Kwalitee Issues

no_pod_errors

Remove the POD errors. You can check for POD errors automatically by including Test::Pod to your test suite.

Error: *** ERROR: empty =head1 at line 123 in file BioPerl-1.7.6/lib/Bio/DB/Fasta.pm *** ERROR: empty =head1 at line 138 in file BioPerl-1.7.6/lib/Bio/DB/Qual.pm

use_strict

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

Error: Bio::CodonUsage::IO, Bio::DB::Flat, Bio::Location::Split, Bio::Matrix::PSM::SiteMatrixI, Bio::Search::BlastUtils, Bio::SearchIO::SearchWriterI, Bio::SearchIO::cross_match, Bio::SeqIO::game, Bio::Tools::Primer::Assessor::Base, Bio::Tools::Primer::AssessorI, Bio::Tools::Primer::Feature, Bio::Tools::Primer::Pair

meta_yml_declares_perl_version

If you are using Build.PL define the {requires}{perl} = VERSION field. If you are using MakeMaker (Makefile.PL) you should upgrade ExtUtils::MakeMaker to 6.48 and use MIN_PERL_VERSION parameter. Perl::MinimumVersion can help you determine which version of Perl your module needs.

use_warnings

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

Error: Bio::Align::AlignI, Bio::Align::DNAStatistics, Bio::Align::PairwiseStatistics, Bio::Align::ProteinStatistics, Bio::Align::StatisticsI, Bio::AlignIO, Bio::AlignIO::arp, Bio::AlignIO::bl2seq, Bio::AlignIO::clustalw, Bio::AlignIO::emboss, Bio::AlignIO::fasta, Bio::AlignIO::largemultifasta, Bio::AlignIO::maf, Bio::AlignIO::mase, Bio::AlignIO::mega, Bio::AlignIO::meme, Bio::AlignIO::metafasta, Bio::AlignIO::msf, Bio::AlignIO::nexus, Bio::AlignIO::pfam, Bio::AlignIO::phylip, Bio::AlignIO::po, Bio::AlignIO::proda, Bio::AlignIO::prodom, Bio::AlignIO::psi, Bio::AlignIO::selex, Bio::AlignIO::xmfa, Bio::AnalysisI, Bio::AnalysisParserI, Bio::AnalysisResultI, Bio::AnnotatableI, Bio::Annotation::AnnotationFactory, Bio::Annotation::Collection, Bio::Annotation::Comment, Bio::Annotation::DBLink, Bio::Annotation::OntologyTerm, Bio::Annotation::Reference, Bio::Annotation::Relation, Bio::Annotation::SimpleValue, Bio::Annotation::StructuredValue, Bio::Annotation::TagTree, Bio::Annotation::Target, Bio::Annotation::Tree, Bio::Annotation::TypeManager, Bio::AnnotationCollectionI, Bio::AnnotationI, Bio::CodonUsage::IO, Bio::CodonUsage::Table, Bio::DB::DBFetch, Bio::DB::Failover, Bio::DB::Fasta, Bio::DB::FileCache, Bio::DB::Flat, Bio::DB::Flat::BDB, Bio::DB::Flat::BDB::embl, Bio::DB::Flat::BDB::fasta, Bio::DB::Flat::BDB::genbank, Bio::DB::Flat::BDB::swiss, Bio::DB::Flat::BinarySearch, Bio::DB::GFF::Util::Binning, Bio::DB::GFF::Util::Rearrange, Bio::DB::InMemoryCache, Bio::DB::LocationI, Bio::DB::Qual, Bio::DB::Query::WebQuery, Bio::DB::QueryI, Bio::DB::RandomAccessI, Bio::DB::ReferenceI, Bio::DB::Registry, Bio::DB::SeqI, Bio::DB::Taxonomy, Bio::DB::Taxonomy::flatfile, Bio::DB::Taxonomy::greengenes, Bio::DB::Taxonomy::list, Bio::DB::Taxonomy::silva, Bio::DB::UpdateableSeqI, Bio::DB::WebDBSeqI, Bio::DBLinkContainerI, Bio::Das::FeatureTypeI, Bio::Das::SegmentI, Bio::DasI, Bio::DescribableI, Bio::Event::EventGeneratorI, Bio::Event::EventHandlerI, Bio::Factory::AnalysisI, Bio::Factory::ApplicationFactoryI, Bio::Factory::DriverFactory, Bio::Factory::FTLocationFactory, Bio::Factory::LocationFactoryI, Bio::Factory::ObjectBuilderI, Bio::Factory::ObjectFactory, Bio::Factory::ObjectFactoryI, Bio::Factory::SeqAnalysisParserFactory, Bio::Factory::SeqAnalysisParserFactoryI, Bio::Factory::SequenceFactoryI, Bio::Factory::SequenceProcessorI, Bio::Factory::SequenceStreamI, Bio::Factory::TreeFactoryI, Bio::FeatureHolderI, Bio::IdCollectionI, Bio::IdentifiableI, Bio::Index::Abstract, Bio::Index::AbstractSeq, Bio::Index::Blast, Bio::Index::BlastTable, Bio::Index::EMBL, Bio::Index::Fastq, Bio::Index::GenBank, Bio::Index::Qual, Bio::Index::SwissPfam, Bio::Index::Swissprot, Bio::LocatableSeq, Bio::Location::Atomic, Bio::Location::AvWithinCoordPolicy, Bio::Location::CoordinatePolicyI, Bio::Location::Fuzzy, Bio::Location::FuzzyLocationI, Bio::Location::NarrowestCoordPolicy, Bio::Location::Simple, Bio::Location::Split, Bio::Location::SplitLocationI, Bio::Location::WidestCoordPolicy, Bio::LocationI, Bio::Matrix::Generic, Bio::Matrix::IO, Bio::Matrix::IO::mlagan, Bio::Matrix::IO::phylip, Bio::Matrix::IO::scoring, Bio::Matrix::MatrixI, Bio::Matrix::Mlagan, Bio::Matrix::PSM::IO, Bio::Matrix::PSM::IO::mast, Bio::Matrix::PSM::IO::masta, Bio::Matrix::PSM::IO::meme, Bio::Matrix::PSM::IO::psiblast, Bio::Matrix::PSM::IO::transfac, Bio::Matrix::PSM::InstanceSite, Bio::Matrix::PSM::InstanceSiteI, Bio::Matrix::PSM::ProtMatrix, Bio::Matrix::PSM::ProtPsm, Bio::Matrix::PSM::Psm, Bio::Matrix::PSM::PsmHeader, Bio::Matrix::PSM::PsmHeaderI, Bio::Matrix::PSM::PsmI, Bio::Matrix::PSM::SiteMatrix, Bio::Matrix::PSM::SiteMatrixI, Bio::Matrix::PhylipDist, Bio::Matrix::Scoring, Bio::Ontology::DocumentRegistry, Bio::Ontology::GOterm, Bio::Ontology::InterProTerm, Bio::Ontology::OBOEngine, Bio::Ontology::OBOterm, Bio::Ontology::Ontology, Bio::Ontology::OntologyEngineI, Bio::Ontology::OntologyI, Bio::Ontology::OntologyStore, Bio::Ontology::Path, Bio::Ontology::PathI, Bio::Ontology::Relationship, Bio::Ontology::RelationshipFactory, Bio::Ontology::RelationshipI, Bio::Ontology::RelationshipType, Bio::Ontology::SimpleGOEngine::GraphAdaptor, Bio::Ontology::SimpleOntologyEngine, Bio::Ontology::Term, Bio::Ontology::TermFactory, Bio::Ontology::TermI, Bio::OntologyIO, Bio::OntologyIO::Handlers::BaseSAXHandler, Bio::OntologyIO::Handlers::InterProHandler, Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler, Bio::OntologyIO::InterProParser, Bio::OntologyIO::dagflat, Bio::OntologyIO::goflat, Bio::OntologyIO::obo, Bio::OntologyIO::simplehierarchy, Bio::OntologyIO::soflat, Bio::PrimarySeq, Bio::PrimarySeqI, Bio::PullParserI, Bio::Range, Bio::RangeI, Bio::Root::Exception, Bio::Root::IO, Bio::Root::Root, Bio::Root::RootI, Bio::Root::Storable, Bio::Root::TestObject, Bio::Root::Utilities, Bio::Root::Version, Bio::Search::BlastStatistics, Bio::Search::BlastUtils, Bio::Search::DatabaseI, Bio::Search::GenericDatabase, Bio::Search::GenericStatistics, Bio::Search::HSP::BlastHSP, Bio::Search::HSP::BlastPullHSP, Bio::Search::HSP::FastaHSP, Bio::Search::HSP::GenericHSP, Bio::Search::HSP::HSPFactory, Bio::Search::HSP::HSPI, Bio::Search::HSP::ModelHSP, Bio::Search::HSP::PSLHSP, Bio::Search::HSP::PsiBlastHSP, Bio::Search::HSP::PullHSPI, Bio::Search::HSP::WABAHSP, Bio::Search::Hit::BlastHit, Bio::Search::Hit::BlastPullHit, Bio::Search::Hit::Fasta, Bio::Search::Hit::GenericHit, Bio::Search::Hit::HitFactory, Bio::Search::Hit::HitI, Bio::Search::Hit::ModelHit, Bio::Search::Hit::PsiBlastHit, Bio::Search::Hit::PullHitI, Bio::Search::Iteration::GenericIteration, Bio::Search::Iteration::IterationI, Bio::Search::Processor, Bio::Search::Result::BlastPullResult, Bio::Search::Result::BlastResult, Bio::Search::Result::CrossMatchResult, Bio::Search::Result::GenericResult, Bio::Search::Result::PullResultI, Bio::Search::Result::ResultFactory, Bio::Search::Result::ResultI, Bio::Search::Result::WABAResult, Bio::Search::SearchUtils, Bio::Search::StatisticsI, Bio::SearchIO::EventHandlerI, Bio::SearchIO::FastHitEventBuilder, Bio::SearchIO::IteratedSearchResultEventBuilder, Bio::SearchIO::SearchResultEventBuilder, Bio::SearchIO::SearchWriterI, Bio::SearchIO::Writer::GbrowseGFF, Bio::SearchIO::Writer::HSPTableWriter, Bio::SearchIO::Writer::HTMLResultWriter, Bio::SearchIO::Writer::HitTableWriter, Bio::SearchIO::Writer::ResultTableWriter, Bio::SearchIO::Writer::TextResultWriter, Bio::SearchIO::axt, Bio::SearchIO::blast, Bio::SearchIO::blast_pull, Bio::SearchIO::blasttable, Bio::SearchIO::cross_match, Bio::SearchIO::erpin, Bio::SearchIO::exonerate, Bio::SearchIO::fasta, Bio::SearchIO::infernal, Bio::SearchIO::megablast, Bio::SearchIO::psl, Bio::SearchIO::rnamotif, Bio::SearchIO::sim4, Bio::SearchIO::waba, Bio::SearchIO::wise, Bio::Seq, Bio::Seq::BaseSeqProcessor, Bio::Seq::EncodedSeq, Bio::Seq::LargeLocatableSeq, Bio::Seq::LargePrimarySeq, Bio::Seq::LargeSeq, Bio::Seq::LargeSeqI, Bio::Seq::Meta, Bio::Seq::Meta::Array, Bio::Seq::MetaI, Bio::Seq::PrimaryQual, Bio::Seq::PrimedSeq, Bio::Seq::QualI, Bio::Seq::Quality, Bio::Seq::RichSeq, Bio::Seq::RichSeqI, Bio::Seq::SeqBuilder, Bio::Seq::SeqFactory, Bio::Seq::SeqFastaSpeedFactory, Bio::Seq::SequenceTrace, Bio::Seq::TraceI, Bio::SeqAnalysisParserI, Bio::SeqFeature::Amplicon, Bio::SeqFeature::AnnotationAdaptor, Bio::SeqFeature::Collection, Bio::SeqFeature::CollectionI, Bio::SeqFeature::Computation, Bio::SeqFeature::FeaturePair, Bio::SeqFeature::Gene::Exon, Bio::SeqFeature::Gene::ExonI, Bio::SeqFeature::Gene::GeneStructure, Bio::SeqFeature::Gene::GeneStructureI, Bio::SeqFeature::Gene::Intron, Bio::SeqFeature::Gene::NC_Feature, Bio::SeqFeature::Gene::Poly_A_site, Bio::SeqFeature::Gene::Promoter, Bio::SeqFeature::Gene::Transcript, Bio::SeqFeature::Gene::TranscriptI, Bio::SeqFeature::Gene::UTR, Bio::SeqFeature::Generic, Bio::SeqFeature::Lite, Bio::SeqFeature::PositionProxy, Bio::SeqFeature::Primer, Bio::SeqFeature::Similarity, Bio::SeqFeature::SimilarityPair, Bio::SeqFeature::SubSeq, Bio::SeqFeature::Tools::FeatureNamer, Bio::SeqFeature::Tools::IDHandler, Bio::SeqFeature::Tools::TypeMapper, Bio::SeqFeature::Tools::Unflattener, Bio::SeqFeature::TypedSeqFeatureI, Bio::SeqFeatureI, Bio::SeqI, Bio::SeqIO::FTHelper, Bio::SeqIO::MultiFile, Bio::SeqIO::ace, Bio::SeqIO::asciitree, Bio::SeqIO::bsml, Bio::SeqIO::bsml_sax, Bio::SeqIO::embl, Bio::SeqIO::embldriver, Bio::SeqIO::fastq, Bio::SeqIO::game, Bio::SeqIO::game::featHandler, Bio::SeqIO::game::gameHandler, Bio::SeqIO::game::gameSubs, Bio::SeqIO::game::gameWriter, Bio::SeqIO::game::seqHandler, Bio::SeqIO::gbxml, Bio::SeqIO::gcg, Bio::SeqIO::genbank, Bio::SeqIO::interpro, Bio::SeqIO::kegg, Bio::SeqIO::largefasta, Bio::SeqIO::locuslink, Bio::SeqIO::mbsout, Bio::SeqIO::metafasta, Bio::SeqIO::msout, Bio::SeqIO::phd, Bio::SeqIO::pir, Bio::SeqIO::qual, Bio::SeqIO::raw, Bio::SeqIO::scf, Bio::SeqIO::seqxml, Bio::SeqIO::swiss, Bio::SeqIO::swissdriver, Bio::SeqIO::tab, Bio::SeqIO::table, Bio::SeqIO::tigr, Bio::SeqIO::tigrxml, Bio::SeqIO::tinyseq, Bio::SimpleAnalysisI, Bio::Taxon, Bio::Tools::Alignment::Consed, Bio::Tools::Alignment::Trim, Bio::Tools::Analysis::SimpleAnalysisBase, Bio::Tools::AnalysisResult, Bio::Tools::Blat, Bio::Tools::CodonTable, Bio::Tools::Coil, Bio::Tools::ECnumber, Bio::Tools::EMBOSS::Palindrome, Bio::Tools::EPCR, Bio::Tools::ESTScan, Bio::Tools::Eponine, Bio::Tools::Est2Genome, Bio::Tools::Fgenesh, Bio::Tools::FootPrinter, Bio::Tools::GFF, Bio::Tools::Geneid, Bio::Tools::Genemark, Bio::Tools::Genewise, Bio::Tools::Genomewise, Bio::Tools::Genscan, Bio::Tools::Glimmer, Bio::Tools::Grail, Bio::Tools::IUPAC, Bio::Tools::Lucy, Bio::Tools::MZEF, Bio::Tools::Match, Bio::Tools::OddCodes, Bio::Tools::Phylo::Gerp, Bio::Tools::Phylo::Molphy, Bio::Tools::Phylo::Molphy::Result, Bio::Tools::Phylo::Phylip::ProtDist, Bio::Tools::Prediction::Exon, Bio::Tools::Prediction::Gene, Bio::Tools::Primer3, Bio::Tools::Primer::Assessor::Base, Bio::Tools::Primer::AssessorI, Bio::Tools::Primer::Feature, Bio::Tools::Primer::Pair, Bio::Tools::Prints, Bio::Tools::Profile, Bio::Tools::Promoterwise, Bio::Tools::PrositeScan, Bio::Tools::Pseudowise, Bio::Tools::QRNA, Bio::Tools::RandomDistFunctions, Bio::Tools::RepeatMasker, Bio::Tools::Run::Analysis, Bio::Tools::Run::AnalysisFactory, Bio::Tools::Run::GenericParameters, Bio::Tools::Run::ParametersI, Bio::Tools::Run::Phylo::PhyloBase, Bio::Tools::Run::WrapperBase, Bio::Tools::Seg, Bio::Tools::SeqPattern, Bio::Tools::SeqStats, Bio::Tools::SeqWords, Bio::Tools::Sigcleave, Bio::Tools::Signalp, Bio::Tools::Signalp::ExtendedSignalp, Bio::Tools::Sim4::Exon, Bio::Tools::Sim4::Results, Bio::Tools::Spidey::Exon, Bio::Tools::Spidey::Results, Bio::Tools::TandemRepeatsFinder, Bio::Tools::TargetP, Bio::Tools::Tmhmm, Bio::Tools::ipcress, Bio::Tools::isPcr, Bio::Tools::pICalculator, Bio::Tools::tRNAscanSE, Bio::Tree::AnnotatableNode, Bio::Tree::Compatible, Bio::Tree::DistanceFactory, Bio::Tree::Node, Bio::Tree::NodeI, Bio::Tree::NodeNHX, Bio::Tree::RandomFactory, Bio::Tree::Statistics, Bio::Tree::Tree, Bio::Tree::TreeFunctionsI, Bio::Tree::TreeI, Bio::TreeIO, Bio::TreeIO::NewickParser, Bio::TreeIO::TreeEventBuilder, Bio::TreeIO::cluster, Bio::TreeIO::lintree, Bio::TreeIO::newick, Bio::TreeIO::nexus, Bio::TreeIO::nhx, Bio::TreeIO::pag, Bio::TreeIO::phyloxml, Bio::TreeIO::tabtree, Bio::UpdateableSeqI, Bio::WebAgent

meta_yml_has_provides

Add all modules contained in this distribution to the META.yml field 'provides'. Module::Build or Dist::Zilla::Plugin::MetaProvides do this automatically for you.

Modules

Name Abstract Version View
Bio::Align::AlignI An interface for describing sequence alignments. 1.007006 metacpan
Bio::Align::DNAStatistics Calculate some statistics for a DNA alignment 1.007006 metacpan
Bio::Align::PairwiseStatistics Base statistic object for Pairwise Alignments 1.007006 metacpan
Bio::Align::ProteinStatistics Calculate Protein Alignment statistics (mostly distances) 1.007006 metacpan
Bio::Align::StatisticsI Calculate some statistics for an alignment 1.007006 metacpan
Bio::Align::Utilities A collection of utilities regarding converting and manipulating alignment objects 1.007006 metacpan
Bio::AlignIO Handler for AlignIO Formats 1.007006 metacpan
Bio::AlignIO::Handler::GenericAlignHandler Bio::HandlerI-based generic data handler class for alignment-based data 1.007006 metacpan
Bio::AlignIO::arp ARP MSA Sequence input/output stream 1.007006 metacpan
Bio::AlignIO::bl2seq bl2seq sequence input/output stream 1.007006 metacpan
Bio::AlignIO::clustalw clustalw sequence input/output stream 1.007006 metacpan
Bio::AlignIO::emboss Parse EMBOSS alignment output (from applications water and needle) 1.007006 metacpan
Bio::AlignIO::fasta fasta MSA Sequence input/output stream 1.007006 metacpan
Bio::AlignIO::largemultifasta Largemultifasta MSA Sequence input/output stream 1.007006 metacpan
Bio::AlignIO::maf Multiple Alignment Format sequence input stream 1.007006 metacpan
Bio::AlignIO::mase mase sequence input/output stream 1.007006 metacpan
Bio::AlignIO::mega Parse and Create MEGA format data files 1.007006 metacpan
Bio::AlignIO::meme meme sequence input/output stream 1.007006 metacpan
Bio::AlignIO::metafasta Metafasta MSA Sequence input/output stream 1.007006 metacpan
Bio::AlignIO::msf msf sequence input/output stream 1.007006 metacpan
Bio::AlignIO::nexus NEXUS format sequence input/output stream 1.007006 metacpan
Bio::AlignIO::pfam pfam sequence input/output stream 1.007006 metacpan
Bio::AlignIO::phylip PHYLIP format sequence input/output stream 1.007006 metacpan
Bio::AlignIO::po po MSA Sequence input/output stream 1.007006 metacpan
Bio::AlignIO::proda proda sequence input/output stream 1.007006 metacpan
Bio::AlignIO::prodom prodom sequence input/output stream 1.007006 metacpan
Bio::AlignIO::psi Read/Write PSI-BLAST profile alignment files 1.007006 metacpan
Bio::AlignIO::selex selex sequence input/output stream 1.007006 metacpan
Bio::AlignIO::xmfa XMFA MSA Sequence input/output stream 1.007006 metacpan
Bio::AnalysisI An interface to any (local or remote) analysis tool 1.007006 metacpan
Bio::AnalysisParserI Generic analysis output parser interface 1.007006 metacpan
Bio::AnalysisResultI Interface for analysis result objects 1.007006 metacpan
Bio::AnnotatableI the base interface an annotatable object must implement 1.007006 metacpan
Bio::Annotation::AnnotationFactory Instantiates a new Bio::AnnotationI (or derived class) through a factory 1.007006 metacpan
Bio::Annotation::Collection Default Perl implementation of AnnotationCollectionI 1.007006 metacpan
Bio::Annotation::Comment A comment object, holding text 1.007006 metacpan
Bio::Annotation::DBLink untyped links between databases 1.007006 metacpan
Bio::Annotation::OntologyTerm An ontology term adapted to AnnotationI 1.007006 metacpan
Bio::Annotation::Reference Specialised DBLink object for Literature References 1.007006 metacpan
Bio::Annotation::Relation Relationship (pairwise) with other objects SeqI and NodeI; 1.007006 metacpan
Bio::Annotation::SimpleValue A simple scalar 1.007006 metacpan
Bio::Annotation::StructuredValue A scalar with embedded structured information 1.007006 metacpan
Bio::Annotation::TagTree AnnotationI with tree-like hierarchal key-value relationships ('structured tags') that can be represented as simple text. 1.007006 metacpan
Bio::Annotation::Target Provides an object which represents a target (ie, a similarity hit) from one object to something in another database 1.007006 metacpan
Bio::Annotation::Tree Provide a tree as an annotation to a Bio::AnnotatableI object 1.007006 metacpan
Bio::Annotation::TypeManager Manages types for annotation collections 1.007006 metacpan
Bio::AnnotationCollectionI Interface for annotation collections 1.007006 metacpan
Bio::AnnotationI Annotation interface 1.007006 metacpan
Bio::CodonUsage::IO for reading and writing codon usage tables to file 1.007006 metacpan
Bio::CodonUsage::Table for access to the Codon usage Database at http://www.kazusa.or.jp/codon. 1.007006 metacpan
Bio::DB::DBFetch Database object for retrieving using the dbfetch script 1.007006 metacpan
Bio::DB::Failover A Bio::DB::RandomAccessI compliant class which wraps a prioritized list of DBs 1.007006 metacpan
Bio::DB::Fasta Fast indexed access to fasta files 1.007006 metacpan
Bio::DB::FileCache In file cache for BioSeq objects 1.007006 metacpan
Bio::DB::Flat Interface for indexed flat files 1.007006 metacpan
Bio::DB::Flat::BDB Interface for BioHackathon standard BDB-indexed flat file 1.007006 metacpan
Bio::DB::Flat::BDB::embl embl adaptor for Open-bio standard BDB-indexed flat file 1.007006 metacpan
Bio::DB::Flat::BDB::fasta fasta adaptor for Open-bio standard BDB-indexed flat file 1.007006 metacpan
Bio::DB::Flat::BDB::genbank genbank adaptor for Open-bio standard BDB-indexed flat file 1.007006 metacpan
Bio::DB::Flat::BDB::swiss swissprot adaptor for Open-bio standard BDB-indexed flat file 1.007006 metacpan
Bio::DB::Flat::BinarySearch BinarySearch search indexing system for sequence files 1.007006 metacpan
Bio::DB::GFF::Util::Binning binning utility for Bio::DB::GFF index 1.007006 metacpan
Bio::DB::GFF::Util::Rearrange rearrange utility 1.007006 metacpan
Bio::DB::GenericWebAgent helper base class for parameter-based remote server access and response retrieval. 1.007006 metacpan
Bio::DB::InMemoryCache Abstract interface for a sequence database 1.007006 metacpan
Bio::DB::IndexedBase Base class for modules using indexed sequence files 1.007006 metacpan
Bio::DB::LocationI A RandomAccessI-like abstract interface for retrieving location data from a sequence database and returning Bio::LocationI objects 1.007006 metacpan
Bio::DB::Qual Fast indexed access to quality files 1.007006 metacpan
Bio::DB::Query::WebQuery Helper class for web-based sequence queryies 1.007006 metacpan
Bio::DB::QueryI Object Interface to queryable sequence databases 1.007006 metacpan
Bio::DB::RandomAccessI Abstract interface for a sequence database 1.007006 metacpan
Bio::DB::ReferenceI A RandomAccessI-like abstract interface for retrieving Reference data from a sequence database and returning Bio::Annotation::Reference objects 1.007006 metacpan
Bio::DB::Registry Access to the Open Bio Database Access registry scheme 1.007006 metacpan
Bio::DB::SeqI Abstract Interface for Sequence databases 1.007006 metacpan
Bio::DB::Taxonomy Access to a taxonomy database 1.007006 metacpan
Bio::DB::Taxonomy::flatfile Use the NCBI taxonomy from local indexed flat files 1.007006 metacpan
Bio::DB::Taxonomy::greengenes Use the Greengenes taxonomy 1.007006 metacpan
Bio::DB::Taxonomy::list An implementation of Bio::DB::Taxonomy that accepts lists of words to build a database 1.007006 metacpan
Bio::DB::Taxonomy::silva Use the Silva taxonomy 1.007006 metacpan
Bio::DB::UpdateableSeqI An interface for writing to a database of sequences. 1.007006 metacpan
Bio::DB::WebDBSeqI Object Interface to generalize Web Databases for retrieving sequences 1.007006 metacpan
Bio::DBLinkContainerI Abstract interface for any object wanting to use database cross references 1.007006 metacpan
Bio::Das::FeatureTypeI Simple interface to Sequence Ontology feature types 1.007006 metacpan
Bio::Das::SegmentI DAS-style access to a feature database 1.007006 metacpan
Bio::DasI DAS-style access to a feature database 1.007006 metacpan
Bio::DescribableI interface for objects with human readable names and descriptions 1.007006 metacpan
Bio::Event::EventGeneratorI This interface describes the basic event generator class. 1.007006 metacpan
Bio::Event::EventHandlerI An Event Handler Interface 1.007006 metacpan
Bio::Factory::AnalysisI An interface to analysis tool factory 1.007006 metacpan
Bio::Factory::ApplicationFactoryI Interface class for Application Factories 1.007006 metacpan
Bio::Factory::DriverFactory Base class for factory classes loading drivers 1.007006 metacpan
Bio::Factory::FTLocationFactory A FeatureTable Location Parser 1.007006 metacpan
Bio::Factory::LocationFactoryI A factory interface for generating locations from a string 1.007006 metacpan
Bio::Factory::ObjectBuilderI Interface for an object builder 1.007006 metacpan
Bio::Factory::ObjectFactory Instantiates a new Bio::Root::RootI (or derived class) through a factory 1.007006 metacpan
Bio::Factory::ObjectFactoryI A General object creator factory 1.007006 metacpan
Bio::Factory::SeqAnalysisParserFactory class capable of creating SeqAnalysisParserI compliant parsers 1.007006 metacpan
Bio::Factory::SeqAnalysisParserFactoryI interface describing objects capable of creating SeqAnalysisParserI compliant parsers 1.007006 metacpan
Bio::Factory::SequenceFactoryI This interface allows for generic building of sequences in factories which create sequences (like SeqIO) 1.007006 metacpan
Bio::Factory::SequenceProcessorI Interface for chained sequence processing algorithms 1.007006 metacpan
Bio::Factory::SequenceStreamI Interface describing the basics of a Sequence Stream. 1.007006 metacpan
Bio::Factory::TreeFactoryI Factory Interface for getting and writing trees from/to a data stream 1.007006 metacpan
Bio::FeatureHolderI the base interface an object with features must implement 1.007006 metacpan
Bio::HandlerBaseI Interface class for handler methods which interact with any event-driven parsers (drivers). 1.007006 metacpan
Bio::IdCollectionI interface for objects with multiple identifiers 1.007006 metacpan
Bio::IdentifiableI interface for objects with identifiers 1.007006 metacpan
Bio::Index::Abstract Abstract interface for indexing a flat file 1.007006 metacpan
Bio::Index::AbstractSeq base class for AbstractSeq 1.007006 metacpan
Bio::Index::Blast Indexes Blast reports and supports retrieval based on query accession(s) 1.007006 metacpan
Bio::Index::BlastTable Indexes tabular Blast reports (-m 8 or -m 9 format) and supports retrieval based on query accession(s) 1.007006 metacpan
Bio::Index::EMBL Interface for indexing (multiple) EMBL/Swissprot .dat files (i.e. flat file EMBL/Swissprot format). 1.007006 metacpan
Bio::Index::Fasta Interface for indexing (multiple) fasta files 1.007006 metacpan
Bio::Index::Fastq Interface for indexing (multiple) fastq files 1.007006 metacpan
Bio::Index::GenBank Interface for indexing one or more GenBank files (i.e. flat file GenBank format). 1.007006 metacpan
Bio::Index::Qual Interface for indexing (multiple) fasta qual files 1.007006 metacpan
Bio::Index::SwissPfam Interface for indexing swisspfam files 1.007006 metacpan
Bio::Index::Swissprot Interface for indexing one or more Swissprot files. 1.007006 metacpan
Bio::LocatableSeq A Bio::PrimarySeq object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq. 1.007006 metacpan
Bio::Location::Atomic Implementation of a Atomic Location on a Sequence 1.007006 metacpan
Bio::Location::AvWithinCoordPolicy class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise 1.007006 metacpan
Bio::Location::CoordinatePolicyI Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location 1.007006 metacpan
Bio::Location::Fuzzy Implementation of a Location on a Sequence which has unclear start and/or end locations 1.007006 metacpan
Bio::Location::FuzzyLocationI Abstract interface of a Location on a Sequence which has unclear start/end location 1.007006 metacpan
Bio::Location::NarrowestCoordPolicy class implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range 1.007006 metacpan
Bio::Location::Simple Implementation of a Simple Location on a Sequence 1.007006 metacpan
Bio::Location::Split Implementation of a Location on a Sequence which has multiple locations (start/end points) 1.007006 metacpan
Bio::Location::SplitLocationI Abstract interface of a Location on a Sequence which has multiple locations (start/end points) 1.007006 metacpan
Bio::Location::WidestCoordPolicy class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable range 1.007006 metacpan
Bio::LocationI Abstract interface of a Location on a Sequence 1.007006 metacpan
Bio::Matrix::Generic A generic matrix implementation 1.007006 metacpan
Bio::Matrix::IO A factory for Matrix parsing 1.007006 metacpan
Bio::Matrix::IO::mlagan A parser for the mlagan substitution matrix 1.007006 metacpan
Bio::Matrix::IO::phylip A parser for PHYLIP distance matricies 1.007006 metacpan
Bio::Matrix::IO::scoring A parser for PAM/BLOSUM matricies 1.007006 metacpan
Bio::Matrix::MatrixI An interface for describing a Matrix 1.007006 metacpan
Bio::Matrix::Mlagan A generic matrix with mlagan fields 1.007006 metacpan
Bio::Matrix::PSM::IO PSM parser 1.007006 metacpan
Bio::Matrix::PSM::IO::mast PSM mast parser implementation 1.007006 metacpan
Bio::Matrix::PSM::IO::masta motif fasta format parser 1.007006 metacpan
Bio::Matrix::PSM::IO::meme PSM meme parser implementation 1.007006 metacpan
Bio::Matrix::PSM::IO::psiblast PSM psiblast parser 1.007006 metacpan
Bio::Matrix::PSM::IO::transfac PSM transfac parser 1.007006 metacpan
Bio::Matrix::PSM::InstanceSite A PSM site occurrence 1.007006 metacpan
Bio::Matrix::PSM::InstanceSiteI InstanceSite interface, holds an instance of a PSM 1.007006 metacpan
Bio::Matrix::PSM::ProtMatrix SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) with log-odds scoring information. 1.007006 metacpan
Bio::Matrix::PSM::ProtPsm handle combination of site matricies 1.007006 metacpan
Bio::Matrix::PSM::Psm handle combination of site matricies 1.007006 metacpan
Bio::Matrix::PSM::PsmHeader PSM mast parser implementation 1.007006 metacpan
Bio::Matrix::PSM::PsmHeaderI handles the header data from a PSM file 1.007006 metacpan
Bio::Matrix::PSM::PsmI abstract interface to handler of site matricies 1.007006 metacpan
Bio::Matrix::PSM::SiteMatrix SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds 1.007006 metacpan
Bio::Matrix::PSM::SiteMatrixI SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds 1.007006 metacpan
Bio::Matrix::PhylipDist A Phylip Distance Matrix object 1.007006 metacpan
Bio::Matrix::Scoring Object which can hold scoring matrix information 1.007006 metacpan
Bio::Ontology::DocumentRegistry Keep track of where to find ontologies. Allows lookups by name. 1.007006 metacpan
Bio::Ontology::GOterm representation of GO terms 1.007006 metacpan
Bio::Ontology::InterProTerm Implementation of InterProI term interface 1.007006 metacpan
Bio::Ontology::OBOEngine An Ontology Engine for OBO style flat file format from the Gene Ontology Consortium 1.007006 metacpan
Bio::Ontology::OBOterm representation of OBO terms 1.007006 metacpan
Bio::Ontology::Ontology standard implementation of an Ontology 1.007006 metacpan
Bio::Ontology::OntologyEngineI Interface a minimal Ontology implementation should satisfy 1.007006 metacpan
Bio::Ontology::OntologyI Interface for an ontology implementation 1.007006 metacpan
Bio::Ontology::OntologyStore A repository of ontologies 1.007006 metacpan
Bio::Ontology::Path a path for an ontology term graph 1.007006 metacpan
Bio::Ontology::PathI Interface for a path between ontology terms 1.007006 metacpan
Bio::Ontology::Relationship a relationship for an ontology 1.007006 metacpan
Bio::Ontology::RelationshipFactory Instantiates a new Bio::Ontology::RelationshipI (or derived class) through a factory 1.007006 metacpan
Bio::Ontology::RelationshipI Interface for a relationship between ontology terms 1.007006 metacpan
Bio::Ontology::RelationshipType a relationship type for an ontology 1.007006 metacpan
Bio::Ontology::SimpleGOEngine::GraphAdaptor Graph adaptor for Bio::Ontology::SimpleGOEngine 1.007006 metacpan
Bio::Ontology::SimpleOntologyEngine Implementation of OntologyEngineI interface 1.007006 metacpan
Bio::Ontology::Term implementation of the interface for ontology terms 1.007006 metacpan
Bio::Ontology::TermFactory Instantiates a new Bio::Ontology::TermI (or derived class) through a factory 1.007006 metacpan
Bio::Ontology::TermI interface for ontology terms 1.007006 metacpan
Bio::OntologyIO Parser factory for Ontology formats 1.007006 metacpan
Bio::OntologyIO::Handlers::BaseSAXHandler base class for SAX Handlers 1.007006 metacpan
Bio::OntologyIO::Handlers::InterProHandler XML handler class for InterProParser 1.007006 metacpan
Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler parse an InterPro XML file and persist the resulting terms to a Biosql database 1.007006 metacpan
Bio::OntologyIO::InterProParser Parser for InterPro xml files. 1.007006 metacpan
Bio::OntologyIO::dagflat a base class parser for GO flat-file type formats 1.007006 metacpan
Bio::OntologyIO::goflat a parser for the Gene Ontology flat-file format 1.007006 metacpan
Bio::OntologyIO::obo parser for OBO flat-file format 1.007006 metacpan
Bio::OntologyIO::simplehierarchy a base class parser for simple hierarchy-by-indentation type formats 1.007006 metacpan
Bio::OntologyIO::soflat a parser for the Sequence Ontology flat-file format 1.007006 metacpan
Bio::ParameterBaseI Simple interface class for any parameter-related data such as IDs, database name, program arguments, and other odds and ends. 1.007006 metacpan
Bio::PrimarySeq Bioperl lightweight sequence object 1.007006 metacpan
Bio::PrimarySeqI Interface definition for a Bio::PrimarySeq 1.007006 metacpan
Bio::PullParserI A base module for fast 'pull' parsing 1.007006 metacpan
Bio::Range Pure perl RangeI implementation 1.007006 metacpan
Bio::RangeI Range interface 1.007006 metacpan
Bio::Root::Exception BioPerl exceptions 1.007006 metacpan
Bio::Root::HTTPget module for fallback HTTP get operations when LWP:: is unavailable 1.007006 metacpan
Bio::Root::IO BioPerl base IO handling class 1.007006 metacpan
Bio::Root::Root implementation of Bio::Root::RootI interface 1.007006 metacpan
Bio::Root::RootI base interface for all BioPerl classes 1.007006 metacpan
Bio::Root::Storable Safely store/retrieve objects from disk 1.007006 metacpan
Bio::Root::Test common base for all BioPerl test scripts 1.007006 metacpan
Bio::Root::TestObject 1.007006 metacpan
Bio::Root::Utilities general-purpose utilities 1.007006 metacpan
Bio::Root::Version don't use, get version from each module 1.007006 metacpan
Bio::Search::BlastStatistics An object for Blast statistics 1.007006 metacpan
Bio::Search::BlastUtils Utility functions for Bio::Search:: BLAST objects 1.007006 metacpan
Bio::Search::DatabaseI Interface for a database used in a sequence search 1.007006 metacpan
Bio::Search::GenericDatabase Generic implementation of Bio::Search::DatabaseI 1.007006 metacpan
Bio::Search::GenericStatistics An object for statistics 1.007006 metacpan
Bio::Search::HSP::BlastHSP Bioperl BLAST High-Scoring Pair object 1.007006 metacpan
Bio::Search::HSP::BlastPullHSP A parser and HSP object for BlastN hsps 1.007006 metacpan
Bio::Search::HSP::FastaHSP HSP object for FASTA specific data 1.007006 metacpan
Bio::Search::HSP::GenericHSP A "Generic" implementation of a High Scoring Pair 1.007006 metacpan
Bio::Search::HSP::HSPFactory A factory to create Bio::Search::HSP::HSPI objects 1.007006 metacpan
Bio::Search::HSP::HSPI Interface for a High Scoring Pair in a similarity search result 1.007006 metacpan
Bio::Search::HSP::ModelHSP A HSP object for model-based searches 1.007006 metacpan
Bio::Search::HSP::PSLHSP A HSP for PSL output 1.007006 metacpan
Bio::Search::HSP::PsiBlastHSP Bioperl BLAST High-Scoring Pair object 1.007006 metacpan
Bio::Search::HSP::PullHSPI Bio::Search::HSP::HSPI interface for pull parsers. 1.007006 metacpan
Bio::Search::HSP::WABAHSP HSP object suitable for describing WABA alignments 1.007006 metacpan
Bio::Search::Hit::BlastHit Blast-specific subclass of Bio::Search::Hit::GenericHit 1.007006 metacpan
Bio::Search::Hit::BlastPullHit A parser and hit object for BLASTN hits 1.007006 metacpan
Bio::Search::Hit::Fasta Hit object specific for Fasta-generated hits 1.007006 metacpan
Bio::Search::Hit::GenericHit A generic implementation of the Bio::Search::Hit::HitI interface 1.007006 metacpan
Bio::Search::Hit::HitFactory A factory to create Bio::Search::Hit::HitI objects 1.007006 metacpan
Bio::Search::Hit::HitI Interface for a hit in a similarity search result 1.007006 metacpan
Bio::Search::Hit::ModelHit A model-based implementation of the Bio::Search::Hit::HitI interface 1.007006 metacpan
Bio::Search::Hit::PsiBlastHit Bioperl BLAST Hit object 1.007006 metacpan
Bio::Search::Hit::PullHitI Bio::Search::Hit::HitI interface for pull parsers. 1.007006 metacpan
Bio::Search::Iteration::GenericIteration A generic implementation of the Bio::Search::Iteration::IterationI interface. 1.007006 metacpan
Bio::Search::Iteration::IterationI Abstract interface to an iteration from an iterated search result, such as PSI-BLAST. 1.007006 metacpan
Bio::Search::Processor DESCRIPTION of Object 1.007006 metacpan
Bio::Search::Result::BlastPullResult A parser and result object for BLASTN results 1.007006 metacpan
Bio::Search::Result::BlastResult Blast-specific subclass of Bio::Search::Result::GenericResult 1.007006 metacpan
Bio::Search::Result::CrossMatchResult CrossMatch-specific subclass of Bio::Search::Result::GenericResult 1.007006 metacpan
Bio::Search::Result::GenericResult Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results. 1.007006 metacpan
Bio::Search::Result::INFERNALResult A Result object for INFERNAL results 1.007006 metacpan
Bio::Search::Result::PullResultI Bio::Search::Result::ResultI interface for 'pull' parsers 1.007006 metacpan
Bio::Search::Result::ResultFactory A factory to create Bio::Search::Result::ResultI objects 1.007006 metacpan
Bio::Search::Result::ResultI Abstract interface to Search Result objects 1.007006 metacpan
Bio::Search::Result::WABAResult Result object for WABA alignment output 1.007006 metacpan
Bio::Search::SearchUtils Utility functions for Bio::Search:: objects 1.007006 metacpan
Bio::Search::StatisticsI A Base object for statistics 1.007006 metacpan
Bio::Search::Tiling::MapTileUtils utilities for manipulating closed intervals for an HSP tiling algorithm 1.007006 metacpan
Bio::Search::Tiling::MapTiling An implementation of an HSP tiling algorithm, with methods to obtain frequently-requested statistics 1.007006 metacpan
Bio::Search::Tiling::TilingI Abstract interface for an HSP tiling module 1.007006 metacpan
Bio::SearchIO Driver for parsing Sequence Database Searches (BLAST, FASTA, ...) 1.007006 metacpan
Bio::SearchIO::EventHandlerI An abstract Event Handler for Search Result parsing 1.007006 metacpan
Bio::SearchIO::FastHitEventBuilder Event Handler for SearchIO events. 1.007006 metacpan
Bio::SearchIO::IteratedSearchResultEventBuilder Event Handler for SearchIO events. 1.007006 metacpan
Bio::SearchIO::SearchResultEventBuilder Event Handler for SearchIO events. 1.007006 metacpan
Bio::SearchIO::SearchWriterI Interface for outputting parsed Search results 1.007006 metacpan
Bio::SearchIO::Writer::GbrowseGFF Interface for outputting parsed search results in Gbrowse GFF format 1.007006 metacpan
Bio::SearchIO::Writer::HSPTableWriter Tab-delimited data for Bio::Search::HSP::HSPI objects 1.007006 metacpan
Bio::SearchIO::Writer::HTMLResultWriter write a Bio::Search::ResultI in HTML 1.007006 metacpan
Bio::SearchIO::Writer::HitTableWriter Tab-delimited data for Bio::Search::Hit::HitI objects 1.007006 metacpan
Bio::SearchIO::Writer::ResultTableWriter Outputs tab-delimited data for each Bio::Search::Result::ResultI object. 1.007006 metacpan
Bio::SearchIO::Writer::TextResultWriter Object to implement writing a Bio::Search::ResultI in Text. 1.007006 metacpan
Bio::SearchIO::axt a parser for axt format reports 1.007006 metacpan
Bio::SearchIO::blast Event generator for event based parsing of blast reports 1.007006 metacpan
Bio::SearchIO::blast_pull A parser for BLAST output 1.007006 metacpan
Bio::SearchIO::blasttable Driver module for SearchIO for parsing NCBI -m 8/9 format 1.007006 metacpan
Bio::SearchIO::cross_match CrossMatch-specific subclass of Bio::SearchIO 1.007006 metacpan
Bio::SearchIO::erpin SearchIO-based ERPIN parser 1.007006 metacpan
Bio::SearchIO::exonerate parser for Exonerate 1.007006 metacpan
Bio::SearchIO::fasta A SearchIO parser for FASTA results 1.007006 metacpan
Bio::SearchIO::gmap_f9 Event generator for parsing gmap reports (Z format) 1.007006 metacpan
Bio::SearchIO::infernal SearchIO-based Infernal parser 1.007006 metacpan
Bio::SearchIO::megablast a driver module for Bio::SearchIO to parse megablast reports (format 0) 1.007006 metacpan
Bio::SearchIO::psl A parser for PSL output (UCSC) 1.007006 metacpan
Bio::SearchIO::rnamotif SearchIO-based RNAMotif parser 1.007006 metacpan
Bio::SearchIO::sim4 parser for Sim4 alignments 1.007006 metacpan
Bio::SearchIO::waba SearchIO parser for Jim Kent WABA program alignment output 1.007006 metacpan
Bio::SearchIO::wise Parsing of wise output as alignments 1.007006 metacpan
Bio::Seq Sequence object, with features 1.007006 metacpan
Bio::Seq::BaseSeqProcessor Base implementation for a SequenceProcessor 1.007006 metacpan
Bio::Seq::EncodedSeq subtype of L<Bio::LocatableSeq|Bio::LocatableSeq> to store DNA that encodes a protein 1.007006 metacpan
Bio::Seq::LargeLocatableSeq LocatableSeq object that stores sequence as files in the tempdir 1.007006 metacpan
Bio::Seq::LargePrimarySeq PrimarySeq object that stores sequence as files in the tempdir (as found by File::Temp) or the default method in Bio::Root::Root 1.007006 metacpan
Bio::Seq::LargeSeq SeqI compliant object that stores sequence as files in /tmp 1.007006 metacpan
Bio::Seq::LargeSeqI Interface class for sequences that cache their residues in a temporary file 1.007006 metacpan
Bio::Seq::Meta Generic superclass for sequence objects with residue-based meta information 1.007006 metacpan
Bio::Seq::Meta::Array array-based generic implementation of a sequence class with residue-based meta information 1.007006 metacpan
Bio::Seq::MetaI Interface for sequence objects with residue-based meta information 1.007006 metacpan
Bio::Seq::PrimaryQual Bioperl lightweight Quality Object 1.007006 metacpan
Bio::Seq::PrimedSeq A sequence and a pair of primers matching on it 1.007006 metacpan
Bio::Seq::QualI Interface definition for a Bio::Seq::Qual 1.007006 metacpan
Bio::Seq::Quality Implementation of sequence with residue quality and trace values 1.007006 metacpan
Bio::Seq::RichSeq Module implementing a sequence created from a rich sequence database entry 1.007006 metacpan
Bio::Seq::RichSeqI interface for sequences from rich data sources, mostly databases 1.007006 metacpan
Bio::Seq::SeqBuilder Configurable object builder for sequence stream parsers 1.007006 metacpan
Bio::Seq::SeqFactory Instantiation of generic Bio::PrimarySeqI (or derived) objects through a factory 1.007006 metacpan
Bio::Seq::SeqFastaSpeedFactory Rapid creation of Bio::Seq objects through a factory 1.007006 metacpan
Bio::Seq::SequenceTrace Bioperl object packaging a sequence with its trace 1.007006 metacpan
Bio::Seq::SimulatedRead Read with sequencing errors taken from a reference sequence 1.007006 metacpan
Bio::Seq::TraceI Interface definition for a Bio::Seq::Trace 1.007006 metacpan
Bio::SeqAnalysisParserI Sequence analysis output parser interface 1.007006 metacpan
Bio::SeqFeature::Amplicon Amplicon feature 1.007006 metacpan
Bio::SeqFeature::AnnotationAdaptor integrates SeqFeatureIs annotation 1.007006 metacpan
Bio::SeqFeature::Collection A container class for SeqFeatures suitable for performing operations such as finding features within a range, that match a certain feature type, etc. 1.007006 metacpan
Bio::SeqFeature::CollectionI An interface for a collection of SeqFeatureI objects. 1.007006 metacpan
Bio::SeqFeature::Computation Computation SeqFeature 1.007006 metacpan
Bio::SeqFeature::FeaturePair hold pair feature information e.g. blast hits 1.007006 metacpan
Bio::SeqFeature::Gene::Exon a feature representing an exon 1.007006 metacpan
Bio::SeqFeature::Gene::ExonI Interface for a feature representing an exon 1.007006 metacpan
Bio::SeqFeature::Gene::GeneStructure A feature representing an arbitrarily complex structure of a gene 1.007006 metacpan
Bio::SeqFeature::Gene::GeneStructureI A feature representing an arbitrarily complex structure of a gene 1.007006 metacpan
Bio::SeqFeature::Gene::Intron An intron feature 1.007006 metacpan
Bio::SeqFeature::Gene::NC_Feature 1.007006 metacpan
Bio::SeqFeature::Gene::Poly_A_site poly A feature 1.007006 metacpan
Bio::SeqFeature::Gene::Promoter Describes a promoter 1.007006 metacpan
Bio::SeqFeature::Gene::Transcript A feature representing a transcript 1.007006 metacpan
Bio::SeqFeature::Gene::TranscriptI Interface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site. 1.007006 metacpan
Bio::SeqFeature::Gene::UTR A feature representing an untranslated region that is part of a transcriptional unit 1.007006 metacpan
Bio::SeqFeature::Generic Generic SeqFeature 1.007006 metacpan
Bio::SeqFeature::Lite Lightweight Bio::SeqFeatureI class 1.007006 metacpan
Bio::SeqFeature::PositionProxy handle features when truncation/revcom sequences span a feature 1.007006 metacpan
Bio::SeqFeature::Primer Primer Generic SeqFeature 1.007006 metacpan
Bio::SeqFeature::Similarity A sequence feature based on similarity 1.007006 metacpan
Bio::SeqFeature::SimilarityPair Sequence feature based on the similarity of two sequences. 1.007006 metacpan
Bio::SeqFeature::SubSeq Feature representing a subsequence 1.007006 metacpan
Bio::SeqFeature::Tools::FeatureNamer generates unique persistent names for features 1.007006 metacpan
Bio::SeqFeature::Tools::IDHandler maps $seq_feature-E<gt>primary_tag 1.007006 metacpan
Bio::SeqFeature::Tools::TypeMapper maps $seq_feature-E<gt>primary_tag 1.007006 metacpan
Bio::SeqFeature::Tools::Unflattener turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy 1.007006 metacpan
Bio::SeqFeature::TypedSeqFeatureI a strongly typed SeqFeature 1.007006 metacpan
Bio::SeqFeatureI Abstract interface of a Sequence Feature 1.007006 metacpan
Bio::SeqI [Developers] Abstract Interface of Sequence (with features) 1.007006 metacpan
Bio::SeqIO Handler for SeqIO Formats 1.007006 metacpan
Bio::SeqIO::FTHelper Helper class for EMBL/Genbank feature tables 1.007006 metacpan
Bio::SeqIO::Handler::GenericRichSeqHandler Bio::HandlerI-based data handler for GenBank/EMBL/UniProt (and other) sequence data 1.007006 metacpan
Bio::SeqIO::MultiFile Treating a set of files as a single input stream 1.007006 metacpan
Bio::SeqIO::ace ace sequence input/output stream 1.007006 metacpan
Bio::SeqIO::asciitree asciitree sequence input/output stream 1.007006 metacpan
Bio::SeqIO::bsml BSML sequence input/output stream 1.007006 metacpan
Bio::SeqIO::bsml_sax BSML sequence input/output stream using SAX 1.007006 metacpan
Bio::SeqIO::embl EMBL sequence input/output stream 1.007006 metacpan
Bio::SeqIO::embldriver EMBL sequence input/output stream 1.007006 metacpan
Bio::SeqIO::fasta fasta sequence input/output stream 1.007006 metacpan
Bio::SeqIO::fastq fastq sequence input/output stream 1.007006 metacpan
Bio::SeqIO::game a class for parsing and writing game-XML 1.007006 metacpan
Bio::SeqIO::game::featHandler a class for handling feature elements 1.007006 metacpan
Bio::SeqIO::game::gameHandler PerlSAX handler for game-XML 1.007006 metacpan
Bio::SeqIO::game::gameSubs a base class for game-XML parsing 1.007006 metacpan
Bio::SeqIO::game::gameWriter a class for writing game-XML 1.007006 metacpan
Bio::SeqIO::game::seqHandler a class for handling game-XML sequences 1.007006 metacpan
Bio::SeqIO::gbdriver GenBank handler-based push parser 1.007006 metacpan
Bio::SeqIO::gbxml GenBank sequence input/output stream using SAX 1.007006 metacpan
Bio::SeqIO::gcg GCG sequence input/output stream 1.007006 metacpan
Bio::SeqIO::genbank GenBank sequence input/output stream 1.007006 metacpan
Bio::SeqIO::interpro InterProScan XML input/output stream 1.007006 metacpan
Bio::SeqIO::kegg KEGG sequence input/output stream 1.007006 metacpan
Bio::SeqIO::largefasta method i/o on very large fasta sequence files 1.007006 metacpan
Bio::SeqIO::locuslink LocusLink input/output stream 1.007006 metacpan
Bio::SeqIO::mbsout input stream for output by Teshima et al.'s mbs. 1.007006 metacpan
Bio::SeqIO::metafasta metafasta sequence input/output stream 1.007006 metacpan
Bio::SeqIO::msout input stream for output by Hudson's ms 1.007006 metacpan
Bio::SeqIO::phd phd file input/output stream 1.007006 metacpan
Bio::SeqIO::pir PIR sequence input/output stream 1.007006 metacpan
Bio::SeqIO::qual .qual file input/output stream 1.007006 metacpan
Bio::SeqIO::raw raw sequence file input/output stream 1.007006 metacpan
Bio::SeqIO::scf .scf file input/output stream 1.007006 metacpan
Bio::SeqIO::seqxml SeqXML sequence input/output stream 1.007006 metacpan
Bio::SeqIO::swiss Swissprot sequence input/output stream 1.007006 metacpan
Bio::SeqIO::swissdriver SwissProt/UniProt handler-based push parser 1.007006 metacpan
Bio::SeqIO::tab nearly raw sequence file input/output stream. Reads/writes id"\t"sequence"\n" 1.007006 metacpan
Bio::SeqIO::table sequence input/output stream from a delimited table 1.007006 metacpan
Bio::SeqIO::tigr TIGR XML sequence input/output stream 1.007006 metacpan
Bio::SeqIO::tigrxml Parse TIGR (new) XML 1.007006 metacpan
Bio::SeqIO::tinyseq reading/writing sequences in NCBI TinySeq format 1.007006 metacpan
Bio::SeqIO::tinyseq::tinyseqHandler XML event handlers to support NCBI TinySeq XML parsing 1.007006 metacpan
Bio::SeqUtils Additional methods for PrimarySeq objects 1.007006 metacpan
Bio::SimpleAlign Multiple alignments held as a set of sequences 1.007006 metacpan
Bio::SimpleAnalysisI A simple interface to any (local or remote) analysis tool 1.007006 metacpan
Bio::Species Generic species object. 1.007006 metacpan
Bio::Taxon A node in a represented taxonomy 1.007006 metacpan
Bio::Tools::Alignment::Consed A module to work with objects from consed .ace files 1.007006 metacpan
Bio::Tools::Alignment::Trim A kludge to do specialized trimming of sequence based on quality. 1.007006 metacpan
Bio::Tools::AmpliconSearch Find amplicons in a template using degenerate PCR primers 1.007006 metacpan
Bio::Tools::Analysis::SimpleAnalysisBase abstract superclass for SimpleAnalysis implementations 1.007006 metacpan
Bio::Tools::AnalysisResult Base class for analysis result objects and parsers 1.007006 metacpan
Bio::Tools::Blat parser for Blat program 1.007006 metacpan
Bio::Tools::CodonTable Codon table object 1.007006 metacpan
Bio::Tools::Coil parser for Coil output 1.007006 metacpan
Bio::Tools::ECnumber representation of EC numbers (Enzyme Classification) 1.007006 metacpan
Bio::Tools::EMBOSS::Palindrome parse EMBOSS palindrome output 1.007006 metacpan
Bio::Tools::EPCR Parse ePCR output and make features 1.007006 metacpan
Bio::Tools::ESTScan Results of one ESTScan run 1.007006 metacpan
Bio::Tools::Eponine Results of one Eponine run 1.007006 metacpan
Bio::Tools::Est2Genome Parse est2genome output, makes simple Bio::SeqFeature::Generic objects 1.007006 metacpan
Bio::Tools::Fgenesh parse results of one Fgenesh run 1.007006 metacpan
Bio::Tools::FootPrinter write sequence features in FootPrinter format 1.007006 metacpan
Bio::Tools::GFF A Bio::SeqAnalysisParserI compliant GFF format parser 1.007006 metacpan
Bio::Tools::Geneid Results of one geneid run 1.007006 metacpan
Bio::Tools::Genemark Results of one Genemark run 1.007006 metacpan
Bio::Tools::Genewise Results of one Genewise run 1.007006 metacpan
Bio::Tools::Genomewise Results of one Genomewise run 1.007006 metacpan
Bio::Tools::Genscan Results of one Genscan run 1.007006 metacpan
Bio::Tools::Glimmer parser for Glimmer 2.X/3.X prokaryotic and GlimmerM/GlimmerHMM eukaryotic gene predictions 1.007006 metacpan
Bio::Tools::Grail Results of one Grail run 1.007006 metacpan
Bio::Tools::GuessSeqFormat Module for determining the sequence format of the contents of a file, a string, or through a filehandle. 1.007006 metacpan
Bio::Tools::IUPAC Generates unique sequence objects or regular expressions from an ambiguous IUPAC sequence 1.007006 metacpan
Bio::Tools::Lucy Object for analyzing the output from Lucy, a vector and quality trimming program from TIGR 1.007006 metacpan
Bio::Tools::MZEF Results of one MZEF run 1.007006 metacpan
Bio::Tools::Match Parses output from Transfac's match(TM) 1.007006 metacpan
Bio::Tools::OddCodes Object holding alternative alphabet coding for one protein sequence 1.007006 metacpan
Bio::Tools::Phylo::Gerp Parses output from GERP 1.007006 metacpan
Bio::Tools::Phylo::Molphy parser for Molphy output 1.007006 metacpan
Bio::Tools::Phylo::Molphy::Result container for data parsed from a ProtML run 1.007006 metacpan
Bio::Tools::Phylo::Phylip::ProtDist parser for ProtDist output 1.007006 metacpan
Bio::Tools::Prediction::Exon A predicted exon feature 1.007006 metacpan
Bio::Tools::Prediction::Gene a predicted gene structure feature 1.007006 metacpan
Bio::Tools::Primer3 Create input for and work with the output from the program primer3 1.007006 metacpan
Bio::Tools::Primer::Assessor::Base base class for common assessor things 1.007006 metacpan
Bio::Tools::Primer::AssessorI interface for assessing primer pairs 1.007006 metacpan
Bio::Tools::Primer::Feature position of a single primer 1.007006 metacpan
Bio::Tools::Primer::Pair two primers on left and right side 1.007006 metacpan
Bio::Tools::Prints Parser for FingerPRINTScanII program 1.007006 metacpan
Bio::Tools::Profile parse Profile output 1.007006 metacpan
Bio::Tools::Promoterwise parser for Promoterwise tab format output 1.007006 metacpan
Bio::Tools::PrositeScan Parser for ps_scan result 1.007006 metacpan
Bio::Tools::Pseudowise Results of one Pseudowise run 1.007006 metacpan
Bio::Tools::QRNA A Parser for qrna output 1.007006 metacpan
Bio::Tools::RandomDistFunctions A set of routines useful for generating random data in different distributions 1.007006 metacpan
Bio::Tools::RepeatMasker a parser for RepeatMasker output 1.007006 metacpan
Bio::Tools::Run::Analysis Module representing any (remote or local) analysis tool 1.007006 metacpan
Bio::Tools::Run::AnalysisFactory A directory of analysis tools 1.007006 metacpan
Bio::Tools::Run::GenericParameters An object for the parameters used to run programs 1.007006 metacpan
Bio::Tools::Run::ParametersI A Base object for the parameters used to run programs 1.007006 metacpan
Bio::Tools::Run::Phylo::PhyloBase 1.007006 metacpan
Bio::Tools::Run::WrapperBase A Base object for wrappers around executables 1.007006 metacpan
Bio::Tools::Seg parse C<seg> output 1.007006 metacpan
Bio::Tools::SeqPattern represent a sequence pattern or motif 1.007006 metacpan
Bio::Tools::SeqPattern::Backtranslate reverse translate protein patterns 1.007006 metacpan
Bio::Tools::SeqStats Object holding statistics for one particular sequence 1.007006 metacpan
Bio::Tools::SeqWords Object holding n-mer statistics for a sequence 1.007006 metacpan
Bio::Tools::Sigcleave Bioperl object for sigcleave analysis 1.007006 metacpan
Bio::Tools::Signalp parser for Signalp output 1.007006 metacpan
Bio::Tools::Signalp::ExtendedSignalp enhanced parser for Signalp output 1.007006 metacpan
Bio::Tools::Sim4::Exon A single exon determined by an alignment 1.007006 metacpan
Bio::Tools::Sim4::Results Results of one Sim4 run 1.007006 metacpan
Bio::Tools::Spidey::Exon A single exon determined by an alignment 1.007006 metacpan
Bio::Tools::Spidey::Results Results of a Spidey run 1.007006 metacpan
Bio::Tools::TandemRepeatsFinder a parser for Tandem Repeats Finder output 1.007006 metacpan
Bio::Tools::TargetP Results of one TargetP run 1.007006 metacpan
Bio::Tools::Tmhmm parse TMHMM output (TransMembrane HMM) 1.007006 metacpan
Bio::Tools::ipcress Parse ipcress output and make features 1.007006 metacpan
Bio::Tools::isPcr Parse isPcr output and make features 1.007006 metacpan
Bio::Tools::pICalculator calculate the isoelectric point of a protein 1.007006 metacpan
Bio::Tools::tRNAscanSE A parser for tRNAscan-SE output 1.007006 metacpan
Bio::Tree::AnnotatableNode A Tree Node with support for annotation 1.007006 metacpan
Bio::Tree::Compatible Testing compatibility of phylogenetic trees with nested taxa. 1.007006 metacpan
Bio::Tree::DistanceFactory Construct a tree using distance based methods 1.007006 metacpan
Bio::Tree::Node A Simple Tree Node 1.007006 metacpan
Bio::Tree::NodeI Interface describing a Tree Node 1.007006 metacpan
Bio::Tree::NodeNHX A Simple Tree Node with support for NHX tags 1.007006 metacpan
Bio::Tree::RandomFactory TreeFactory for generating Random Trees 1.007006 metacpan
Bio::Tree::Statistics Calculate certain statistics for a Tree 1.007006 metacpan
Bio::Tree::Tree An implementation of the TreeI interface. 1.007006 metacpan
Bio::Tree::TreeFunctionsI Decorated Interface implementing basic Tree exploration methods 1.007006 metacpan
Bio::Tree::TreeI A Tree object suitable for lots of things, designed originally for Phylogenetic Trees. 1.007006 metacpan
Bio::TreeIO Parser for Tree files 1.007006 metacpan
Bio::TreeIO::NewickParser newick string parser 1.007006 metacpan
Bio::TreeIO::TreeEventBuilder Build Bio::Tree::Tree's and Bio::Tree::Node's from Events 1.007006 metacpan
Bio::TreeIO::cluster A TreeIO driver module for parsing Algorithm::Cluster::treecluster() output 1.007006 metacpan
Bio::TreeIO::lintree Parser for lintree output trees 1.007006 metacpan
Bio::TreeIO::newick parsing and writing of Newick/PHYLIP/New Hampshire format 1.007006 metacpan
Bio::TreeIO::nexus A TreeIO driver module for parsing Nexus tree output from PAUP 1.007006 metacpan
Bio::TreeIO::nhx TreeIO implementation for parsing Newick/New Hampshire eXtendend (NHX) format. 1.007006 metacpan
Bio::TreeIO::pag Bio::TreeIO driver for Pagel format 1.007006 metacpan
Bio::TreeIO::phyloxml TreeIO implementation for parsing PhyloXML format. 1.007006 metacpan
Bio::TreeIO::tabtree A simple output format which displays a tree as an ASCII drawing 1.007006 metacpan
Bio::UpdateableSeqI Descendant of Bio::SeqI that allows updates 1.007006 metacpan
Bio::WebAgent A base class for Web (any protocol) access 1.007006 metacpan
BioPerl Perl modules for biology 1.007006 metacpan

Provides

Name File View
Bio::AnalysisI::JobI lib/Bio/AnalysisI.pm metacpan
Bio::DB::Indexed::Stream lib/Bio/DB/IndexedBase.pm metacpan
Bio::PrimarySeq::Fasta lib/Bio/DB/Fasta.pm metacpan
Bio::Seq::PrimaryQual::Qual lib/Bio/DB/Qual.pm metacpan
Bio::Tools::Run::Analysis::Job lib/Bio/Tools/Run/Analysis.pm metacpan
Bio::Tools::Run::Analysis::Utils lib/Bio/Tools/Run/Analysis.pm metacpan

Other Files

Changes metacpan
MANIFEST metacpan
META.json metacpan
META.yml metacpan
Makefile.PL metacpan
README.md metacpan
dist.ini metacpan