpan | |
Bio::Coordinate::Pair | Continuous match between two coordinate sets | metacpan | |
Bio::Coordinate::Result | Results from coordinate transformation | metacpan | |
Bio::Coordinate::Result::Gap | Another name for Bio::Location::Simple | metacpan | |
Bio::Coordinate::Result::Match | Another name for Bio::Location::Simple | metacpan | |
Bio::Coordinate::ResultI | Interface to identify coordinate mapper results | metacpan | |
Bio::Coordinate::Utils | Additional methods to create Bio::Coordinate objects | metacpan | |
Bio::DB::Ace | Database object interface to ACeDB servers | metacpan | |
Bio::DB::BioFetch | Database object interface to BioFetch retrieval | metacpan | |
Bio::DB::CUTG | for access to the Codon usage Database at http://www.kazusa.or.jp/codon. | metacpan | |
Bio::DB::DBFetch | Database object for retrieving using the dbfetch script | metacpan | |
Bio::DB::EMBL | Database object interface for EMBL entry retrieval | metacpan | |
Bio::DB::EntrezGene | Database object interface to Entrez Gene | metacpan | |
Bio::DB::Expression | DESCRIPTION of Object | metacpan | |
Bio::DB::Expression::geo | *** DESCRIPTION of Class | metacpan | |
Bio::DB::Failover | A Bio::DB::RandomAccessI compliant class which wraps a prioritized list of DBs | metacpan | |
Bio::DB::Fasta | Fast indexed access to fasta files | metacpan | |
Bio::DB::FileCache | In file cache for BioSeq objects | metacpan | |
Bio::DB::Flat | Interface for indexed flat files | metacpan | |
Bio::DB::Flat::BDB | Interface for BioHackathon standard BDB-indexed flat file | metacpan | |
Bio::DB::Flat::BDB::embl | embl adaptor for Open-bio standard BDB-indexed flat file | metacpan | |
Bio::DB::Flat::BDB::fasta | fasta adaptor for Open-bio standard BDB-indexed flat file | metacpan | |
Bio::DB::Flat::BDB::genbank | genbank adaptor for Open-bio standard BDB-indexed flat file | metacpan | |
Bio::DB::Flat::BDB::swiss | swissprot adaptor for Open-bio standard BDB-indexed flat file | metacpan | |
Bio::DB::Flat::BinarySearch | BinarySearch search indexing system for sequence files | metacpan | |
Bio::DB::GFF | Storage and retrieval of sequence annotation data | metacpan | |
Bio::DB::GFF::Adaptor::ace | ace interface (for multiple inheritance) | metacpan | |
Bio::DB::GFF::Adaptor::berkeleydb | Bio::DB::GFF database adaptor for in-memory databases | metacpan | |
Bio::DB::GFF::Adaptor::berkeleydb::iterator | iterator for Bio::DB::GFF::Adaptor::berkeleydb | metacpan | |
Bio::DB::GFF::Adaptor::biofetch | Cache BioFetch objects in a Bio::DB::GFF database | metacpan | |
Bio::DB::GFF::Adaptor::biofetch_oracle | Cache BioFetch objects in a Bio::DB::GFF database | metacpan | |
Bio::DB::GFF::Adaptor::dbi | Database adaptor for DBI (SQL) databases | metacpan | |
Bio::DB::GFF::Adaptor::dbi::caching_handle | Cache for database handles | metacpan | |
Bio::DB::GFF::Adaptor::dbi::iterator | iterator for Bio::DB::GFF::Adaptor::dbi | metacpan | |
Bio::DB::GFF::Adaptor::dbi::mysql | Database adaptor for a specific mysql schema | metacpan | |
Bio::DB::GFF::Adaptor::dbi::mysqlace | Unholy union between mysql GFF database and acedb database | metacpan | |
Bio::DB::GFF::Adaptor::dbi::mysqlcmap | Database adaptor for an integraded CMap/GBrowse mysql schema | metacpan | |
Bio::DB::GFF::Adaptor::dbi::mysqlopt | Deprecated database adaptor | metacpan | |
Bio::DB::GFF::Adaptor::dbi::oracle | Database adaptor for a specific oracle schema | metacpan | |
Bio::DB::GFF::Adaptor::dbi::oracleace | Unholy union between oracle GFF database and acedb database | metacpan | |
Bio::DB::GFF::Adaptor::dbi::pg | Database adaptor for a specific postgres schema | metacpan | |
Bio::DB::GFF::Adaptor::dbi::pg_fts | Database adaptor for a specific postgres schema with a TSearch2 implementation | metacpan | |
Bio::DB::GFF::Adaptor::memory | Bio::DB::GFF database adaptor for in-memory databases | metacpan | |
Bio::DB::GFF::Adaptor::memory::feature_serializer | utility methods for serializing and deserializing GFF features | metacpan | |
Bio::DB::GFF::Adaptor::memory::iterator | iterator for Bio::DB::GFF::Adaptor::memory | metacpan | |
Bio::DB::GFF::Aggregator | Aggregate GFF groups into composite features | metacpan | |
Bio::DB::GFF::Aggregator::alignment | Alignment aggregator | metacpan | |
Bio::DB::GFF::Aggregator::clone | Clone aggregator | metacpan | |
Bio::DB::GFF::Aggregator::coding | The Coding Region Aggregator | metacpan | |
Bio::DB::GFF::Aggregator::gene | Sequence Ontology Geene | metacpan | |
Bio::DB::GFF::Aggregator::match | Match aggregator | metacpan | |
Bio::DB::GFF::Aggregator::none | No aggregation | metacpan | |
Bio::DB::GFF::Aggregator::orf | An aggregator for orf regions | metacpan | |
Bio::DB::GFF::Aggregator::processed_transcript | Sequence Ontology Transcript | metacpan | |
Bio::DB::GFF::Aggregator::so_transcript | Sequence Ontology Transcript | metacpan | |
Bio::DB::GFF::Aggregator::transcript | Transcript aggregator | metacpan | |
Bio::DB::GFF::Aggregator::ucsc_acembly | UCSC acembly aggregator | metacpan | |
Bio::DB::GFF::Aggregator::ucsc_ensgene | UCSC ensGene aggregator | metacpan | |
Bio::DB::GFF::Aggregator::ucsc_genscan | UCSC genscan aggregator | metacpan | |
Bio::DB::GFF::Aggregator::ucsc_refgene | UCSC refGene aggregator | metacpan | |
Bio::DB::GFF::Aggregator::ucsc_sanger22 | UCSC sanger22 aggregator | metacpan | |
Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo | UCSC sanger22pseudo aggregator | metacpan | |
Bio::DB::GFF::Aggregator::ucsc_softberry | UCSC softberry aggregator | metacpan | |
Bio::DB::GFF::Aggregator::ucsc_twinscan | UCSC twinscan aggregator | metacpan | |
Bio::DB::GFF::Aggregator::ucsc_unigene | UCSC UniGene aggregator | metacpan | |
Bio::DB::GFF::Featname | The name of a feature | metacpan | |
Bio::DB::GFF::Feature | A relative segment identified by a feature type | metacpan | |
Bio::DB::GFF::Homol | A segment of DNA that is homologous to another | metacpan | |
Bio::DB::GFF::RelSegment | Sequence segment with relative coordinate support | metacpan | |
Bio::DB::GFF::Segment | Simple DNA segment object | metacpan | |
Bio::DB::GFF::Typename | The name of a feature type | metacpan | |
Bio::DB::GFF::Util::Binning | binning utility for Bio::DB::GFF index | metacpan | |
Bio::DB::GFF::Util::Rearrange | rearrange utility | metacpan | |
Bio::DB::GenBank | Database object interface to GenBank | metacpan | |
Bio::DB::GenPept | Database object interface to GenPept | metacpan | |
Bio::DB::GenericWebAgent | helper base class for parameter-based remote server access and response retrieval. | metacpan | |
Bio::DB::HIV | Database object interface to the Los Alamos HIV Sequence Database | metacpan | |
Bio::DB::HIV::HIVAnnotProcessor | metacpan | ||
Bio::DB::HIV::HIVQueryHelper | Routines and packages used by Bio::DB::HIV and Bio::DB::Query::HIVQuery | metacpan | |
Bio::DB::InMemoryCache | Abstract interface for a sequence database | metacpan | |
Bio::DB::IndexedBase | Base class for modules using indexed sequence files | metacpan | |
Bio::DB::LocationI | A RandomAccessI-like abstract interface for retrieving location data from a sequence database and returning Bio::LocationI objects | metacpan | |
Bio::DB::MeSH | Term retrieval from a Web MeSH database | metacpan | |
Bio::DB::NCBIHelper | A collection of routines useful for queries to NCBI databases. | metacpan | |
Bio::DB::Qual | Fast indexed access to quality files | metacpan | |
Bio::DB::Query::GenBank | Build a GenBank Entrez Query | metacpan | |
Bio::DB::Query::HIVQuery | Query interface to the Los Alamos HIV Sequence Database | metacpan | |
Bio::DB::Query::WebQuery | Helper class for web-based sequence queryies | metacpan | |
Bio::DB::QueryI | Object Interface to queryable sequence databases | metacpan | |
Bio::DB::RandomAccessI | Abstract interface for a sequence database | metacpan | |
Bio::DB::RefSeq | Database object interface for RefSeq retrieval | metacpan | |
Bio::DB::ReferenceI | A RandomAccessI-like abstract interface for retrieving Reference data from a sequence database and returning Bio::Annotation::Reference objects | metacpan | |
Bio::DB::Registry | Access to the Open Bio Database Access registry scheme | metacpan | |
Bio::DB::SeqFeature | Normalized feature for use with Bio::DB::SeqFeature::Store | metacpan | |
Bio::DB::SeqFeature::NormalizedFeature | Normalized feature for use with Bio::DB::SeqFeature::Store | metacpan | |
Bio::DB::SeqFeature::NormalizedFeatureI | Interface for normalized features | metacpan | |
Bio::DB::SeqFeature::NormalizedTableFeatureI | Interface for normalized features whose hierarchy is stored in a table | metacpan | |
Bio::DB::SeqFeature::Segment | Location-based access to genome annotation data | metacpan | |
Bio::DB::SeqFeature::Store | Storage and retrieval of sequence annotation data | metacpan | |
Bio::DB::SeqFeature::Store::DBI::Iterator | utility methods for creating and iterating over SeqFeature records | metacpan | |
Bio::DB::SeqFeature::Store::DBI::Pg | PostgreSQL implementation of Bio::DB::SeqFeature::Store | metacpan | |
Bio::DB::SeqFeature::Store::DBI::SQLite | SQLite implementation of Bio::DB::SeqFeature::Store | metacpan | |
Bio::DB::SeqFeature::Store::DBI::mysql | Mysql implementation of Bio::DB::SeqFeature::Store | metacpan | |
Bio::DB::SeqFeature::Store::FeatureFileLoader | feature file loader for Bio::DB::SeqFeature::Store | metacpan | |
Bio::DB::SeqFeature::Store::GFF2Loader | GFF2 file loader for Bio::DB::SeqFeature::Store | metacpan | |
Bio::DB::SeqFeature::Store::GFF3Loader | GFF3 file loader for Bio::DB::SeqFeature::Store | metacpan | |
Bio::DB::SeqFeature::Store::LoadHelper | Internal utility for Bio::DB::SeqFeature::Store | 1.10 | metacpan |
Bio::DB::SeqFeature::Store::Loader | Loader | metacpan | |
Bio::DB::SeqFeature::Store::bdb | fetch and store objects from a BerkeleyDB | metacpan | |
Bio::DB::SeqFeature::Store::berkeleydb | Storage and retrieval of sequence annotation data in Berkeleydb files | metacpan | |
Bio::DB::SeqFeature::Store::berkeleydb3 | Storage and retrieval of sequence annotation data in Berkeleydb files | metacpan | |
Bio::DB::SeqFeature::Store::memory | In-memory implementation of Bio::DB::SeqFeature::Store | metacpan | |
Bio::DB::SeqHound | Database object interface to SeqHound | metacpan | |
Bio::DB::SeqI | Abstract Interface for Sequence databases | metacpan | |
Bio::DB::SeqVersion | front end to querying databases for identifier versions | metacpan | |
Bio::DB::SeqVersion::gi | interface to NCBI Sequence Revision History page | metacpan | |
Bio::DB::SwissProt | Database object interface to SwissProt retrieval | metacpan | |
Bio::DB::TFBS | Access to a Transcription Factor Binding Site database | metacpan | |
Bio::DB::TFBS::transfac_pro | An implementation of Bio::DB::TFBS which uses local flat files for transfac pro | metacpan | |
Bio::DB::Taxonomy | Access to a taxonomy database | metacpan | |
Bio::DB::Taxonomy::entrez | Taxonomy Entrez driver | metacpan | |
Bio::DB::Taxonomy::flatfile | Use the NCBI taxonomy from local indexed flat files | metacpan | |
Bio::DB::Taxonomy::greengenes | Use the Greengenes taxonomy | metacpan | |
Bio::DB::Taxonomy::list | An implementation of Bio::DB::Taxonomy that accepts lists of words to build a database | metacpan | |
Bio::DB::Taxonomy::silva | Use the Silva taxonomy | metacpan | |
Bio::DB::Universal | Artificial database that delegates to specific databases | metacpan | |
Bio::DB::UpdateableSeqI | An interface for writing to a database of sequences. | metacpan | |
Bio::DB::WebDBSeqI | Object Interface to generalize Web Databases for retrieving sequences | metacpan | |
Bio::DBLinkContainerI | Abstract interface for any object wanting to use database cross references | metacpan | |
Bio::Das::FeatureTypeI | Simple interface to Sequence Ontology feature types | metacpan | |
Bio::Das::SegmentI | DAS-style access to a feature database | metacpan | |
Bio::DasI | DAS-style access to a feature database | metacpan | |
Bio::DescribableI | interface for objects with human readable names and descriptions | metacpan | |
Bio::Draw::Pictogram | generate SVG output of Pictogram display for consensus motifs | metacpan | |
Bio::Event::EventGeneratorI | This interface describes the basic event generator class. | metacpan | |
Bio::Event::EventHandlerI | An Event Handler Interface | metacpan | |
Bio::Factory::AnalysisI | An interface to analysis tool factory | metacpan | |
Bio::Factory::ApplicationFactoryI | Interface class for Application Factories | metacpan | |
Bio::Factory::DriverFactory | Base class for factory classes loading drivers | metacpan | |
Bio::Factory::FTLocationFactory | A FeatureTable Location Parser | metacpan | |
Bio::Factory::LocationFactoryI | A factory interface for generating locations from a string | metacpan | |
Bio::Factory::MapFactoryI | A Factory for getting markers | metacpan | |
Bio::Factory::ObjectBuilderI | Interface for an object builder | metacpan | |
Bio::Factory::ObjectFactory | Instantiates a new Bio::Root::RootI (or derived class) through a factory | metacpan | |
Bio::Factory::ObjectFactoryI | A General object creator factory | metacpan | |
Bio::Factory::SeqAnalysisParserFactory | class capable of creating SeqAnalysisParserI compliant parsers | metacpan | |
Bio::Factory::SeqAnalysisParserFactoryI | interface describing objects capable of creating SeqAnalysisParserI compliant parsers | metacpan | |
Bio::Factory::SequenceFactoryI | This interface allows for generic building of sequences in factories which create sequences (like SeqIO) | metacpan | |
Bio::Factory::SequenceProcessorI | Interface for chained sequence processing algorithms | metacpan | |
Bio::Factory::SequenceStreamI | Interface describing the basics of a Sequence Stream. | metacpan | |
Bio::Factory::TreeFactoryI | Factory Interface for getting and writing trees from/to a data stream | metacpan | |
Bio::FeatureHolderI | the base interface an object with features must implement | metacpan | |
Bio::HandlerBaseI | Interface class for handler methods which interact with any event-driven parsers (drivers). | metacpan | |
Bio::IdCollectionI | interface for objects with multiple identifiers | metacpan | |
Bio::IdentifiableI | interface for objects with identifiers | metacpan | |
Bio::Index::Abstract | Abstract interface for indexing a flat file | metacpan | |
Bio::Index::AbstractSeq | base class for AbstractSeq | metacpan | |
Bio::Index::Blast | Indexes Blast reports and supports retrieval based on query accession(s) | metacpan | |
Bio::Index::BlastTable | Indexes tabular Blast reports (-m 8 or -m 9 format) and supports retrieval based on query accession(s) | metacpan | |
Bio::Index::EMBL | Interface for indexing (multiple) EMBL/Swissprot .dat files (i.e. flat file EMBL/Swissprot format). | metacpan | |
Bio::Index::Fasta | Interface for indexing (multiple) fasta files | metacpan | |
Bio::Index::Fastq | Interface for indexing (multiple) fastq files | metacpan | |
Bio::Index::GenBank | Interface for indexing one or more GenBank files (i.e. flat file GenBank format). | metacpan | |
Bio::Index::Hmmer | indexes HMMER reports and supports retreival based on query | metacpan | |
Bio::Index::Qual | Interface for indexing (multiple) fasta qual files | metacpan | |
Bio::Index::Stockholm | metacpan | ||
Bio::Index::SwissPfam | Interface for indexing swisspfam files | metacpan | |
Bio::Index::Swissprot | Interface for indexing one or more Swissprot files. | metacpan | |
Bio::LiveSeq::AARange | AARange abstract class for LiveSeq | metacpan | |
Bio::LiveSeq::Chain | DoubleChain DataStructure for Perl | metacpan | |
Bio::LiveSeq::ChainI | Double linked chain data structure | metacpan | |
Bio::LiveSeq::DNA | DNA object for LiveSeq | metacpan | |
Bio::LiveSeq::Exon | Range abstract class for LiveSeq | metacpan | |
Bio::LiveSeq::Gene | Range abstract class for LiveSeq | metacpan | |
Bio::LiveSeq::IO::BioPerl | Loader for LiveSeq from EMBL entries with BioPerl | metacpan | |
Bio::LiveSeq::IO::Loader | Parent Loader for LiveSeq | metacpan | |
Bio::LiveSeq::Intron | Range abstract class for LiveSeq | metacpan | |
Bio::LiveSeq::Mutation | Mutation event descriptor class | metacpan | |
Bio::LiveSeq::Mutator | Package mutating LiveSequences | metacpan | |
Bio::LiveSeq::Prim_Transcript | Prim_Transcript class for LiveSeq | metacpan | |
Bio::LiveSeq::Range | Range abstract class for LiveSeq | metacpan | |
Bio::LiveSeq::Repeat_Region | Repeat_Region class for LiveSeq | metacpan | |
Bio::LiveSeq::Repeat_Unit | Repeat_Unit class for LiveSeq | metacpan | |
Bio::LiveSeq::SeqI | Abstract sequence interface class for LiveSeq | metacpan | |
Bio::LiveSeq::Transcript | Transcript class for LiveSeq | metacpan | |
Bio::LiveSeq::Translation | Translation class for LiveSeq | metacpan | |
Bio::LocatableSeq | A Bio::PrimarySeq object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq. | metacpan | |
Bio::Location::Atomic | Implementation of a Atomic Location on a Sequence | metacpan | |
Bio::Location::AvWithinCoordPolicy | class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise | metacpan | |
Bio::Location::CoordinatePolicyI | Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location | metacpan | |
Bio::Location::Fuzzy | Implementation of a Location on a Sequence which has unclear start and/or end locations | metacpan | |
Bio::Location::FuzzyLocationI | Abstract interface of a Location on a Sequence which has unclear start/end location | metacpan | |
Bio::Location::NarrowestCoordPolicy | class implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range | metacpan | |
Bio::Location::Simple | Implementation of a Simple Location on a Sequence | metacpan | |
Bio::Location::Split | Implementation of a Location on a Sequence which has multiple locations (start/end points) | metacpan | |
Bio::Location::SplitLocationI | Abstract interface of a Location on a Sequence which has multiple locations (start/end points) | metacpan | |
Bio::Location::WidestCoordPolicy | class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable range | metacpan | |
Bio::LocationI | Abstract interface of a Location on a Sequence | metacpan | |
Bio::Map::Clone | An central map object representing a clone | metacpan | |
Bio::Map::Contig | A MapI implementation handling the contigs of a Physical Map (such as FPC) | metacpan | |
Bio::Map::CytoMap | A Bio::MapI compliant map implementation handling cytogenic bands | metacpan | |
Bio::Map::CytoMarker | An object representing a marker. | metacpan | |
Bio::Map::CytoPosition | Marker class with cytogenetic band storing attributes | metacpan | |
Bio::Map::EntityI | An Entity Interface | metacpan | |
Bio::Map::FPCMarker | An central map object representing a marker | metacpan | |
Bio::Map::Gene | An gene modelled as a mappable element. | metacpan | |
Bio::Map::GeneMap | A MapI implementation to represent the area around a gene | metacpan | |
Bio::Map::GenePosition | A typed position, suitable for modelling the various regions of a gene. | metacpan | |
Bio::Map::GeneRelative | Represents being relative to named sub-regions of a gene. | metacpan | |
Bio::Map::LinkageMap | A representation of a genetic linkage map. | metacpan | |
Bio::Map::LinkagePosition | Create a Position for a Marker that will be placed on a Bio::Map::LinkageMap | metacpan | |
Bio::Map::MapI | Interface for describing Map objects in bioperl | metacpan | |
Bio::Map::Mappable | An object representing a generic map element that can have multiple locations in several maps. | metacpan | |
Bio::Map::MappableI | An object that can be placed in a map | metacpan | |
Bio::Map::Marker | An central map object representing a generic marker that can have multiple location in several maps. | metacpan | |
Bio::Map::MarkerI | Interface for basic marker functionality | metacpan | |
Bio::Map::Microsatellite | An object representing a Microsatellite marker. | metacpan | |
Bio::Map::OrderedPosition | Abstracts the notion of a member of an ordered list of markers. Each marker is a certain distance from the one in the ordered list before it. | metacpan | |
Bio::Map::OrderedPositionWithDistance | Abstracts the notion of a member of an ordered list of markers. Each marker is a certain distance from the one in the ordered list before it. | metacpan | |
Bio::Map::Physical | A class for handling a Physical Map (such as FPC) | metacpan | |
Bio::Map::Position | A single position of a Marker, or the range over which that marker lies, in a Map | metacpan | |
Bio::Map::PositionHandler | A Position Handler Implementation | metacpan | |
Bio::Map::PositionHandlerI | A Position Handler Interface | metacpan | |
Bio::Map::PositionI | Abstracts the notion of a position having a value in the context of a marker and a Map | metacpan | |
Bio::Map::PositionWithSequence | A position with a sequence. | metacpan | |
Bio::Map::Prediction | An object representing the predictions of something that can have multiple locations in several maps. | metacpan | |
Bio::Map::Relative | Represents what a Position's coordiantes are relative to. | metacpan | |
Bio::Map::RelativeI | Interface for describing what a Position's coordiantes are relative to. | metacpan | |
Bio::Map::SimpleMap | A MapI implementation handling the basics of a Map | metacpan | |
Bio::Map::TranscriptionFactor | A transcription factor modelled as a mappable element | metacpan | |
Bio::MapIO | A Map Factory object | metacpan | |
Bio::MapIO::fpc | A FPC Map reader | metacpan | |
Bio::MapIO::mapmaker | A Mapmaker Map reader | metacpan | |
Bio::Matrix::Generic | A generic matrix implementation | metacpan | |
Bio::Matrix::IO | A factory for Matrix parsing | metacpan | |
Bio::Matrix::IO::mlagan | A parser for the mlagan substitution matrix | metacpan | |
Bio::Matrix::IO::phylip | A parser for PHYLIP distance matricies | metacpan | |
Bio::Matrix::IO::scoring | A parser for PAM/BLOSUM matricies | metacpan | |
Bio::Matrix::MatrixI | An interface for describing a Matrix | metacpan | |
Bio::Matrix::Mlagan | A generic matrix with mlagan fields | metacpan | |
Bio::Matrix::PSM::IO | PSM parser | metacpan | |
Bio::Matrix::PSM::IO::mast | PSM mast parser implementation | metacpan | |
Bio::Matrix::PSM::IO::masta | motif fasta format parser | metacpan | |
Bio::Matrix::PSM::IO::meme | PSM meme parser implementation | metacpan | |
Bio::Matrix::PSM::IO::psiblast | PSM psiblast parser | metacpan | |
Bio::Matrix::PSM::IO::transfac | PSM transfac parser | metacpan | |
Bio::Matrix::PSM::InstanceSite | A PSM site occurance | metacpan | |
Bio::Matrix::PSM::InstanceSiteI | InstanceSite interface, holds an instance of a PSM | metacpan | |
Bio::Matrix::PSM::ProtMatrix | SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) with log-odds scoring information. | metacpan | |
Bio::Matrix::PSM::ProtPsm | handle combination of site matricies | metacpan | |
Bio::Matrix::PSM::Psm | handle combination of site matricies | metacpan | |
Bio::Matrix::PSM::PsmHeader | PSM mast parser implementation | metacpan | |
Bio::Matrix::PSM::PsmHeaderI | handles the header data from a PSM file | metacpan | |
Bio::Matrix::PSM::PsmI | abstract interface to handler of site matricies | metacpan | |
Bio::Matrix::PSM::SiteMatrix | SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds | metacpan | |
Bio::Matrix::PSM::SiteMatrixI | SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds | metacpan | |
Bio::Matrix::PhylipDist | A Phylip Distance Matrix object | metacpan | |
Bio::Matrix::Scoring | Object which can hold scoring matrix information | metacpan | |
Bio::MolEvol::CodonModel | Codon Evolution Models | metacpan | |
Bio::Nexml::Factory | A factory module for creating BioPerl and Bio::Phylo objects from/to nexml documents | metacpan | |
Bio::NexmlIO | stream handler for NeXML documents | metacpan | |
Bio::Ontology::DocumentRegistry | Keep track of where to find ontologies. Allows lookups by name. | metacpan | |
Bio::Ontology::GOterm | representation of GO terms | metacpan | |
Bio::Ontology::InterProTerm | Implementation of InterProI term interface | metacpan | |
Bio::Ontology::OBOEngine | An Ontology Engine for OBO style flat file format from the Gene Ontology Consortium | metacpan | |
Bio::Ontology::OBOterm | representation of OBO terms | metacpan | |
Bio::Ontology::Ontology | standard implementation of an Ontology | metacpan | |
Bio::Ontology::OntologyEngineI | Interface a minimal Ontology implementation should satisfy | metacpan | |
Bio::Ontology::OntologyI | Interface for an ontology implementation | metacpan | |
Bio::Ontology::OntologyStore | A repository of ontologies | metacpan | |
Bio::Ontology::Path | a path for an ontology term graph | metacpan | |
Bio::Ontology::PathI | Interface for a path between ontology terms | metacpan | |
Bio::Ontology::Relationship | a relationship for an ontology | metacpan | |
Bio::Ontology::RelationshipFactory | Instantiates a new Bio::Ontology::RelationshipI (or derived class) through a factory | metacpan | |
Bio::Ontology::RelationshipI | Interface for a relationship between ontology terms | metacpan | |
Bio::Ontology::RelationshipType | a relationship type for an ontology | metacpan | |
Bio::Ontology::SimpleGOEngine::GraphAdaptor | Graph adaptor for Bio::Ontology::SimpleGOEngine | metacpan | |
Bio::Ontology::SimpleOntologyEngine | Implementation of OntologyEngineI interface | metacpan | |
Bio::Ontology::Term | implementation of the interface for ontology terms | metacpan | |
Bio::Ontology::TermFactory | Instantiates a new Bio::Ontology::TermI (or derived class) through a factory | metacpan | |
Bio::Ontology::TermI | interface for ontology terms | metacpan | |
Bio::OntologyIO | Parser factory for Ontology formats | metacpan | |
Bio::OntologyIO::Handlers::BaseSAXHandler | metacpan | ||
Bio::OntologyIO::Handlers::InterProHandler | XML handler class for InterProParser | metacpan | |
Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler | parse an InterPro XML file and persist the resulting terms to a Biosql database | metacpan | |
Bio::OntologyIO::InterProParser | Parser for InterPro xml files. | metacpan | |
Bio::OntologyIO::dagflat | a base class parser for GO flat-file type formats | metacpan | |
Bio::OntologyIO::goflat | a parser for the Gene Ontology flat-file format | metacpan | |
Bio::OntologyIO::obo | a parser for OBO flat-file format from Gene Ontology Consortium | metacpan | |
Bio::OntologyIO::simplehierarchy | a base class parser for simple hierarchy-by-indentation type formats | metacpan | |
Bio::OntologyIO::soflat | a parser for the Sequence Ontology flat-file format | metacpan | |
Bio::ParameterBaseI | Simple interface class for any parameter-related data such as IDs, database name, program arguments, and other odds and ends. | metacpan | |
Bio::Perl | Functional access to BioPerl for people who don't know objects | metacpan | |
Bio::Phenotype::Correlate | Representation of a correlating phenotype in a given species | metacpan | |
Bio::Phenotype::MeSH::Term | A MeSH term | metacpan | |
Bio::Phenotype::MeSH::Twig | Context for a MeSH term | metacpan | |
Bio::Phenotype::Measure | Representation of context/value(-range)/unit triplets | metacpan | |
Bio::Phenotype::OMIM::MiniMIMentry | Representation of a Mini MIM entry | metacpan | |
Bio::Phenotype::OMIM::OMIMentry | represents OMIM (Online Mendelian Inheritance in Man) database entries | metacpan | |
Bio::Phenotype::OMIM::OMIMentryAllelicVariant | Representation of a allelic variant of the OMIM database | metacpan | |
Bio::Phenotype::OMIM::OMIMparser | parser for the OMIM database | metacpan | |
Bio::Phenotype::Phenotype | A class for modeling phenotypes | metacpan | |
Bio::Phenotype::PhenotypeI | An interface for classes modeling phenotypes | metacpan | |
Bio::PhyloNetwork | Module to compute with Phylogenetic Networks | metacpan | |
Bio::PhyloNetwork::Factory | Module to sequentially generate Phylogenetic Networks | metacpan | |
Bio::PhyloNetwork::FactoryX | Module to sequentially generate Phylogenetic Networks | metacpan | |
Bio::PhyloNetwork::GraphViz | Interface between PhyloNetwork and GraphViz | metacpan | |
Bio::PhyloNetwork::RandomFactory | Module to generate random Phylogenetic Networks | metacpan | |
Bio::PhyloNetwork::TreeFactory | Module to sequentially generate Phylogenetic Trees | metacpan | |
Bio::PhyloNetwork::TreeFactoryMulti | Module to sequentially generate Phylogenetic Trees | metacpan | |
Bio::PhyloNetwork::TreeFactoryX | Module to sequentially generate Phylogenetic Trees | metacpan | |
Bio::PhyloNetwork::muVector | Module to compute with vectors of arbitrary dimension | metacpan | |
Bio::PopGen::Genotype | An implementation of GenotypeI which is just an allele container | metacpan | |
Bio::PopGen::GenotypeI | A marker and alleles for a specific individual | metacpan | |
Bio::PopGen::HtSNP | metacpan | ||
Bio::PopGen::IO | Input individual,marker,allele information | metacpan | |
Bio::PopGen::IO::csv | metacpan | ||
Bio::PopGen::IO::hapmap | A parser for HapMap output data | metacpan | |
Bio::PopGen::IO::phase | A parser for Phase format data | metacpan | |
Bio::PopGen::IO::prettybase | Extract individual allele data from PrettyBase format | metacpan | |
Bio::PopGen::Individual | An implementation of an Individual who has Genotype or Sequence Results | metacpan | |
Bio::PopGen::IndividualI | An individual who has Genotype or Sequence Results | metacpan | |
Bio::PopGen::Marker | A genetic marker which one uses to generate genotypes | metacpan | |
Bio::PopGen::MarkerI | A Population Genetic conceptual marker | metacpan | |
Bio::PopGen::PopStats | A collection of methods for calculating statistics about a population or sets of populations | metacpan | |
Bio::PopGen::Population | A population of individuals | metacpan | |
Bio::PopGen::PopulationI | Interface for Populations | metacpan | |
Bio::PopGen::Simulation::Coalescent | A Coalescent simulation factory | metacpan | |
Bio::PopGen::Simulation::GeneticDrift | A simple genetic drift simulation | metacpan | |
Bio::PopGen::Statistics | Population Genetics statistical tests | metacpan | |
Bio::PopGen::TagHaplotype | metacpan | ||
Bio::PopGen::Utilities | Utilities for working with PopGen data and objects | metacpan | |
Bio::PrimarySeq | Bioperl lightweight sequence object | metacpan | |
Bio::PrimarySeqI | Interface definition for a Bio::PrimarySeq | metacpan | |
Bio::PullParserI | A base module for fast 'pull' parsing | metacpan | |
Bio::Range | Pure perl RangeI implementation | metacpan | |
Bio::RangeI | Range interface | metacpan | |
Bio::Restriction::Analysis | cutting sequences with restriction enzymes | metacpan | |
Bio::Restriction::Enzyme | A single restriction endonuclease (cuts DNA at specific locations) | metacpan | |
Bio::Restriction::Enzyme::MultiCut | A single restriction endonuclease | metacpan | |
Bio::Restriction::Enzyme::MultiSite | A single restriction endonuclease | metacpan | |
Bio::Restriction::EnzymeCollection | Set of restriction endonucleases | metacpan | |
Bio::Restriction::EnzymeI | Interface class for restriction endonuclease | metacpan | |
Bio::Restriction::IO | Handler for sequence variation IO Formats | metacpan | |
Bio::Restriction::IO::bairoch | bairoch enzyme set | metacpan | |
Bio::Restriction::IO::base | base enzyme set | metacpan | |
Bio::Restriction::IO::itype2 | itype2 enzyme set | metacpan | |
Bio::Restriction::IO::prototype | prototype enzyme set | metacpan | |
Bio::Restriction::IO::withrefm | withrefm enzyme set | metacpan | |
Bio::Root::Build | A common Module::Build subclass base for BioPerl distributions | 1.006923 | metacpan |
Bio::Root::Exception | Generic exception objects for Bioperl | metacpan | |
Bio::Root::HTTPget | module for fallback HTTP get operations when LWP:: is unavailable | metacpan | |
Bio::Root::IO | module providing several methods often needed when dealing with file IO | metacpan | |
Bio::Root::Root | Hash-based implementation of Bio::Root::RootI | metacpan | |
Bio::Root::RootI | Abstract interface to root object code | metacpan | |
Bio::Root::Storable | object serialisation methods | metacpan | |
Bio::Root::Test | A common base for all Bioperl test scripts. | metacpan | |
Bio::Root::Utilities | General-purpose utility module | metacpan | |
Bio::Root::Version | provide global, distribution-level versioning | 1.006923 | metacpan |
Bio::Search::BlastStatistics | An object for Blast statistics | metacpan | |
Bio::Search::BlastUtils | Utility functions for Bio::Search:: BLAST objects | metacpan | |
Bio::Search::DatabaseI | Interface for a database used in a sequence search | metacpan | |
Bio::Search::GenericDatabase | Generic implementation of Bio::Search::DatabaseI | metacpan | |
Bio::Search::GenericStatistics | An object for statistics | metacpan | |
Bio::Search::HSP::BlastHSP | Bioperl BLAST High-Scoring Pair object | metacpan | |
Bio::Search::HSP::BlastPullHSP | A parser and HSP object for BlastN hsps | metacpan | |
Bio::Search::HSP::FastaHSP | HSP object for FASTA specific data | metacpan | |
Bio::Search::HSP::GenericHSP | A "Generic" implementation of a High Scoring Pair | metacpan | |
Bio::Search::HSP::HMMERHSP | A HSP object for HMMER results | metacpan | |
Bio::Search::HSP::HSPFactory | A factory to create Bio::Search::HSP::HSPI objects | metacpan | |
Bio::Search::HSP::HSPI | Interface for a High Scoring Pair in a similarity search result | metacpan | |
Bio::Search::HSP::HmmpfamHSP | A parser and HSP object for hmmpfam hsps | metacpan | |
Bio::Search::HSP::ModelHSP | A HSP object for model-based searches | metacpan | |
Bio::Search::HSP::PSLHSP | A HSP for PSL output | metacpan | |
Bio::Search::HSP::PsiBlastHSP | Bioperl BLAST High-Scoring Pair object | metacpan | |
Bio::Search::HSP::PullHSPI | Bio::Search::HSP::HSPI interface for pull parsers. | metacpan | |
Bio::Search::HSP::WABAHSP | HSP object suitable for describing WABA alignments | metacpan | |
Bio::Search::Hit::BlastHit | Blast-specific subclass of Bio::Search::Hit::GenericHit | metacpan | |
Bio::Search::Hit::BlastPullHit | A parser and hit object for BLASTN hits | metacpan | |
Bio::Search::Hit::Fasta | Hit object specific for Fasta-generated hits | metacpan | |
Bio::Search::Hit::GenericHit | A generic implementation of the Bio::Search::Hit::HitI interface | metacpan | |
Bio::Search::Hit::HMMERHit | A Hit module for HMMER hits | metacpan | |
Bio::Search::Hit::HitFactory | A factory to create Bio::Search::Hit::HitI objects | metacpan | |
Bio::Search::Hit::HitI | Interface for a hit in a similarity search result | metacpan | |
Bio::Search::Hit::HmmpfamHit | A parser and hit object for hmmpfam hits | metacpan | |
Bio::Search::Hit::ModelHit | A model-based implementation of the Bio::Search::Hit::HitI interface | metacpan | |
Bio::Search::Hit::PsiBlastHit | Bioperl BLAST Hit object | metacpan | |
Bio::Search::Hit::PullHitI | Bio::Search::Hit::HitI interface for pull parsers. | metacpan | |
Bio::Search::Hit::hmmer3Hit | DESCRIPTION of Object | metacpan | |
Bio::Search::Iteration::GenericIteration | A generic implementation of the Bio::Search::Iteration::IterationI interface. | metacpan | |
Bio::Search::Iteration::IterationI | Abstract interface to an iteration from an iterated search result, such as PSI-BLAST. | metacpan | |
Bio::Search::Processor | DESCRIPTION of Object | metacpan | |
Bio::Search::Result::BlastPullResult | A parser and result object for BLASTN results | metacpan | |
Bio::Search::Result::BlastResult | Blast-specific subclass of Bio::Search::Result::GenericResult | metacpan | |
Bio::Search::Result::CrossMatchResult | CrossMatch-specific subclass of Bio::Search::Result::GenericResult | metacpan | |
Bio::Search::Result::GenericResult | Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results. | metacpan | |
Bio::Search::Result::HMMERResult | A Result object for HMMER results | metacpan | |
Bio::Search::Result::HmmpfamResult | A parser and result object for hmmpfam results | metacpan | |
Bio::Search::Result::PullResultI | Bio::Search::Result::ResultI interface for 'pull' parsers | metacpan | |
Bio::Search::Result::ResultFactory | A factory to create Bio::Search::Result::ResultI objects | metacpan | |
Bio::Search::Result::ResultI | Abstract interface to Search Result objects | metacpan | |
Bio::Search::Result::WABAResult | Result object for WABA alignment output | metacpan | |
Bio::Search::Result::hmmer3Result | DESCRIPTION of Object | metacpan | |
Bio::Search::SearchUtils | Utility functions for Bio::Search:: objects | metacpan | |
Bio::Search::StatisticsI | A Base object for statistics | metacpan | |
Bio::Search::Tiling::MapTileUtils | utilities for manipulating closed intervals for an HSP tiling algorithm | metacpan | |
Bio::Search::Tiling::MapTiling | An implementation of an HSP tiling algorithm, with methods to obtain frequently-requested statistics | metacpan | |
Bio::Search::Tiling::TilingI | Abstract interface for an HSP tiling module | metacpan | |
Bio::SearchDist | A perl wrapper around Sean Eddy's histogram object | metacpan | |
Bio::SearchIO | Driver for parsing Sequence Database Searches (BLAST, FASTA, ...) | metacpan | |
Bio::SearchIO::EventHandlerI | An abstract Event Handler for Search Result parsing | metacpan | |
Bio::SearchIO::FastHitEventBuilder | Event Handler for SearchIO events. | metacpan | |
Bio::SearchIO::IteratedSearchResultEventBuilder | Event Handler for SearchIO events. | metacpan | |
Bio::SearchIO::SearchResultEventBuilder | Event Handler for SearchIO events. | metacpan | |
Bio::SearchIO::SearchWriterI | Interface for outputting parsed Search results | metacpan | |
Bio::SearchIO::Writer::BSMLResultWriter | BSML output writer | metacpan | |
Bio::SearchIO::Writer::GbrowseGFF | Interface for outputting parsed search results in Gbrowse GFF format | metacpan | |
Bio::SearchIO::Writer::HSPTableWriter | Tab-delimited data for Bio::Search::HSP::HSPI objects | metacpan | |
Bio::SearchIO::Writer::HTMLResultWriter | write a Bio::Search::ResultI in HTML | metacpan | |
Bio::SearchIO::Writer::HitTableWriter | Tab-delimited data for Bio::Search::Hit::HitI objects | metacpan | |
Bio::SearchIO::Writer::ResultTableWriter | Outputs tab-delimited data for each Bio::Search::Result::ResultI object. | metacpan | |
Bio::SearchIO::Writer::TextResultWriter | Object to implement writing a Bio::Search::ResultI in Text. | metacpan | |
Bio::SearchIO::XML::BlastHandler | XML Handler for NCBI Blast XML parsing. | metacpan | |
Bio::SearchIO::XML::PsiBlastHandler | XML Handler for NCBI Blast PSIBLAST XML parsing. | metacpan | |
Bio::SearchIO::axt | a parser for axt format reports | metacpan | |
Bio::SearchIO::blast | Event generator for event based parsing of blast reports | metacpan | |
Bio::SearchIO::blast_pull | A parser for BLAST output | metacpan | |
Bio::SearchIO::blasttable | Driver module for SearchIO for parsing NCBI -m 8/9 format | metacpan | |
Bio::SearchIO::blastxml | A SearchIO implementation of NCBI Blast XML parsing. | metacpan | |
Bio::SearchIO::cross_match | CrossMatch-specific subclass of Bio::SearchIO | metacpan | |
Bio::SearchIO::erpin | SearchIO-based ERPIN parser | metacpan | |
Bio::SearchIO::exonerate | parser for Exonerate | metacpan | |
Bio::SearchIO::fasta | A SearchIO parser for FASTA results | metacpan | |
Bio::SearchIO::gmap_f9 | Event generator for parsing gmap reports (Z format) | metacpan | |
Bio::SearchIO::hmmer | A parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam) | metacpan | |
Bio::SearchIO::hmmer2 | A parser for HMMER output (hmmpfam, hmmsearch) | metacpan | |
Bio::SearchIO::hmmer3 | metacpan | ||
Bio::SearchIO::hmmer_pull | A parser for HMMER output | metacpan | |
Bio::SearchIO::infernal | SearchIO-based Infernal parser | metacpan | |
Bio::SearchIO::megablast | a driver module for Bio::SearchIO to parse megablast reports (format 0) | metacpan | |
Bio::SearchIO::psl | A parser for PSL output (UCSC) | metacpan | |
Bio::SearchIO::rnamotif | SearchIO-based RNAMotif parser | metacpan | |
Bio::SearchIO::sim4 | parser for Sim4 alignments | metacpan | |
Bio::SearchIO::waba | SearchIO parser for Jim Kent WABA program alignment output | metacpan | |
Bio::SearchIO::wise | Parsing of wise output as alignments | metacpan | |
Bio::Seq | Sequence object, with features | metacpan | |
Bio::Seq::BaseSeqProcessor | Base implementation for a SequenceProcessor | metacpan | |
Bio::Seq::EncodedSeq | subtype of L<Bio::LocatableSeq|Bio::LocatableSeq> to store DNA that encodes a protein | metacpan | |
Bio::Seq::LargeLocatableSeq | LocatableSeq object that stores sequence as files in the tempdir | metacpan | |
Bio::Seq::LargePrimarySeq | PrimarySeq object that stores sequence as files in the tempdir (as found by File::Temp) or the default method in Bio::Root::Root | metacpan | |
Bio::Seq::LargeSeq | SeqI compliant object that stores sequence as files in /tmp | metacpan | |
Bio::Seq::LargeSeqI | Interface class for sequences that cache their residues in a temporary file | metacpan | |
Bio::Seq::Meta | Generic superclass for sequence objects with residue-based meta information | metacpan | |
Bio::Seq::Meta::Array | array-based generic implementation of a sequence class with residue-based meta information | metacpan | |
Bio::Seq::MetaI | Interface for sequence objects with residue-based meta information | metacpan | |
Bio::Seq::PrimaryQual | Bioperl lightweight Quality Object | metacpan | |
Bio::Seq::PrimedSeq | A sequence and a pair of primers matching on it | metacpan | |
Bio::Seq::QualI | Interface definition for a Bio::Seq::Qual | metacpan | |
Bio::Seq::Quality | Implementation of sequence with residue quality and trace values | metacpan | |
Bio::Seq::RichSeq | Module implementing a sequence created from a rich sequence database entry | metacpan | |
Bio::Seq::RichSeqI | interface for sequences from rich data sources, mostly databases | metacpan | |
Bio::Seq::SeqBuilder | Configurable object builder for sequence stream parsers | metacpan | |
Bio::Seq::SeqFactory | Instantiation of generic Bio::PrimarySeqI (or derived) objects through a factory | metacpan | |
Bio::Seq::SeqFastaSpeedFactory | Rapid creation of Bio::Seq objects through a factory | metacpan | |
Bio::Seq::SeqWithQuality | Bioperl object packaging a sequence with its quality. Deprecated class, use Bio::Seq::Quality instead! | metacpan | |
Bio::Seq::SequenceTrace | Bioperl object packaging a sequence with its trace | metacpan | |
Bio::Seq::SimulatedRead | Read with sequencing errors taken from a reference sequence | metacpan | |
Bio::Seq::TraceI | Interface definition for a Bio::Seq::Trace | metacpan | |
Bio::SeqAnalysisParserI | Sequence analysis output parser interface | metacpan | |
Bio::SeqEvolution::DNAPoint | evolve a sequence by point mutations | metacpan | |
Bio::SeqEvolution::EvolutionI | the interface for evolving sequences | metacpan | |
Bio::SeqEvolution::Factory | Factory object to instantiate sequence evolving classes | metacpan | |
Bio::SeqFeature::Amplicon | Amplicon feature | metacpan | |
Bio::SeqFeature::AnnotationAdaptor | integrates SeqFeatureIs annotation | metacpan | |
Bio::SeqFeature::Collection | A container class for SeqFeatures suitable for performing operations such as finding features within a range, that match a certain feature type, etc. | metacpan | |
Bio::SeqFeature::CollectionI | An interface for a collection of SeqFeatureI objects. | metacpan | |
Bio::SeqFeature::Computation | Computation SeqFeature | metacpan | |
Bio::SeqFeature::FeaturePair | hold pair feature information e.g. blast hits | metacpan | |
Bio::SeqFeature::Gene::Exon | a feature representing an exon | metacpan | |
Bio::SeqFeature::Gene::ExonI | Interface for a feature representing an exon | metacpan | |
Bio::SeqFeature::Gene::GeneStructure | A feature representing an arbitrarily complex structure of a gene | metacpan | |
Bio::SeqFeature::Gene::GeneStructureI | A feature representing an arbitrarily complex structure of a gene | metacpan | |
Bio::SeqFeature::Gene::Intron | An intron feature | metacpan | |
Bio::SeqFeature::Gene::NC_Feature | metacpan | ||
Bio::SeqFeature::Gene::Poly_A_site | poly A feature | metacpan | |
Bio::SeqFeature::Gene::Promoter | Describes a promoter | metacpan | |
Bio::SeqFeature::Gene::Transcript | A feature representing a transcript | metacpan | |
Bio::SeqFeature::Gene::TranscriptI | Interface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site. | metacpan | |
Bio::SeqFeature::Gene::UTR | A feature representing an untranslated region that is part of a transcriptional unit | metacpan | |
Bio::SeqFeature::Generic | Generic SeqFeature | metacpan | |
Bio::SeqFeature::Lite | Lightweight Bio::SeqFeatureI class | metacpan | |
Bio::SeqFeature::PositionProxy | handle features when truncation/revcom sequences span a feature | metacpan | |
Bio::SeqFeature::Primer | Primer Generic SeqFeature | metacpan | |
Bio::SeqFeature::SiRNA::Oligo | Perl object for small inhibitory RNAs. | metacpan | |
Bio::SeqFeature::SiRNA::Pair | Perl object for small inhibitory RNA (SiRNA) oligo pairs | metacpan | |
Bio::SeqFeature::Similarity | A sequence feature based on similarity | metacpan | |
Bio::SeqFeature::SimilarityPair | Sequence feature based on the similarity of two sequences. | metacpan | |
Bio::SeqFeature::SubSeq | Feature representing a subsequence | metacpan | |
Bio::SeqFeature::Tools::FeatureNamer | generates unique persistent names for features | metacpan | |
Bio::SeqFeature::Tools::IDHandler | maps $seq_feature->primary_tag | metacpan | |
Bio::SeqFeature::Tools::TypeMapper | maps $seq_feature->primary_tag | metacpan | |
Bio::SeqFeature::Tools::Unflattener | turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy | metacpan | |
Bio::SeqFeature::TypedSeqFeatureI | a strongly typed SeqFeature | metacpan | |
Bio::SeqFeatureI | Abstract interface of a Sequence Feature | metacpan | |
Bio::SeqI | [Developers] Abstract Interface of Sequence (with features) | metacpan | |
Bio::SeqIO | Handler for SeqIO Formats | metacpan | |
Bio::SeqIO::FTHelper | Helper class for Embl/Genbank feature tables | metacpan | |
Bio::SeqIO::Handler::GenericRichSeqHandler | Bio::HandlerI-based data handler for GenBank/EMBL/UniProt (and other) sequence data | metacpan | |
Bio::SeqIO::MultiFile | Treating a set of files as a single input stream | metacpan | |
Bio::SeqIO::abi | abi trace sequence input/output stream | metacpan | |
Bio::SeqIO::ace | ace sequence input/output stream | metacpan | |
Bio::SeqIO::agave | AGAVE sequence output stream. | metacpan | |
Bio::SeqIO::alf | alf trace sequence input/output stream | metacpan | |
Bio::SeqIO::asciitree | asciitree sequence input/output stream | metacpan | |
Bio::SeqIO::bsml | BSML sequence input/output stream | metacpan | |
Bio::SeqIO::bsml_sax | BSML sequence input/output stream using SAX | metacpan | |
Bio::SeqIO::chadoxml | chadoxml sequence output stream | metacpan | |
Bio::SeqIO::chaos | chaos sequence input/output stream | metacpan | |
Bio::SeqIO::chaosxml | chaosxml sequence input/output stream | metacpan | |
Bio::SeqIO::ctf | ctf trace sequence input/output stream | metacpan | |
Bio::SeqIO::embl | EMBL sequence input/output stream | metacpan | |
Bio::SeqIO::embldriver | EMBL sequence input/output stream | metacpan | |
Bio::SeqIO::entrezgene | Entrez Gene ASN1 parser | metacpan | |
Bio::SeqIO::excel | sequence input/output stream from a MSExcel-formatted table | metacpan | |
Bio::SeqIO::exp | exp trace sequence input/output stream | metacpan | |
Bio::SeqIO::fasta | fasta sequence input/output stream | metacpan | |
Bio::SeqIO::fastq | fastq sequence input/output stream | metacpan | |
Bio::SeqIO::flybase_chadoxml | FlyBase variant of chadoxml with sequence output stream | metacpan | |
Bio::SeqIO::game | a class for parsing and writing game-XML | metacpan | |
Bio::SeqIO::game::featHandler | a class for handling feature elements | metacpan | |
Bio::SeqIO::game::gameHandler | PerlSAX handler for game-XML | metacpan | |
Bio::SeqIO::game::gameSubs | a base class for game-XML parsing | metacpan | |
Bio::SeqIO::game::gameWriter | a class for writing game-XML | metacpan | |
Bio::SeqIO::game::seqHandler | a class for handling game-XML sequences | metacpan | |
Bio::SeqIO::gbdriver | GenBank handler-based push parser | metacpan | |
Bio::SeqIO::gbxml | GenBank sequence input/output stream using SAX | metacpan | |
Bio::SeqIO::gcg | GCG sequence input/output stream | metacpan | |
Bio::SeqIO::genbank | GenBank sequence input/output stream | metacpan | |
Bio::SeqIO::interpro | InterProScan XML input/output stream | metacpan | |
Bio::SeqIO::kegg | KEGG sequence input/output stream | metacpan | |
Bio::SeqIO::largefasta | method i/o on very large fasta sequence files | metacpan | |
Bio::SeqIO::lasergene | Lasergene sequence file input/output stream | metacpan | |
Bio::SeqIO::locuslink | LocusLink input/output stream | metacpan | |
Bio::SeqIO::mbsout | input stream for output by Teshima et al.'s mbs. | metacpan | |
Bio::SeqIO::metafasta | metafasta sequence input/output stream | metacpan | |
Bio::SeqIO::msout | input stream for output by Hudson's ms | metacpan | |
Bio::SeqIO::nexml | NeXML sequence input/output stream | metacpan | |
Bio::SeqIO::phd | phd file input/output stream | metacpan | |
Bio::SeqIO::pir | PIR sequence input/output stream | metacpan | |
Bio::SeqIO::pln | pln trace sequence input/output stream | metacpan | |
Bio::SeqIO::qual | .qual file input/output stream | metacpan | |
Bio::SeqIO::raw | raw sequence file input/output stream | metacpan | |
Bio::SeqIO::scf | .scf file input/output stream | metacpan | |
Bio::SeqIO::seqxml | SeqXML sequence input/output stream | metacpan | |
Bio::SeqIO::strider | DNA strider sequence input/output stream | metacpan | |
Bio::SeqIO::swiss | Swissprot sequence input/output stream | metacpan | |
Bio::SeqIO::swissdriver | SwissProt/UniProt handler-based push parser | metacpan | |
Bio::SeqIO::tab | nearly raw sequence file input/output stream. Reads/writes id"\t"sequence"\n" | metacpan | |
Bio::SeqIO::table | sequence input/output stream from a delimited table | metacpan | |
Bio::SeqIO::tigr | TIGR XML sequence input/output stream | metacpan | |
Bio::SeqIO::tigrxml | Parse TIGR (new) XML | metacpan | |
Bio::SeqIO::tinyseq | reading/writing sequences in NCBI TinySeq format | metacpan | |
Bio::SeqIO::tinyseq::tinyseqHandler | XML event handlers to support NCBI TinySeq XML parsing | metacpan | |
Bio::SeqIO::ztr | ztr trace sequence input/output stream | metacpan | |
Bio::SeqUtils | Additional methods for PrimarySeq objects | metacpan | |
Bio::SimpleAlign | Multiple alignments held as a set of sequences | metacpan | |
Bio::SimpleAnalysisI | A simple interface to any (local or remote) analysis tool | metacpan | |
Bio::Species | Generic species object. | metacpan | |
Bio::Structure::Atom | Bioperl structure Object, describes an Atom | metacpan | |
Bio::Structure::Chain | Bioperl structure Object, describes a chain | metacpan | |
Bio::Structure::Entry | Bioperl structure Object, describes the whole entry | metacpan | |
Bio::Structure::IO | Handler for Structure Formats | metacpan | |
Bio::Structure::IO::pdb | PDB input/output stream | metacpan | |
Bio::Structure::Model | Bioperl structure Object, describes a Model | metacpan | |
Bio::Structure::Residue | Bioperl structure Object, describes a Residue | metacpan | |
Bio::Structure::SecStr::DSSP::Res | Module for parsing/accessing dssp output | metacpan | |
Bio::Structure::SecStr::STRIDE::Res | Module for parsing/accessing stride output | metacpan | |
Bio::Structure::StructureI | Abstract Interface for a Structure objects | metacpan | |
Bio::Symbol::Alphabet | BSANE/BioCORBA compliant symbol list alphabet | metacpan | |
Bio::Symbol::AlphabetI | A Symbol Alphabet | metacpan | |
Bio::Symbol::DNAAlphabet | A ready made DNA alphabet | metacpan | |
Bio::Symbol::ProteinAlphabet | A ready made Protein alphabet | metacpan | |
Bio::Symbol::Symbol | A biological symbol | metacpan | |
Bio::Symbol::SymbolI | Interface for a Symbol | metacpan | |
Bio::Taxon | A node in a represented taxonomy | metacpan | |
Bio::Taxonomy | representing Taxonomy. | metacpan | |
Bio::Taxonomy::FactoryI | interface to define how to access NCBI Taxonoy | metacpan | |
Bio::Taxonomy::Node | A node in a represented taxonomy | metacpan | |
Bio::Taxonomy::Taxon | Generic Taxonomic Entity object | metacpan | |
Bio::Taxonomy::Tree | An Organism Level Implementation of TreeI interface. | metacpan | |
Bio::Tools::AlignFactory | Base object for alignment factories | metacpan | |
Bio::Tools::Alignment::Consed | A module to work with objects from consed .ace files | metacpan | |
Bio::Tools::Alignment::Trim | A kludge to do specialized trimming of sequence based on quality. | metacpan | |
Bio::Tools::AmpliconSearch | Find amplicons in a template using degenerate PCR primers | metacpan | |
Bio::Tools::Analysis::DNA::ESEfinder | a wrapper around ESEfinder server | metacpan | |
Bio::Tools::Analysis::Protein::Domcut | a wrapper around Domcut server | metacpan | |
Bio::Tools::Analysis::Protein::ELM | a wrapper around the ELM server which predicts short functional motifs on amino acid sequences | metacpan | |
Bio::Tools::Analysis::Protein::GOR4 | a wrapper around GOR4 protein secondary structure prediction server | metacpan | |
Bio::Tools::Analysis::Protein::HNN | a wrapper around the HNN protein secondary structure prediction server | metacpan | |
Bio::Tools::Analysis::Protein::Mitoprot | a wrapper around Mitoprot server | metacpan | |
Bio::Tools::Analysis::Protein::NetPhos | a wrapper around NetPhos server | metacpan | |
Bio::Tools::Analysis::Protein::Scansite | a wrapper around the Scansite server | metacpan | |
Bio::Tools::Analysis::Protein::Sopma | a wrapper around the Sopma protein secondary structure prediction server | metacpan | |
Bio::Tools::Analysis::SimpleAnalysisBase | abstract superclass for SimpleAnalysis implementations | metacpan | |
Bio::Tools::AnalysisResult | Base class for analysis result objects and parsers | metacpan | |
Bio::Tools::Blat | parser for Blat program | metacpan | |
Bio::Tools::CodonTable | Codon table object | metacpan | |
Bio::Tools::Coil | parser for Coil output | metacpan | |
Bio::Tools::ECnumber | representation of EC numbers (Enzyme Classification) | metacpan | |
Bio::Tools::EMBOSS::Palindrome | parse EMBOSS palindrome output | metacpan | |
Bio::Tools::EPCR | Parse ePCR output and make features | metacpan | |
Bio::Tools::ERPIN | a parser for ERPIN output | metacpan | |
Bio::Tools::ESTScan | Results of one ESTScan run | metacpan | |
Bio::Tools::Eponine | Results of one Eponine run | metacpan | |
Bio::Tools::Est2Genome | Parse est2genome output, makes simple Bio::SeqFeature::Generic objects | metacpan | |
Bio::Tools::Fgenesh | parse results of one Fgenesh run | metacpan | |
Bio::Tools::FootPrinter | write sequence features in FootPrinter format | metacpan | |
Bio::Tools::GFF | A Bio::SeqAnalysisParserI compliant GFF format parser | metacpan | |
Bio::Tools::Gel | Calculates relative electrophoretic migration distances | metacpan | |
Bio::Tools::Geneid | Results of one geneid run | metacpan | |
Bio::Tools::Genemark | Results of one Genemark run | metacpan | |
Bio::Tools::Genewise | Results of one Genewise run | metacpan | |
Bio::Tools::Genomewise | Results of one Genomewise run | metacpan | |
Bio::Tools::Genscan | Results of one Genscan run | metacpan | |
Bio::Tools::Glimmer | parser for Glimmer 2.X/3.X prokaryotic and GlimmerM/GlimmerHMM eukaryotic gene predictions | metacpan | |
Bio::Tools::Grail | Results of one Grail run | metacpan | |
Bio::Tools::GuessSeqFormat | Module for determining the sequence format of the contents of a file, a string, or through a filehandle. | metacpan | |
Bio::Tools::HMMER::Domain | One particular domain hit from HMMER | metacpan | |
Bio::Tools::HMMER::Results | Object representing HMMER output results | metacpan | |
Bio::Tools::HMMER::Set | Set of identical domains from HMMER matches | metacpan | |
Bio::Tools::Hmmpfam | Parser for Hmmpfam program | metacpan | |
Bio::Tools::IUPAC | Generates unique sequence objects or regular expressions from an ambiguous IUPAC sequence | metacpan | |
Bio::Tools::Infernal | A parser for Infernal output | metacpan | |
Bio::Tools::Lucy | Object for analyzing the output from Lucy, a vector and quality trimming program from TIGR | metacpan | |
Bio::Tools::MZEF | Results of one MZEF run | metacpan | |
Bio::Tools::Match | Parses output from Transfac's match(TM) | metacpan | |
Bio::Tools::OddCodes | Object holding alternative alphabet coding for one protein sequence | metacpan | |
Bio::Tools::Phylo::Gerp | Parses output from GERP | metacpan | |
Bio::Tools::Phylo::Gumby | Parses output from gumby | metacpan | |
Bio::Tools::Phylo::Molphy | parser for Molphy output | metacpan | |
Bio::Tools::Phylo::Molphy::Result | container for data parsed from a ProtML run | metacpan | |
Bio::Tools::Phylo::PAML | Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00 | metacpan | |
Bio::Tools::Phylo::PAML::Codeml | Parses output from the PAML program codeml. | metacpan | |
Bio::Tools::Phylo::PAML::ModelResult | A container for NSSite Model Result from PAML | metacpan | |
Bio::Tools::Phylo::PAML::Result | A PAML result set object | metacpan | |
Bio::Tools::Phylo::Phylip::ProtDist | parser for ProtDist output | metacpan | |
Bio::Tools::Prediction::Exon | A predicted exon feature | metacpan | |
Bio::Tools::Prediction::Gene | a predicted gene structure feature | metacpan | |
Bio::Tools::Primer3 | Create input for and work with the output from the program primer3 | metacpan | |
Bio::Tools::Primer::Assessor::Base | base class for common assessor things | metacpan | |
Bio::Tools::Primer::AssessorI | interface for assessing primer pairs | metacpan | |
Bio::Tools::Primer::Feature | position of a single primer | metacpan | |
Bio::Tools::Primer::Pair | two primers on left and right side | metacpan | |
Bio::Tools::Prints | Parser for FingerPRINTScanII program | metacpan | |
Bio::Tools::Profile | parse Profile output | metacpan | |
Bio::Tools::Promoterwise | parser for Promoterwise tab format output | metacpan | |
Bio::Tools::PrositeScan | Parser for ps_scan result | metacpan | |
Bio::Tools::Protparam | submit to and parse output from protparam ; | metacpan | |
Bio::Tools::Pseudowise | Results of one Pseudowise run | metacpan | |
Bio::Tools::QRNA | A Parser for qrna output | metacpan | |
Bio::Tools::RNAMotif | A parser for RNAMotif output | metacpan | |
Bio::Tools::RandomDistFunctions | A set of routines useful for generating random data in different distributions | metacpan | |
Bio::Tools::RepeatMasker | a parser for RepeatMasker output | metacpan | |
Bio::Tools::Run::GenericParameters | An object for the parameters used to run programs | metacpan | |
Bio::Tools::Run::ParametersI | A Base object for the parameters used to run programs | metacpan | |
Bio::Tools::Run::RemoteBlast | Object for remote execution of the NCBI Blast via HTTP | metacpan | |
Bio::Tools::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. | 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. | metacpan | |
Bio::Tools::Run::StandAloneWUBlast | Object for the local execution of WU-Blast. | metacpan | |
Bio::Tools::Run::WrapperBase | A Base object for wrappers around executables | metacpan | |
Bio::Tools::Seg | parse C<seg> output | metacpan | |
Bio::Tools::SeqPattern | represent a sequence pattern or motif | metacpan | |
Bio::Tools::SeqPattern::Backtranslate | metacpan | ||
Bio::Tools::SeqStats | Object holding statistics for one particular sequence | metacpan | |
Bio::Tools::SeqWords | Object holding n-mer statistics for a sequence | metacpan | |
Bio::Tools::SiRNA | metacpan | ||
Bio::Tools::SiRNA::Ruleset::saigo | Perl object implementing the Saigo group's rules for designing small inhibitory RNAs | metacpan | |
Bio::Tools::SiRNA::Ruleset::tuschl | Perl object implementing the tuschl group's rules for designing small inhibitory RNAs | metacpan | |
Bio::Tools::Sigcleave | Bioperl object for sigcleave analysis | metacpan | |
Bio::Tools::Signalp | parser for Signalp output | metacpan | |
Bio::Tools::Signalp::ExtendedSignalp | enhanced parser for Signalp output | metacpan | |
Bio::Tools::Sim4::Exon | A single exon determined by an alignment | metacpan | |
Bio::Tools::Sim4::Results | Results of one Sim4 run | metacpan | |
Bio::Tools::Spidey::Exon | A single exon determined by an alignment | metacpan | |
Bio::Tools::Spidey::Results | Results of a Spidey run | metacpan | |
Bio::Tools::TandemRepeatsFinder | a parser for Tandem Repeats Finder output | metacpan | |
Bio::Tools::TargetP | Results of one TargetP run | metacpan | |
Bio::Tools::Tmhmm | parse TMHMM output (TransMembrane HMM) | metacpan | |
Bio::Tools::dpAlign | Perl extension to do pairwise dynamic programming sequence alignment | metacpan | |
Bio::Tools::ipcress | Parse ipcress output and make features | metacpan | |
Bio::Tools::isPcr | Parse isPcr output and make features | metacpan | |
Bio::Tools::pICalculator | calculate the isoelectric point of a protein | metacpan | |
Bio::Tools::pSW | pairwise Smith Waterman object | metacpan | |
Bio::Tools::tRNAscanSE | A parser for tRNAscan-SE output | metacpan | |
Bio::Tree::AlleleNode | A Node with Alleles attached | metacpan | |
Bio::Tree::AnnotatableNode | A Tree Node with support for annotation | metacpan | |
Bio::Tree::Compatible | Testing compatibility of phylogenetic trees with nested taxa. | metacpan | |
Bio::Tree::DistanceFactory | Construct a tree using distance based methods | metacpan | |
Bio::Tree::Draw::Cladogram | Drawing phylogenetic trees in Encapsulated PostScript (EPS) format. | metacpan | |
Bio::Tree::Node | A Simple Tree Node | metacpan | |
Bio::Tree::NodeI | Interface describing a Tree Node | metacpan | |
Bio::Tree::NodeNHX | A Simple Tree Node with support for NHX tags | metacpan | |
Bio::Tree::RandomFactory | TreeFactory for generating Random Trees | metacpan | |
Bio::Tree::Statistics | Calculate certain statistics for a Tree | metacpan | |
Bio::Tree::Tree | An implementation of the TreeI interface. | metacpan | |
Bio::Tree::TreeFunctionsI | Decorated Interface implementing basic Tree exploration methods | metacpan | |
Bio::Tree::TreeI | A Tree object suitable for lots of things, designed originally for Phylogenetic Trees. | metacpan | |
Bio::TreeIO | Parser for Tree files | metacpan | |
Bio::TreeIO::NewickParser | metacpan | ||
Bio::TreeIO::TreeEventBuilder | Build Bio::Tree::Tree's and Bio::Tree::Node's from Events | metacpan | |
Bio::TreeIO::cluster | A TreeIO driver module for parsing Algorithm::Cluster::treecluster() output | metacpan | |
Bio::TreeIO::lintree | Parser for lintree output trees | metacpan | |
Bio::TreeIO::newick | metacpan | ||
Bio::TreeIO::nexml | A TreeIO driver module for parsing NeXML tree files | metacpan | |
Bio::TreeIO::nexus | A TreeIO driver module for parsing Nexus tree output from PAUP | metacpan | |
Bio::TreeIO::nhx | TreeIO implementation for parsing Newick/New Hampshire eXtendend (NHX) format. | metacpan | |
Bio::TreeIO::pag | Bio::TreeIO driver for Pagel format | metacpan | |
Bio::TreeIO::phyloxml | TreeIO implementation for parsing PhyloXML format. | metacpan | |
Bio::TreeIO::svggraph | A simple output format that converts a Tree object to an SVG output | metacpan | |
Bio::TreeIO::tabtree | A simple output format which displays a tree as an ASCII drawing | metacpan | |
Bio::UpdateableSeqI | Descendant of Bio::SeqI that allows updates | metacpan | |
Bio::Variation::AAChange | Sequence change class for polypeptides | metacpan | |
Bio::Variation::AAReverseMutate | point mutation and codon information from single amino acid changes | metacpan | |
Bio::Variation::Allele | Sequence object with allele-specific attributes | metacpan | |
Bio::Variation::DNAMutation | DNA level mutation class | metacpan | |
Bio::Variation::IO | Handler for sequence variation IO Formats | metacpan | |
Bio::Variation::IO::flat | flat file sequence variation input/output stream | metacpan | |
Bio::Variation::IO::xml | XML sequence variation input/output stream | metacpan | |
Bio::Variation::RNAChange | Sequence change class for RNA level | metacpan | |
Bio::Variation::SNP | submitted SNP | metacpan | |
Bio::Variation::SeqDiff | Container class for mutation/variant descriptions | metacpan | |
Bio::Variation::VariantI | Sequence Change SeqFeature abstract class | metacpan | |
Bio::WebAgent | A base class for Web (any protocol) access | metacpan | |
BioPerl | Perl Modules for Biology | metacpan | |
Deobfuscator | get BioPerl method and package information from a Berkeley DB | 0.000003 | metacpan |
Provides
Name | File | View |
---|---|---|
Bio::AnalysisI::JobI | Bio/AnalysisI.pm | metacpan |
Bio::DB::Fasta::Subdir | Bio/DB/SeqFeature/Store/berkeleydb.pm | metacpan |
Bio::DB::GFF::Adaptor::dbi::faux_dbh | Bio/DB/GFF/Adaptor/dbi/caching_handle.pm | metacpan |
Bio::DB::GFF::FeatureIterator | Bio/DB/GFF.pm | metacpan |
Bio::DB::GFF::ID_Iterator | Bio/DB/GFF.pm | metacpan |
Bio::DB::Indexed::Stream | Bio/DB/IndexedBase.pm | metacpan |
Bio::DB::SeqFeature::Store::FeatureIterator | Bio/DB/SeqFeature/Store.pm | metacpan |
Bio::DB::SeqFeature::Store::berkeleydb::Iterator | Bio/DB/SeqFeature/Store/berkeleydb.pm | metacpan |
Bio::DB::SeqFeature::Store::memory::Iterator | Bio/DB/SeqFeature/Store/memory.pm | metacpan |
Bio::PrimarySeq::Fasta | Bio/DB/Fasta.pm | metacpan |
Bio::Seq::PrimaryQual::Qual | Bio/DB/Qual.pm | metacpan |
FeatureStore | Bio/DB/GFF/Adaptor/berkeleydb.pm | metacpan |