Kwalitee Issues

main_module_version_matches_dist_version

Fix the version(s).

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_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

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

no_invalid_versions

Fix the version numbers so that version::is_lax($version) returns true.

Error:

  • BioPerl.pm: HASH(0x736b9c0)

use_warnings

Add 'use warnings' (or its equivalents) to all modules (this will require perl > 5.6), or convince us that your favorite module is well-known enough and people can easily see the modules warn when something bad happens.

Error: Bio::Align::AlignI, Bio::Align::DNAStatistics, Bio::Align::PairwiseStatistics, Bio::Align::ProteinStatistics, Bio::Align::StatisticsI, Bio::AlignIO, Bio::AlignIO::arp, Bio::AlignIO::bl2seq, Bio::AlignIO::clustalw, Bio::AlignIO::emboss, Bio::AlignIO::fasta, Bio::AlignIO::largemultifasta, Bio::AlignIO::maf, Bio::AlignIO::mase, Bio::AlignIO::mega, Bio::AlignIO::meme, Bio::AlignIO::metafasta, Bio::AlignIO::msf, Bio::AlignIO::nexml, Bio::AlignIO::nexus, Bio::AlignIO::pfam, Bio::AlignIO::phylip, Bio::AlignIO::po, Bio::AlignIO::proda, Bio::AlignIO::prodom, Bio::AlignIO::psi, Bio::AlignIO::selex, Bio::AlignIO::stockholm, Bio::AlignIO::xmfa, Bio::AnalysisI, Bio::AnalysisParserI, Bio::AnalysisResultI, Bio::AnnotatableI, Bio::Annotation::AnnotationFactory, Bio::Annotation::Collection, Bio::Annotation::Comment, Bio::Annotation::DBLink, Bio::Annotation::OntologyTerm, Bio::Annotation::Reference, Bio::Annotation::Relation, Bio::Annotation::SimpleValue, Bio::Annotation::StructuredValue, Bio::Annotation::TagTree, Bio::Annotation::Target, Bio::Annotation::Tree, Bio::Annotation::TypeManager, Bio::AnnotationCollectionI, Bio::AnnotationI, Bio::Assembly::Contig, Bio::Assembly::ContigAnalysis, Bio::Assembly::IO, Bio::Assembly::IO::ace, Bio::Assembly::IO::maq, Bio::Assembly::IO::phrap, Bio::Assembly::IO::tigr, Bio::Assembly::Scaffold, Bio::Assembly::ScaffoldI, Bio::Assembly::Singlet, Bio::Assembly::Tools::ContigSpectrum, Bio::Cluster::ClusterFactory, Bio::Cluster::FamilyI, Bio::Cluster::UniGene, Bio::Cluster::UniGeneI, Bio::ClusterI, Bio::ClusterIO, Bio::ClusterIO::dbsnp, Bio::ClusterIO::unigene, Bio::CodonUsage::IO, Bio::CodonUsage::Table, Bio::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::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::mutant, 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::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::Storable, Bio::Root::Utilities, 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::NiftyFeature, 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, Foo, MyShinyNewIndexer

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::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::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::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::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-E<gt>primary_tag metacpan
Bio::SeqFeature::Tools::TypeMapper maps $seq_feature-E<gt>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::Aggregator Bio/DB/GFF/Aggregator.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::Index::AbstractSeq Bio/Index/AbstractSeq.pm metacpan
Bio::PrimarySeq::Fasta Bio/DB/Fasta.pm metacpan
Bio::Root::RootI Bio/Root/RootI.pm metacpan
Bio::Root::Version Bio/Root/Version.pm metacpan
Bio::Seq::PrimaryQual::Qual Bio/DB/Qual.pm metacpan
FeatureStore Bio/DB/GFF/Adaptor/berkeleydb.pm metacpan

Other Files

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