📦 libbio-perl-perl

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Bio::Align::AlignI(3pm)An interface for describing sequence alignments.✨
Bio::Align::DNAStatistics(3pm)Calculate some statistics for a DNA alignment✨
Bio::Align::PairwiseStatistics(3pm)Base statistic object for Pairwise Alignments✨
Bio::Align::ProteinStatistics(3pm)Calculate Protein Alignment statistics (mostly distances)✨
Bio::Align::StatisticsI(3pm)Calculate some statistics for an alignment✨
Bio::Align::Utilities(3pm)A collection of utilities regarding converting and manipulating alignment objects✨
Bio::AlignIO(3pm)Handler for AlignIO Formats✨
Bio::AlignIO::arp(3pm)ARP MSA Sequence input/output stream✨
Bio::AlignIO::bl2seq(3pm)bl2seq sequence input/output stream✨
Bio::AlignIO::clustalw(3pm)clustalw sequence input/output stream✨
Bio::AlignIO::emboss(3pm)Parse EMBOSS alignment output (from applications water and needle)✨
Bio::AlignIO::fasta(3pm)fasta MSA Sequence input/output stream✨
Bio::AlignIO::Handler::GenericAlignHandler(3pm)Bio::HandlerI-based generic data handler class for alignment-based data✨
Bio::AlignIO::largemultifasta(3pm)Largemultifasta MSA Sequence input/output stream✨
Bio::AlignIO::maf(3pm)Multiple Alignment Format sequence input stream✨
Bio::AlignIO::mase(3pm)mase sequence input/output stream✨
Bio::AlignIO::mega(3pm)Parse and Create MEGA format data files✨
Bio::AlignIO::meme(3pm)meme sequence input/output stream✨
Bio::AlignIO::metafasta(3pm)Metafasta MSA Sequence input/output stream✨
Bio::AlignIO::msf(3pm)msf sequence input/output stream✨
Bio::AlignIO::nexus(3pm)NEXUS format sequence input/output stream✨
Bio::AlignIO::pfam(3pm)pfam sequence input/output stream✨
Bio::AlignIO::phylip(3pm)PHYLIP format sequence input/output stream✨
Bio::AlignIO::po(3pm)po MSA Sequence input/output stream✨
Bio::AlignIO::proda(3pm)proda sequence input/output stream This provides the basic capabilities to parse the output alignments from the ProDA multiple sequence alignment program (http://proda.stanford.edu)✨
Bio::AlignIO::prodom(3pm)prodom sequence input/output stream✨
Bio::AlignIO::psi(3pm)Read/Write PSI-BLAST profile alignment files✨
Bio::AlignIO::selex(3pm)selex sequence input/output stream✨
Bio::AlignIO::xmfa(3pm)XMFA MSA Sequence input/output stream✨
Bio::AnalysisI(3pm)An interface to any (local or remote) analysis tool✨
Bio::AnalysisParserI(3pm)Generic analysis output parser interface✨
Bio::AnalysisResultI(3pm)Interface for analysis result objects✨
Bio::AnnotatableI(3pm)the base interface an annotatable object must implement✨
Bio::Annotation::AnnotationFactory(3pm)Instantiates a new Bio::AnnotationI (or derived class) through a factory✨
Bio::Annotation::Collection(3pm)Default Perl implementation of AnnotationCollectionI✨
Bio::Annotation::Comment(3pm)A comment object, holding text✨
Bio::Annotation::DBLink(3pm)untyped links between databases✨
Bio::Annotation::OntologyTerm(3pm)An ontology term adapted to AnnotationI✨
Bio::Annotation::Reference(3pm)Specialised DBLink object for Literature References✨
Bio::Annotation::Relation(3pm)Relationship (pairwise) with other objects SeqI and NodeI;✨
Bio::Annotation::SimpleValue(3pm)A simple scalar✨
Bio::Annotation::StructuredValue(3pm)A scalar with embedded structured information✨
Bio::Annotation::TagTree(3pm)AnnotationI with tree-like hierarchal key-value relationships ('structured tags') that can be represented as simple text.✨
Bio::Annotation::Target(3pm)Provides an object which represents a target (ie, a similarity hit) from one object to something in another database✨
Bio::Annotation::Tree(3pm)Provide a tree as an annotation to a Bio::AnnotatableI object✨
Bio::Annotation::TypeManager(3pm)Manages types for annotation collections✨
Bio::AnnotationCollectionI(3pm)Interface for annotation collections✨
Bio::AnnotationI(3pm)Annotation interface✨
Bio::CodonUsage::IO(3pm)for reading and writing codon usage tables to file✨
Bio::CodonUsage::Table(3pm)for access to the Codon usage Database at http://www.kazusa.or.jp/codon.✨
Bio::Das::FeatureTypeI(3pm)Simple interface to Sequence Ontology feature types✨
Bio::Das::SegmentI(3pm)DAS-style access to a feature database✨
Bio::DasI(3pm)DAS-style access to a feature database✨
Bio::DB::DBFetch(3pm)Database object for retrieving using the dbfetch script✨
Bio::DB::Failover(3pm)A Bio::DB::RandomAccessI compliant class which wraps a prioritized list of DBs✨
Bio::DB::Fasta(3pm)Fast indexed access to fasta files✨
Bio::DB::FileCache(3pm)In file cache for BioSeq objects✨
Bio::DB::Flat(3pm)Interface for indexed flat files✨
Bio::DB::Flat::BDB(3pm)Interface for BioHackathon standard BDB-indexed flat file✨
Bio::DB::Flat::BDB::embl(3pm)embl adaptor for Open-bio standard BDB-indexed flat file✨
Bio::DB::Flat::BDB::fasta(3pm)fasta adaptor for Open-bio standard BDB-indexed flat file✨
Bio::DB::Flat::BDB::genbank(3pm)genbank adaptor for Open-bio standard BDB-indexed flat file✨
Bio::DB::Flat::BDB::swiss(3pm)swissprot adaptor for Open-bio standard BDB-indexed flat file✨
Bio::DB::Flat::BinarySearch(3pm)BinarySearch search indexing system for sequence files✨
Bio::DB::GenericWebAgent(3pm)helper base class for parameter-based remote server access and response retrieval.✨
Bio::DB::GFF::Util::Binning(3pm)binning utility for Bio::DB::GFF index✨
Bio::DB::GFF::Util::Rearrange(3pm)rearrange utility✨
Bio::DB::IndexedBase(3pm)Base class for modules using indexed sequence files✨
Bio::DB::InMemoryCache(3pm)Abstract interface for a sequence database✨
Bio::DB::LocationI(3pm)A RandomAccessI-like abstract interface for retrieving location data from a sequence database and returning Bio::LocationI objects✨
Bio::DB::Qual(3pm)Fast indexed access to quality files✨
Bio::DB::Query::WebQuery(3pm)Helper class for web-based sequence queryies✨
Bio::DB::QueryI(3pm)Object Interface to queryable sequence databases✨
Bio::DB::RandomAccessI(3pm)Abstract interface for a sequence database✨
Bio::DB::ReferenceI(3pm)A RandomAccessI-like abstract interface for retrieving Reference data from a sequence database and returning Bio::Annotation::Reference objects✨
Bio::DB::Registry(3pm)Access to the Open Bio Database Access registry scheme✨
Bio::DB::SeqI(3pm)Abstract Interface for Sequence databases✨
Bio::DB::Taxonomy(3pm)Access to a taxonomy database✨
Bio::DB::Taxonomy::flatfile(3pm)Use the NCBI taxonomy from local indexed flat files✨
Bio::DB::Taxonomy::greengenes(3pm)Use the Greengenes taxonomy✨
Bio::DB::Taxonomy::list(3pm)An implementation of Bio::DB::Taxonomy that accepts lists of words to build a database✨
Bio::DB::Taxonomy::silva(3pm)Use the Silva taxonomy✨
Bio::DB::UpdateableSeqI(3pm)An interface for writing to a database of sequences.✨
Bio::DB::WebDBSeqI(3pm)Object Interface to generalize Web Databases for retrieving sequences✨
Bio::DBLinkContainerI(3pm)Abstract interface for any object wanting to use database cross references✨
Bio::DescribableI(3pm)interface for objects with human readable names and descriptions✨
Bio::Event::EventGeneratorI(3pm)This interface describes the basic event generator class.✨
Bio::Event::EventHandlerI(3pm)An Event Handler Interface✨
Bio::Factory::AnalysisI(3pm)An interface to analysis tool factory✨
Bio::Factory::ApplicationFactoryI(3pm)Interface class for Application Factories✨
Bio::Factory::DriverFactory(3pm)Base class for factory classes loading drivers✨
Bio::Factory::FTLocationFactory(3pm)A FeatureTable Location Parser✨
Bio::Factory::LocationFactoryI(3pm)A factory interface for generating locations from a string✨
Bio::Factory::ObjectBuilderI(3pm)Interface for an object builder✨
Bio::Factory::ObjectFactory(3pm)Instantiates a new Bio::Root::RootI (or derived class) through a factory✨
Bio::Factory::ObjectFactoryI(3pm)A General object creator factory✨
Bio::Factory::SeqAnalysisParserFactory(3pm)class capable of creating SeqAnalysisParserI compliant parsers✨
Bio::Factory::SeqAnalysisParserFactoryI(3pm)interface describing objects capable of creating SeqAnalysisParserI compliant parsers✨
Bio::Factory::SequenceFactoryI(3pm)This interface allows for generic building of sequences in factories which create sequences (like SeqIO)✨
Bio::Factory::SequenceProcessorI(3pm)Interface for chained sequence processing algorithms✨
Bio::Factory::SequenceStreamI(3pm)Interface describing the basics of a Sequence Stream.✨
Bio::Factory::TreeFactoryI(3pm)Factory Interface for getting and writing trees from/to a data stream✨
Bio::FeatureHolderI(3pm)the base interface an object with features must implement✨
Bio::HandlerBaseI(3pm)Interface class for handler methods which interact with any event-driven parsers (drivers).✨
Bio::IdCollectionI(3pm)interface for objects with multiple identifiers✨
Bio::IdentifiableI(3pm)interface for objects with identifiers✨
Bio::Index::Abstract(3pm)Abstract interface for indexing a flat file✨
Bio::Index::AbstractSeq(3pm)base class for AbstractSeq✨
Bio::Index::Blast(3pm)Indexes Blast reports and supports retrieval based on query accession(s)✨
Bio::Index::BlastTable(3pm)Indexes tabular Blast reports (-m 8 or -m 9 format) and supports retrieval based on query accession(s)✨
Bio::Index::EMBL(3pm)Interface for indexing (multiple) EMBL/Swissprot .dat files (i.e. flat file EMBL/Swissprot format).✨
Bio::Index::Fasta(3pm)Interface for indexing (multiple) fasta files✨
Bio::Index::Fastq(3pm)Interface for indexing (multiple) fastq files✨
Bio::Index::GenBank(3pm)Interface for indexing one or more GenBank files (i.e. flat file GenBank format).✨
Bio::Index::Qual(3pm)Interface for indexing (multiple) fasta qual files✨
Bio::Index::SwissPfam(3pm)Interface for indexing swisspfam files✨
Bio::Index::Swissprot(3pm)Interface for indexing one or more Swissprot files.✨
Bio::LocatableSeq(3pm)A Bio::PrimarySeq object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq.✨
Bio::Location::Atomic(3pm)Implementation of a Atomic Location on a Sequence✨
Bio::Location::AvWithinCoordPolicy(3pm)class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise✨
Bio::Location::CoordinatePolicyI(3pm)Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location✨
Bio::Location::Fuzzy(3pm)Implementation of a Location on a Sequence which has unclear start and/or end locations✨
Bio::Location::FuzzyLocationI(3pm)Abstract interface of a Location on a Sequence which has unclear start/end location✨
Bio::Location::NarrowestCoordPolicy(3pm)class implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range✨
Bio::Location::Simple(3pm)Implementation of a Simple Location on a Sequence✨
Bio::Location::Split(3pm)Implementation of a Location on a Sequence which has multiple locations (start/end points)✨
Bio::Location::SplitLocationI(3pm)Abstract interface of a Location on a Sequence which has multiple locations (start/end points)✨
Bio::Location::WidestCoordPolicy(3pm)class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable range✨
Bio::LocationI(3pm)Abstract interface of a Location on a Sequence✨
Bio::Matrix::Generic(3pm)A generic matrix implementation✨
Bio::Matrix::IO(3pm)A factory for Matrix parsing✨
Bio::Matrix::IO::mlagan(3pm)A parser for the mlagan substitution matrix✨
Bio::Matrix::IO::phylip(3pm)A parser for PHYLIP distance matricies✨
Bio::Matrix::IO::scoring(3pm)A parser for PAM/BLOSUM matricies✨
Bio::Matrix::MatrixI(3pm)An interface for describing a Matrix✨
Bio::Matrix::Mlagan(3pm)A generic matrix with mlagan fields✨
Bio::Matrix::PhylipDist(3pm)A Phylip Distance Matrix object✨
Bio::Matrix::PSM::InstanceSite(3pm)A PSM site occurrence✨
Bio::Matrix::PSM::InstanceSiteI(3pm)InstanceSite interface, holds an instance of a PSM✨
Bio::Matrix::PSM::IO(3pm)PSM parser✨
Bio::Matrix::PSM::IO::mast(3pm)PSM mast parser implementation✨
Bio::Matrix::PSM::IO::masta(3pm)motif fasta format parser✨
Bio::Matrix::PSM::IO::meme(3pm)PSM meme parser implementation✨
Bio::Matrix::PSM::IO::psiblast(3pm)PSM psiblast parser✨
Bio::Matrix::PSM::IO::transfac(3pm)PSM transfac parser✨
Bio::Matrix::PSM::ProtMatrix(3pm)SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) with log-odds scoring information.✨
Bio::Matrix::PSM::ProtPsm(3pm)handle combination of site matricies✨
Bio::Matrix::PSM::Psm(3pm)handle combination of site matricies✨
Bio::Matrix::PSM::PsmHeader(3pm)PSM mast parser implementation✨
Bio::Matrix::PSM::PsmHeaderI(3pm)handles the header data from a PSM file✨
Bio::Matrix::PSM::PsmI(3pm)abstract interface to handler of site matricies✨
Bio::Matrix::PSM::SiteMatrix(3pm)SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds✨
Bio::Matrix::PSM::SiteMatrixI(3pm)SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds✨
Bio::Matrix::Scoring(3pm)Object which can hold scoring matrix information✨
Bio::Ontology::DocumentRegistry(3pm)Keep track of where to find ontologies. Allows lookups by name.✨
Bio::Ontology::GOterm(3pm)representation of GO terms✨
Bio::Ontology::InterProTerm(3pm)Implementation of InterProI term interface✨
Bio::Ontology::OBOEngine(3pm)An Ontology Engine for OBO style flat file format from the Gene Ontology Consortium✨
Bio::Ontology::OBOterm(3pm)representation of OBO terms✨
Bio::Ontology::Ontology(3pm)standard implementation of an Ontology✨
Bio::Ontology::OntologyEngineI(3pm)Interface a minimal Ontology implementation should satisfy✨
Bio::Ontology::OntologyI(3pm)Interface for an ontology implementation✨
Bio::Ontology::OntologyStore(3pm)A repository of ontologies✨
Bio::Ontology::Path(3pm)a path for an ontology term graph✨
Bio::Ontology::PathI(3pm)Interface for a path between ontology terms✨
Bio::Ontology::Relationship(3pm)a relationship for an ontology✨
Bio::Ontology::RelationshipFactory(3pm)Instantiates a new Bio::Ontology::RelationshipI (or derived class) through a factory✨
Bio::Ontology::RelationshipI(3pm)Interface for a relationship between ontology terms✨
Bio::Ontology::RelationshipType(3pm)a relationship type for an ontology✨
Bio::Ontology::SimpleGOEngine::GraphAdaptor(3pm)Graph adaptor for Bio::Ontology::SimpleGOEngine✨
Bio::Ontology::SimpleOntologyEngine(3pm)Implementation of OntologyEngineI interface✨
Bio::Ontology::Term(3pm)implementation of the interface for ontology terms✨
Bio::Ontology::TermFactory(3pm)Instantiates a new Bio::Ontology::TermI (or derived class) through a factory✨
Bio::Ontology::TermI(3pm)interface for ontology terms✨
Bio::OntologyIO(3pm)Parser factory for Ontology formats✨
Bio::OntologyIO::dagflat(3pm)a base class parser for GO flat-file type formats✨
Bio::OntologyIO::goflat(3pm)a parser for the Gene Ontology flat-file format✨
Bio::OntologyIO::Handlers::BaseSAXHandler(3pm)base class for SAX Handlers✨
Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler(3pm)parse an InterPro XML file and persist the resulting terms to a Biosql database✨
Bio::OntologyIO::Handlers::InterProHandler(3pm)XML handler class for InterProParser✨
Bio::OntologyIO::InterProParser(3pm)Parser for InterPro xml files.✨
Bio::OntologyIO::obo(3pm)parser for OBO flat-file format✨
Bio::OntologyIO::simplehierarchy(3pm)a base class parser for simple hierarchy-by-indentation type formats✨
Bio::OntologyIO::soflat(3pm)a parser for the Sequence Ontology flat-file format✨
Bio::ParameterBaseI(3pm)Simple interface class for any parameter-related data such as IDs, database name, program arguments, and other odds and ends.✨
Bio::PrimarySeq(3pm)Bioperl lightweight sequence object✨
Bio::PrimarySeqI(3pm)Interface definition for a Bio::PrimarySeq✨
Bio::PullParserI(3pm)A base module for fast 'pull' parsing✨
Bio::Range(3pm)Pure perl RangeI implementation✨
Bio::RangeI(3pm)Range interface✨
Bio::Root::Exception(3pm)BioPerl exceptions✨
Bio::Root::HTTPget(3pm)module for fallback HTTP get operations when LWP:: is unavailable✨
Bio::Root::IO(3pm)BioPerl base IO handling class✨
Bio::Root::Root(3pm)implementation of Bio::Root::RootI interface✨
Bio::Root::RootI(3pm)base interface for all BioPerl classes✨
Bio::Root::Storable(3pm)Safely store/retrieve objects from disk✨
Bio::Root::Test(3pm)common base for all BioPerl test scripts✨
Bio::Root::TestObject(3pm)An implementation of TestInterface✨
Bio::Root::Utilities(3pm)general-purpose utilities✨
Bio::Root::Version(3pm)don't use, get version from each module✨