Modules

• Bio::Align::AlignI - An interface for describing sequence alignments.
• Bio::Align::DNAStatistics - Calculate some statistics for a DNA alignment
• Bio::Align::PairwiseStatistics - Base statistic object for Pairwise Alignments
• Bio::Align::ProteinStatistics - Calculate Protein Alignment statistics (mostly distances)
• Bio::Align::StatisticsI - Calculate some statistics for an alignment
• Bio::Align::Utilities - A collection of utilities regarding converting and manipulating alignment objects
• Bio::AlignIO - Handler for AlignIO Formats
• Bio::AlignIO::Handler::GenericAlignHandler - Bio::HandlerI-based generic data handler class for alignment-based data
• Bio::AlignIO::arp - ARP MSA Sequence input/output stream
• Bio::AlignIO::bl2seq - bl2seq sequence input/output stream
• Bio::AlignIO::clustalw - clustalw sequence input/output stream
• Bio::AlignIO::emboss - Parse EMBOSS alignment output (from applications water and needle)
• Bio::AlignIO::fasta - fasta MSA Sequence input/output stream
• Bio::AlignIO::largemultifasta - Largemultifasta MSA Sequence input/output stream
• Bio::AlignIO::maf - Multiple Alignment Format sequence input stream
• Bio::AlignIO::mase - mase sequence input/output stream
• Bio::AlignIO::mega - Parse and Create MEGA format data files
• Bio::AlignIO::meme - meme sequence input/output stream
• Bio::AlignIO::metafasta - Metafasta MSA Sequence input/output stream
• Bio::AlignIO::msf - msf sequence input/output stream
• Bio::AlignIO::nexus - NEXUS format sequence input/output stream
• Bio::AlignIO::pfam - pfam sequence input/output stream
• Bio::AlignIO::phylip - PHYLIP format sequence input/output stream
• Bio::AlignIO::po - po MSA Sequence input/output stream
• Bio::AlignIO::proda - proda sequence input/output stream
• Bio::AlignIO::prodom - prodom sequence input/output stream
• Bio::AlignIO::psi - Read/Write PSI-BLAST profile alignment files
• Bio::AlignIO::selex - selex sequence input/output stream
• Bio::AlignIO::stockholm - stockholm sequence input/output stream
• Bio::AlignIO::xmfa - XMFA MSA Sequence input/output stream
• Bio::AnalysisI - An interface to any (local or remote) analysis tool
• Bio::AnalysisParserI - Generic analysis output parser interface
• Bio::AnalysisResultI - Interface for analysis result objects
• Bio::AnnotatableI - the base interface an annotatable object must implement
• Bio::Annotation::AnnotationFactory - Instantiates a new Bio::AnnotationI (or derived class) through a factory
• Bio::Annotation::Collection - Default Perl implementation of AnnotationCollectionI
• Bio::Annotation::Comment - A comment object, holding text
• Bio::Annotation::DBLink - untyped links between databases
• Bio::Annotation::OntologyTerm - An ontology term adapted to AnnotationI
• Bio::Annotation::Reference - Specialised DBLink object for Literature References
• Bio::Annotation::Relation - Relationship (pairwise) with other objects SeqI and NodeI;
• Bio::Annotation::SimpleValue - A simple scalar
• Bio::Annotation::StructuredValue - A scalar with embedded structured information
• Bio::Annotation::TagTree - AnnotationI with tree-like hierarchal key-value relationships ('structured tags') that can be represented as simple text.
• Bio::Annotation::Target - Provides an object which represents a target (ie, a similarity hit) from one object to something in another database
• Bio::Annotation::Tree - Provide a tree as an annotation to a Bio::AnnotatableI object
• Bio::Annotation::TypeManager - Manages types for annotation collections
• Bio::AnnotationCollectionI - Interface for annotation collections
• Bio::AnnotationI - Annotation interface
• Bio::Assembly::Contig - Perl module to hold and manipulate sequence assembly contigs.
• Bio::Assembly::ContigAnalysis - Perform analysis on sequence assembly contigs.
• Bio::Assembly::IO - Handler for Assembly::IO Formats
• Bio::Assembly::IO::ace - module to load ACE files from various assembly programs
• Bio::Assembly::IO::phrap - driver to load phrap.out files.
• Bio::Assembly::IO::tigr - Driver to read and write assembly files in the TIGR Assembler v2 default format.
• Bio::Assembly::Scaffold - Perl module to hold and manipulate sequence assembly data.
• Bio::Assembly::ScaffoldI - Abstract Inteface of Sequence Assemblies
• Bio::Assembly::Singlet - Perl module to hold and manipulate singlets from sequence assembly contigs.
• Bio::Assembly::Tools::ContigSpectrum - create and manipulate contig spectra
• Bio::Biblio - A Bibliographic Query Service module
• Bio::Biblio::Article - Representation of a general article
• Bio::Biblio::BiblioBase - An abstract base for other biblio classes
• Bio::Biblio::Book - Representation of a book
• Bio::Biblio::BookArticle - Representation of a book article
• Bio::Biblio::IO - Handling the bibliographic references
• Bio::Biblio::IO::medline2ref - A converter of a raw hash to MEDLINE citations
• Bio::Biblio::IO::medlinexml - A converter of XML files with MEDLINE citations
• Bio::Biblio::IO::pubmed2ref - A converter of a raw hash to PUBMED citations
• Bio::Biblio::IO::pubmedxml - A converter of XML files with PUBMED citations
• Bio::Biblio::Journal - Representation of a journal
• Bio::Biblio::JournalArticle - Representation of a journal article
• Bio::Biblio::MedlineArticle - Representation of a MEDLINE article
• Bio::Biblio::MedlineBook - Representation of a MEDLINE book
• Bio::Biblio::MedlineBookArticle - Representation of a MEDLINE book article
• Bio::Biblio::MedlineJournal - Representation of a MEDLINE journal
• Bio::Biblio::MedlineJournalArticle - Representation of a MEDLINE journal article
• Bio::Biblio::Organisation - Representation of an organisation
• Bio::Biblio::Patent - Representation of a patent
• Bio::Biblio::Person - Representation of a person
• Bio::Biblio::Proceeding - Representation of a conference proceeding
• Bio::Biblio::Provider - Representation of a general provider
• Bio::Biblio::PubmedArticle - Representation of a PUBMED article
• Bio::Biblio::PubmedBookArticle - Representation of a PUBMED book article
• Bio::Biblio::PubmedJournalArticle - Representation of a PUBMED journal article
• Bio::Biblio::Ref - Representation of a bibliographic reference
• Bio::Biblio::Service - Representation of a provider of type service
• Bio::Biblio::TechReport - Representation of a technical report
• Bio::Biblio::Thesis - Representation of thesis
• Bio::Biblio::WebResource - Representation of a web resource
• Bio::Cluster::ClusterFactory - Instantiates a new Bio::ClusterI (or derived class) through a factory
• Bio::Cluster::FamilyI - Family Interface
• Bio::Cluster::SequenceFamily - Sequence Family object
• Bio::Cluster::UniGene - UniGene object
• Bio::Cluster::UniGeneI - abstract interface of UniGene object
• Bio::ClusterI - Cluster Interface
• Bio::ClusterIO - Handler for Cluster Formats
• Bio::ClusterIO::dbsnp - dbSNP input stream
• Bio::ClusterIO::unigene - UniGene input stream
• Bio::CodonUsage::IO - for reading and writing codon usage tables to file
• Bio::CodonUsage::Table - for access to the Codon usage Database at http://www.kazusa.or.jp/codon.
• Bio::Coordinate::Chain - Mapping locations through a chain of coordinate mappers
• Bio::Coordinate::Collection - Noncontinuous match between two coordinate sets
• Bio::Coordinate::ExtrapolatingPair - Continuous match between two coordinate sets
• Bio::Coordinate::GeneMapper - transformations between gene related coordinate systems
• Bio::Coordinate::Graph - Finds shortest path between nodes in a graph
• Bio::Coordinate::MapperI - Interface describing coordinate mappers
• Bio::Coordinate::Pair - Continuous match between two coordinate sets
• Bio::Coordinate::Result - Results from coordinate transformation
• Bio::Coordinate::Result::Gap - Another name for Bio::Location::Simple
• Bio::Coordinate::Result::Match - Another name for Bio::Location::Simple
• Bio::Coordinate::ResultI - Interface to identify coordinate mapper results
• Bio::Coordinate::Utils - Additional methods to create Bio::Coordinate objects
• Bio::DB::Ace - Database object interface to ACeDB servers
• Bio::DB::Biblio::biofetch - A BioFetch-based access to a bibliographic citation retrieval
• Bio::DB::Biblio::eutils - Access to PubMed's bibliographic query service
• Bio::DB::Biblio::soap - A SOAP-based access to a bibliographic query service
• Bio::DB::BiblioI - An interface to a Bibliographic Query Service
• Bio::DB::BioFetch - Database object interface to BioFetch retrieval
• Bio::DB::CUTG - for access to the Codon usage Database at http://www.kazusa.or.jp/codon.
• Bio::DB::DBFetch - Database object for retrieving using the dbfetch script
• Bio::DB::EMBL - Database object interface for EMBL entry retrieval
• Bio::DB::EUtilities - webagent which interacts with and retrieves data from NCBI's eUtils
• Bio::DB::EntrezGene - Database object interface to Entrez Gene
• Bio::DB::Expression - DESCRIPTION of Object
• Bio::DB::Expression::geo - *** DESCRIPTION of Class
• Bio::DB::Failover - A Bio::DB::RandomAccessI compliant class which wraps a prioritized list of DBs
• Bio::DB::Fasta - Fast indexed access to a directory of fasta files
• Bio::DB::FileCache - In file cache for BioSeq objects
• Bio::DB::Flat - Interface for indexed flat files
• Bio::DB::Flat::BDB - Interface for BioHackathon standard BDB-indexed flat file
• Bio::DB::Flat::BDB::embl - embl adaptor for Open-bio standard BDB-indexed flat file
• Bio::DB::Flat::BDB::fasta - fasta adaptor for Open-bio standard BDB-indexed flat file
• Bio::DB::Flat::BDB::genbank - genbank adaptor for Open-bio standard BDB-indexed flat file
• Bio::DB::Flat::BDB::swiss - swissprot adaptor for Open-bio standard BDB-indexed flat file
• Bio::DB::Flat::BinarySearch - BinarySearch search indexing system for sequence files
• Bio::DB::GFF - Storage and retrieval of sequence annotation data
• Bio::DB::GFF::Adaptor::ace - ace interface (for multiple inheritance)
• Bio::DB::GFF::Adaptor::berkeleydb - Bio::DB::GFF database adaptor for in-memory databases
• Bio::DB::GFF::Adaptor::berkeleydb::iterator - iterator for Bio::DB::GFF::Adaptor::berkeleydb
• Bio::DB::GFF::Adaptor::biofetch - Cache BioFetch objects in a Bio::DB::GFF database
• Bio::DB::GFF::Adaptor::biofetch_oracle - Cache BioFetch objects in a Bio::DB::GFF database
• Bio::DB::GFF::Adaptor::dbi - Database adaptor for DBI (SQL) databases
• Bio::DB::GFF::Adaptor::dbi::caching_handle - Cache for database handles
• Bio::DB::GFF::Adaptor::dbi::iterator - iterator for Bio::DB::GFF::Adaptor::dbi
• Bio::DB::GFF::Adaptor::dbi::mysql - Database adaptor for a specific mysql schema
• Bio::DB::GFF::Adaptor::dbi::mysqlace - Unholy union between mysql GFF database and acedb database
• Bio::DB::GFF::Adaptor::dbi::mysqlcmap - Database adaptor for an integraded CMap/GBrowse mysql schema
• Bio::DB::GFF::Adaptor::dbi::mysqlopt - Deprecated database adaptor
• Bio::DB::GFF::Adaptor::dbi::oracle - Database adaptor for a specific oracle schema
• Bio::DB::GFF::Adaptor::dbi::oracleace - Unholy union between oracle GFF database and acedb database
• Bio::DB::GFF::Adaptor::dbi::pg - Database adaptor for a specific postgres schema
• Bio::DB::GFF::Adaptor::dbi::pg_fts - Database adaptor for a specific postgres schema with a TSearch2 implementation
• Bio::DB::GFF::Adaptor::memory - Bio::DB::GFF database adaptor for in-memory databases
• Bio::DB::GFF::Adaptor::memory::feature_serializer - utility methods for serializing and deserializing GFF features
• Bio::DB::GFF::Adaptor::memory::iterator - iterator for Bio::DB::GFF::Adaptor::memory
• Bio::DB::GFF::Aggregator - Aggregate GFF groups into composite features
• Bio::DB::GFF::Aggregator::alignment - Alignment aggregator
• Bio::DB::GFF::Aggregator::clone - Clone aggregator
• Bio::DB::GFF::Aggregator::coding - The Coding Region Aggregator
• Bio::DB::GFF::Aggregator::gene - Sequence Ontology Geene
• Bio::DB::GFF::Aggregator::match - Match aggregator
• Bio::DB::GFF::Aggregator::none - No aggregation
• Bio::DB::GFF::Aggregator::orf - An aggregator for orf regions
• Bio::DB::GFF::Aggregator::processed_transcript - Sequence Ontology Transcript
• Bio::DB::GFF::Aggregator::so_transcript - Sequence Ontology Transcript
• Bio::DB::GFF::Aggregator::transcript - Transcript aggregator
• Bio::DB::GFF::Aggregator::ucsc_acembly - UCSC acembly aggregator
• Bio::DB::GFF::Aggregator::ucsc_ensgene - UCSC ensGene aggregator
• Bio::DB::GFF::Aggregator::ucsc_genscan - UCSC genscan aggregator
• Bio::DB::GFF::Aggregator::ucsc_refgene - UCSC refGene aggregator
• Bio::DB::GFF::Aggregator::ucsc_sanger22 - UCSC sanger22 aggregator
• Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo - UCSC sanger22pseudo aggregator
• Bio::DB::GFF::Aggregator::ucsc_softberry - UCSC softberry aggregator
• Bio::DB::GFF::Aggregator::ucsc_twinscan - UCSC twinscan aggregator
• Bio::DB::GFF::Aggregator::ucsc_unigene - UCSC UniGene aggregator
• Bio::DB::GFF::Featname - The name of a feature
• Bio::DB::GFF::Feature - A relative segment identified by a feature type
• Bio::DB::GFF::Homol - A segment of DNA that is homologous to another
• Bio::DB::GFF::RelSegment - Sequence segment with relative coordinate support
• Bio::DB::GFF::Segment - Simple DNA segment object
• Bio::DB::GFF::Typename - The name of a feature type
• Bio::DB::GFF::Util::Binning - binning utility for Bio::DB::GFF index
• Bio::DB::GFF::Util::Rearrange - rearrange utility
• Bio::DB::GenBank - Database object interface to GenBank
• Bio::DB::GenPept - Database object interface to GenPept
• Bio::DB::GenericWebAgent - helper base class for parameter-based remote server access and response retrieval.
• Bio::DB::HIV - Database object interface to the Los Alamos HIV Sequence Database
• Bio::DB::HIV::HIVAnnotProcessor - Adds HIV-specific annotations to Bio::SeqIO streams
• Bio::DB::HIV::HIVQueryHelper - Routines and packages used by Bio::DB::HIV and Bio::DB::Query::HIVQuery
• Bio::DB::InMemoryCache - Abstract interface for a sequence database
• Bio::DB::LocationI - A RandomAccessI-like abstract interface for retrieving location data from a sequence database and returning Bio::LocationI objects
• Bio::DB::MeSH - Term retrieval from a Web MeSH database
• Bio::DB::NCBIHelper - A collection of routines useful for queries to NCBI databases.
• Bio::DB::Qual - Fast indexed access to a directory of quality files
• Bio::DB::Query::GenBank - Build a GenBank Entrez Query
• Bio::DB::Query::HIVQuery - Query interface to the Los Alamos HIV Sequence Database
• Bio::DB::Query::WebQuery - Helper class for web-based sequence queryies
• Bio::DB::QueryI - Object Interface to queryable sequence databases
• Bio::DB::RandomAccessI - Abstract interface for a sequence database
• Bio::DB::RefSeq - Database object interface for RefSeq retrieval
• Bio::DB::ReferenceI - A RandomAccessI-like abstract interface for retrieving Reference data from a sequence database and returning Bio::Annotation::Reference objects
• Bio::DB::Registry - Access to the Open Bio Database Access registry scheme
• Bio::DB::SeqFeature - Normalized feature for use with Bio::DB::SeqFeature::Store
• Bio::DB::SeqFeature::NormalizedFeature - Normalized feature for use with Bio::DB::SeqFeature::Store
• Bio::DB::SeqFeature::NormalizedFeatureI - Interface for normalized features
• Bio::DB::SeqFeature::NormalizedTableFeatureI - Interface for normalized features whose hierarchy is stored in a table
• Bio::DB::SeqFeature::Segment - Location-based access to genome annotation data
• Bio::DB::SeqFeature::Store - Storage and retrieval of sequence annotation data
• Bio::DB::SeqFeature::Store::DBI::Iterator - utility methods for creating and iterating over SeqFeature records
• Bio::DB::SeqFeature::Store::DBI::Pg - Mysql implementation of Bio::DB::SeqFeature::Store
• Bio::DB::SeqFeature::Store::DBI::SQLite - SQLite implementation of Bio::DB::SeqFeature::Store
• Bio::DB::SeqFeature::Store::DBI::mysql - Mysql implementation of Bio::DB::SeqFeature::Store
• Bio::DB::SeqFeature::Store::FeatureFileLoader - feature file loader for Bio::DB::SeqFeature::Store
• Bio::DB::SeqFeature::Store::GFF2Loader - GFF2 file loader for Bio::DB::SeqFeature::Store
• Bio::DB::SeqFeature::Store::GFF3Loader - GFF3 file loader for Bio::DB::SeqFeature::Store
• Bio::DB::SeqFeature::Store::LoadHelper - Internal utility for Bio::DB::SeqFeature::Store
• Bio::DB::SeqFeature::Store::Loader - Loader
• Bio::DB::SeqFeature::Store::bdb - fetch and store objects from a BerkeleyDB
• Bio::DB::SeqFeature::Store::berkeleydb - Storage and retrieval of sequence annotation data in Berkeleydb files
• Bio::DB::SeqFeature::Store::berkeleydb3 - Storage and retrieval of sequence annotation data in Berkeleydb files
• Bio::DB::SeqFeature::Store::memory - In-memory implementation of Bio::DB::SeqFeature::Store
• Bio::DB::SeqHound - Database object interface to SeqHound
• Bio::DB::SeqI - Abstract Interface for Sequence databases
• Bio::DB::SeqVersion - front end to querying databases for identifier versions
• Bio::DB::SeqVersion::gi - interface to NCBI Sequence Revision History page
• Bio::DB::SwissProt - Database object interface to SwissProt retrieval
• Bio::DB::TFBS - Access to a Transcription Factor Binding Site database
• Bio::DB::TFBS::transfac_pro - An implementation of Bio::DB::TFBS which uses local flat files for transfac pro
• Bio::DB::Taxonomy - Access to a taxonomy database
• Bio::DB::Taxonomy::entrez - Taxonomy Entrez driver
• Bio::DB::Taxonomy::flatfile - An implementation of Bio::DB::Taxonomy which uses local flat files
• Bio::DB::Taxonomy::list - An implementation of Bio::DB::Taxonomy that accepts lists of words to build a database
• Bio::DB::Universal - Artificial database that delegates to specific databases
• Bio::DB::UpdateableSeqI - An interface for writing to a database of sequences.
• Bio::DB::WebDBSeqI - Object Interface to generalize Web Databases for retrieving sequences
• Bio::DBLinkContainerI - Abstract interface for any object wanting to use database cross references
• Bio::Das::FeatureTypeI - Simple interface to Sequence Ontology feature types
• Bio::Das::SegmentI - DAS-style access to a feature database
• Bio::DasI - DAS-style access to a feature database
• Bio::DescribableI - interface for objects with human readable names and descriptions
• Bio::Event::EventGeneratorI - This interface describes the basic event generator class.
• Bio::Event::EventHandlerI - An Event Handler Interface
• Bio::Expression::Contact - DESCRIPTION of Object
• Bio::Expression::DataSet - DESCRIPTION of Object
• Bio::Expression::FeatureGroup - a set of DNA/RNA features. ISA Bio::Expression::FeatureI
• Bio::Expression::FeatureGroup::FeatureGroupMas50 - utility class for Mas50 FeatureGroup
• Bio::Expression::FeatureI - an interface class for DNA/RNA features
• Bio::Expression::FeatureSet::FeatureSetMas50 - utility class for Mas50 FeatureSet
• Bio::Expression::Platform - DESCRIPTION of Object
• Bio::Expression::ProbeI - an interface class for DNA/RNA probes
• Bio::Expression::Sample - DESCRIPTION of Object
• Bio::Factory::AnalysisI - An interface to analysis tool factory
• Bio::Factory::ApplicationFactoryI - Interface class for Application Factories
• Bio::Factory::DriverFactory - Base class for factory classes loading drivers
• Bio::Factory::FTLocationFactory - A FeatureTable Location Parser
• Bio::Factory::LocationFactoryI - A factory interface for generating locations from a string
• Bio::Factory::MapFactoryI - A Factory for getting markers
• Bio::Factory::ObjectBuilderI - Interface for an object builder
• Bio::Factory::ObjectFactory - Instantiates a new Bio::Root::RootI (or derived class) through a factory
• Bio::Factory::ObjectFactoryI - A General object creator factory
• Bio::Factory::SeqAnalysisParserFactory - class capable of creating SeqAnalysisParserI compliant parsers
• Bio::Factory::SeqAnalysisParserFactoryI - interface describing objects capable of creating SeqAnalysisParserI compliant parsers
• Bio::Factory::SequenceFactoryI - This interface allows for generic building of sequences in factories which create sequences (like SeqIO)
• Bio::Factory::SequenceProcessorI - Interface for chained sequence processing algorithms
• Bio::Factory::SequenceStreamI - Interface describing the basics of a Sequence Stream.
• Bio::Factory::TreeFactoryI - Factory Interface for getting and writing trees from/to a data stream
• Bio::FeatureHolderI - the base interface an object with features must implement
• Bio::FeatureIO - Handler for FeatureIO
• Bio::FeatureIO::bed - read/write features from UCSC BED format
• Bio::FeatureIO::gff - read/write GFF feature files
• Bio::FeatureIO::gtf - read write features in GTF format
• Bio::FeatureIO::interpro - read features from InterPro XML
• Bio::FeatureIO::ptt - read/write features in PTT format
• Bio::FeatureIO::vecscreen_simple - read/write features from NCBI vecscreen -f 3 output
• Bio::HandlerBaseI - Interface class for handler methods which interact with any event-driven parsers (drivers).
• Bio::IdCollectionI - interface for objects with multiple identifiers
• Bio::IdentifiableI - interface for objects with identifiers
• Bio::Index::Abstract - Abstract interface for indexing a flat file
• Bio::Index::AbstractSeq - base class for AbstractSeq
• Bio::Index::Blast - Indexes Blast reports and supports retrieval based on query accession(s)
• Bio::Index::BlastTable - Indexes tabular Blast reports (-m 9 format) and supports retrieval based on query accession(s)
• Bio::Index::EMBL - Interface for indexing (multiple) EMBL/Swissprot .dat files (i.e. flat file EMBL/Swissprot format).
• Bio::Index::Fasta - Interface for indexing (multiple) fasta files
• Bio::Index::Fastq - Interface for indexing (multiple) fastq files
• Bio::Index::GenBank - Interface for indexing one or more GenBank files (i.e. flat file GenBank format).
• Bio::Index::Hmmer - indexes HMMER reports and supports retreival based on query
• Bio::Index::Qual - Interface for indexing (multiple) fasta qual files
• Bio::Index::Stockholm - Indexes Stockholm format alignments (such as those from Pfam and Rfam. Retrieves raw stream data using the ID or a Bio::SimpleAlign (via Bio::AlignIO)
• Bio::Index::SwissPfam - Interface for indexing swisspfam files
• Bio::Index::Swissprot - Interface for indexing one or more Swissprot files.
• Bio::LiveSeq::AARange - AARange abstract class for LiveSeq
• Bio::LiveSeq::Chain - DoubleChain DataStructure for Perl
• Bio::LiveSeq::ChainI - Double linked chain data structure
• Bio::LiveSeq::DNA - DNA object for LiveSeq
• Bio::LiveSeq::Exon - Range abstract class for LiveSeq
• Bio::LiveSeq::Gene - Range abstract class for LiveSeq
• Bio::LiveSeq::IO::BioPerl - Loader for LiveSeq from EMBL entries with BioPerl
• Bio::LiveSeq::IO::Loader - Parent Loader for LiveSeq
• Bio::LiveSeq::Intron - Range abstract class for LiveSeq
• Bio::LiveSeq::Mutation - Mutation event descriptor class
• Bio::LiveSeq::Mutator - Package mutating LiveSequences
• Bio::LiveSeq::Prim_Transcript - Prim_Transcript class for LiveSeq
• Bio::LiveSeq::Range - Range abstract class for LiveSeq
• Bio::LiveSeq::Repeat_Region - Repeat_Region class for LiveSeq
• Bio::LiveSeq::Repeat_Unit - Repeat_Unit class for LiveSeq
• Bio::LiveSeq::SeqI - Abstract sequence interface class for LiveSeq
• Bio::LiveSeq::Transcript - Transcript class for LiveSeq
• Bio::LiveSeq::Translation - Translation class for LiveSeq
• 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.
• Bio::Location::Atomic - Implementation of a Atomic Location on a Sequence
• Bio::Location::AvWithinCoordPolicy - class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise
• Bio::Location::CoordinatePolicyI - Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location
• Bio::Location::Fuzzy - Implementation of a Location on a Sequence which has unclear start and/or end locations
• Bio::Location::FuzzyLocationI - Abstract interface of a Location on a Sequence which has unclear start/end location
• Bio::Location::NarrowestCoordPolicy - class implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range
• Bio::Location::Simple - Implementation of a Simple Location on a Sequence
• Bio::Location::Split - Implementation of a Location on a Sequence which has multiple locations (start/end points)
• Bio::Location::SplitLocationI - Abstract interface of a Location on a Sequence which has multiple locations (start/end points)
• Bio::Location::WidestCoordPolicy - class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable range
• Bio::LocationI - Abstract interface of a Location on a Sequence
• Bio::Map::Clone - An central map object representing a clone
• Bio::Map::Contig - A MapI implementation handling the contigs of a Physical Map (such as FPC)
• Bio::Map::CytoMap - A Bio::MapI compliant map implementation handling cytogenic bands
• Bio::Map::CytoMarker - An object representing a marker.
• Bio::Map::CytoPosition - Marker class with cytogenetic band storing attributes
• Bio::Map::EntityI - An Entity Interface
• Bio::Map::FPCMarker - An central map object representing a marker
• Bio::Map::Gene - An gene modelled as a mappable element.
• Bio::Map::GeneMap - A MapI implementation to represent the area around a gene
• Bio::Map::GenePosition - A typed position, suitable for modelling the various regions of a gene.
• Bio::Map::GeneRelative - Represents being relative to named sub-regions of a gene.
• Bio::Map::LinkageMap - A representation of a genetic linkage map.
• Bio::Map::LinkagePosition - Create a Position for a Marker that will be placed on a Bio::Map::LinkageMap
• Bio::Map::MapI - Interface for describing Map objects in bioperl
• Bio::Map::Mappable - An object representing a generic map element that can have multiple locations in several maps.
• Bio::Map::MappableI - An object that can be placed in a map
• Bio::Map::Marker - An central map object representing a generic marker that can have multiple location in several maps.
• Bio::Map::MarkerI - Interface for basic marker functionality
• Bio::Map::Microsatellite - An object representing a Microsatellite marker.
• 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.
• 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.
• Bio::Map::Physical - A class for handling a Physical Map (such as FPC)
• Bio::Map::Position - A single position of a Marker, or the range over which that marker lies, in a Map
• Bio::Map::PositionHandler - A Position Handler Implementation
• Bio::Map::PositionHandlerI - A Position Handler Interface
• Bio::Map::PositionI - Abstracts the notion of a position having a value in the context of a marker and a Map
• Bio::Map::PositionWithSequence - A position with a sequence.
• Bio::Map::Prediction - An object representing the predictions of something that can have multiple locations in several maps.
• Bio::Map::Relative - Represents what a Position's coordiantes are relative to.
• Bio::Map::RelativeI - Interface for describing what a Position's coordiantes are relative to.
• Bio::Map::SimpleMap - A MapI implementation handling the basics of a Map
• Bio::Map::TranscriptionFactor - A transcription factor modelled as a mappable element
• Bio::MapIO - A Map Factory object
• Bio::MapIO::fpc - A FPC Map reader
• Bio::MapIO::mapmaker - A Mapmaker Map reader
• Bio::Matrix::Generic - A generic matrix implementation
• Bio::Matrix::IO - A factory for Matrix parsing
• Bio::Matrix::IO::mlagan - A parser for the mlagan substitution matrix
• Bio::Matrix::IO::phylip - A parser for PHYLIP distance matricies
• Bio::Matrix::IO::scoring - A parser for PAM/BLOSUM matricies
• Bio::Matrix::MatrixI - An interface for describing a Matrix
• Bio::Matrix::Mlagan - A generic matrix with mlagan fields
• Bio::Matrix::PSM::IO - PSM parser
• Bio::Matrix::PSM::IO::mast - PSM mast parser implementation
• Bio::Matrix::PSM::IO::masta - motif fasta format parser
• Bio::Matrix::PSM::IO::meme - PSM meme parser implementation
• Bio::Matrix::PSM::IO::psiblast - PSM psiblast parser
• Bio::Matrix::PSM::IO::transfac - PSM transfac parser
• Bio::Matrix::PSM::InstanceSite - A PSM site occurance
• Bio::Matrix::PSM::InstanceSiteI - InstanceSite interface, holds an instance of a PSM
• Bio::Matrix::PSM::ProtMatrix - SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) with log-odds scoring information.
• Bio::Matrix::PSM::ProtPsm - handle combination of site matricies
• Bio::Matrix::PSM::Psm - handle combination of site matricies
• Bio::Matrix::PSM::PsmHeader - PSM mast parser implementation
• Bio::Matrix::PSM::PsmHeaderI - handles the header data from a PSM file
• Bio::Matrix::PSM::PsmI - abstract interface to handler of site matricies
• Bio::Matrix::PSM::SiteMatrix - SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds
• Bio::Matrix::PSM::SiteMatrixI - SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds
• Bio::Matrix::PhylipDist - A Phylip Distance Matrix object
• Bio::Matrix::Scoring - Object which can hold scoring matrix information
• Bio::MolEvol::CodonModel - Codon Evolution Models
• Bio::Ontology::DocumentRegistry - Keep track of where to find ontologies. Allows lookups by name.
• Bio::Ontology::GOterm - representation of GO terms
• Bio::Ontology::InterProTerm - Implementation of InterProI term interface
• Bio::Ontology::OBOEngine - An Ontology Engine for OBO style flat file format from the Gene Ontology Consortium
• Bio::Ontology::OBOterm - representation of OBO terms
• Bio::Ontology::Ontology - standard implementation of an Ontology
• Bio::Ontology::OntologyEngineI - Interface a minimal Ontology implementation should satisfy
• Bio::Ontology::OntologyI - Interface for an ontology implementation
• Bio::Ontology::OntologyStore - A repository of ontologies
• Bio::Ontology::Path - a path for an ontology term graph
• Bio::Ontology::PathI - Interface for a path between ontology terms
• Bio::Ontology::Relationship - a relationship for an ontology
• Bio::Ontology::RelationshipFactory - Instantiates a new Bio::Ontology::RelationshipI (or derived class) through a factory
• Bio::Ontology::RelationshipI - Interface for a relationship between ontology terms
• Bio::Ontology::RelationshipType - a relationship type for an ontology
• Bio::Ontology::SimpleGOEngine::GraphAdaptor - Graph adaptor for Bio::Ontology::SimpleGOEngine
• Bio::Ontology::SimpleGOEngine::GraphAdaptor02 - Graph adaptor (v02.x) for Bio::Ontology::SimpleGOEngine
• Bio::Ontology::SimpleOntologyEngine - Implementation of OntologyEngineI interface
• Bio::Ontology::Term - implementation of the interface for ontology terms
• Bio::Ontology::TermFactory - Instantiates a new Bio::Ontology::TermI (or derived class) through a factory
• Bio::Ontology::TermI - interface for ontology terms
• Bio::OntologyIO - Parser factory for Ontology formats
• Bio::OntologyIO::Handlers::BaseSAXHandler
• Bio::OntologyIO::Handlers::InterProHandler - XML handler class for InterProParser
• Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler - parse an InterPro XML file and persist the resulting terms to a Biosql database
• Bio::OntologyIO::InterProParser - Parser for InterPro xml files.
• Bio::OntologyIO::dagflat - a base class parser for GO flat-file type formats
• Bio::OntologyIO::goflat - a parser for the Gene Ontology flat-file format
• Bio::OntologyIO::obo - a parser for OBO flat-file format from Gene Ontology Consortium
• Bio::OntologyIO::simplehierarchy - a base class parser for simple hierarchy-by-indentation type formats
• Bio::OntologyIO::soflat - a parser for the Sequence Ontology flat-file format
• Bio::ParameterBaseI - Simple interface class for any parameter-related data such as IDs, database name, program arguments, and other odds and ends.
• Bio::Perl - Functional access to BioPerl for people who don't know objects
• Bio::Phenotype::Correlate - Representation of a correlating phenotype in a given species
• Bio::Phenotype::MeSH::Term - A MeSH term
• Bio::Phenotype::MeSH::Twig - Context for a MeSH term
• Bio::Phenotype::Measure - Representation of context/value(-range)/unit triplets
• Bio::Phenotype::OMIM::MiniMIMentry - Representation of a Mini MIM entry
• Bio::Phenotype::OMIM::OMIMentry - represents OMIM (Online Mendelian Inheritance in Man) database entries
• Bio::Phenotype::OMIM::OMIMentryAllelicVariant - Representation of a allelic variant of the OMIM database
• Bio::Phenotype::OMIM::OMIMparser - parser for the OMIM database
• Bio::Phenotype::Phenotype - A class for modeling phenotypes
• Bio::Phenotype::PhenotypeI - An interface for classes modeling phenotypes
• Bio::PhyloNetwork - Module to compute with Phylogenetic Networks
• Bio::PhyloNetwork::Factory - Module to sequentially generate Phylogenetic Networks
• Bio::PhyloNetwork::FactoryX - Module to sequentially generate Phylogenetic Networks
• Bio::PhyloNetwork::GraphViz - Interface between PhyloNetwork and GraphViz
• Bio::PhyloNetwork::RandomFactory - Module to generate random Phylogenetic Networks
• Bio::PhyloNetwork::TreeFactory - Module to sequentially generate Phylogenetic Trees
• Bio::PhyloNetwork::TreeFactoryMulti - Module to sequentially generate Phylogenetic Trees
• Bio::PhyloNetwork::TreeFactoryX - Module to sequentially generate Phylogenetic Trees
• Bio::PhyloNetwork::muVector - Module to compute with vectors of arbitrary dimension
• Bio::PopGen::Genotype - An implementation of GenotypeI which is just an allele container
• Bio::PopGen::GenotypeI - A marker and alleles for a specific individual
• Bio::PopGen::HtSNP
• Bio::PopGen::IO - Input individual,marker,allele information
• Bio::PopGen::IO::csv
• Bio::PopGen::IO::hapmap - A parser for HapMap output data
• Bio::PopGen::IO::phase - A parser for Phase format data
• Bio::PopGen::IO::prettybase - Extract individual allele data from PrettyBase format
• Bio::PopGen::Individual - An implementation of an Individual who has Genotype or Sequence Results
• Bio::PopGen::IndividualI - An individual who has Genotype or Sequence Results
• Bio::PopGen::Marker - A genetic marker which one uses to generate genotypes
• Bio::PopGen::MarkerI - A Population Genetic conceptual marker
• Bio::PopGen::PopStats - A collection of methods for calculating statistics about a population or sets of populations
• Bio::PopGen::Population - A population of individuals
• Bio::PopGen::PopulationI - Interface for Populations
• Bio::PopGen::Simulation::Coalescent - A Coalescent simulation factory
• Bio::PopGen::Simulation::GeneticDrift - A simple genetic drift simulation
• Bio::PopGen::Statistics - Population Genetics statistical tests
• Bio::PopGen::TagHaplotype - Haplotype tag object.
• Bio::PopGen::Utilities - Utilities for working with PopGen data and objects
• Bio::PrimarySeq - Bioperl lightweight Sequence Object
• Bio::PrimarySeqI - Interface definition for a Bio::PrimarySeq
• Bio::PullParserI - A base module for fast 'pull' parsing
• Bio::Range - Pure perl RangeI implementation
• Bio::RangeI - Range interface
• Bio::Restriction::Analysis - cutting sequences with restriction enzymes
• Bio::Restriction::Enzyme - A single restriction endonuclease (cuts DNA at specific locations)
• Bio::Restriction::Enzyme::MultiCut - A single restriction endonuclease
• Bio::Restriction::Enzyme::MultiSite - A single restriction endonuclease
• Bio::Restriction::EnzymeCollection - Set of restriction endonucleases
• Bio::Restriction::EnzymeI - Interface class for restriction endonuclease
• Bio::Restriction::IO - Handler for sequence variation IO Formats
• Bio::Restriction::IO::bairoch - bairoch enzyme set
• Bio::Restriction::IO::base - base enzyme set
• Bio::Restriction::IO::itype2 - itype2 enzyme set
• Bio::Restriction::IO::prototype - prototype enzyme set
• Bio::Restriction::IO::withrefm - withrefm enzyme set
• Bio::Root::Build - A common Module::Build subclass base for BioPerl distributions
• Bio::Root::Exception - Generic exception objects for Bioperl
• Bio::Root::HTTPget - module for fallback HTTP get operations when LWP:: is unavailable
• Bio::Root::IO - module providing several methods often needed when dealing with file IO
• Bio::Root::Root - Hash-based implementation of Bio::Root::RootI
• Bio::Root::RootI - Abstract interface to root object code
• Bio::Root::Storable - object serialisation methods
• Bio::Root::Test - A common base for all Bioperl test scripts.
• Bio::Root::Test::Warn - Perl extension to test Bioperl methods for warnings
• Bio::Root::Utilities - General-purpose utility module
• Bio::Root::Version - provide global, distribution-level versioning
• Bio::Search::BlastStatistics - An object for Blast statistics
• Bio::Search::BlastUtils - Utility functions for Bio::Search:: BLAST objects
• Bio::Search::DatabaseI - Interface for a database used in a sequence search
• Bio::Search::GenericDatabase - Generic implementation of Bio::Search::DatabaseI
• Bio::Search::GenericStatistics - An object for statistics
• Bio::Search::HSP::BlastHSP - Bioperl BLAST High-Scoring Pair object
• Bio::Search::HSP::BlastPullHSP - A parser and HSP object for BlastN hsps
• Bio::Search::HSP::FastaHSP - HSP object for FASTA specific data
• Bio::Search::HSP::GenericHSP - A "Generic" implementation of a High Scoring Pair
• Bio::Search::HSP::HMMERHSP - A HSP object for HMMER results
• Bio::Search::HSP::HSPFactory - A factory to create Bio::Search::HSP::HSPI objects
• Bio::Search::HSP::HSPI - Interface for a High Scoring Pair in a similarity search result
• Bio::Search::HSP::HmmpfamHSP - A parser and HSP object for hmmpfam hsps
• Bio::Search::HSP::ModelHSP - A HSP object for model-based searches
• Bio::Search::HSP::PSLHSP - A HSP for PSL output
• Bio::Search::HSP::PsiBlastHSP - Bioperl BLAST High-Scoring Pair object
• Bio::Search::HSP::PullHSPI - Bio::Search::HSP::HSPI interface for pull parsers.
• Bio::Search::HSP::WABAHSP - HSP object suitable for describing WABA alignments
• Bio::Search::Hit::BlastHit - Blast-specific subclass of Bio::Search::Hit::GenericHit
• Bio::Search::Hit::BlastPullHit - A parser and hit object for BLASTN hits
• Bio::Search::Hit::Fasta - Hit object specific for Fasta-generated hits
• Bio::Search::Hit::GenericHit - A generic implementation of the Bio::Search::Hit::HitI interface
• Bio::Search::Hit::HMMERHit - A Hit module for HMMER hits
• Bio::Search::Hit::HitFactory - A factory to create Bio::Search::Hit::HitI objects
• Bio::Search::Hit::HitI - Interface for a hit in a similarity search result
• Bio::Search::Hit::HmmpfamHit - A parser and hit object for hmmpfam hits
• Bio::Search::Hit::ModelHit - A model-based implementation of the Bio::Search::Hit::HitI interface
• Bio::Search::Hit::PsiBlastHit - Bioperl BLAST Hit object
• Bio::Search::Hit::PullHitI - Bio::Search::Hit::HitI interface for pull parsers.
• Bio::Search::Iteration::GenericIteration - A generic implementation of the Bio::Search::Iteration::IterationI interface.
• Bio::Search::Iteration::IterationI - Abstract interface to an iteration from an iterated search result, such as PSI-BLAST.
• Bio::Search::Processor - DESCRIPTION of Object
• Bio::Search::Result::BlastPullResult - A parser and result object for BLASTN results
• Bio::Search::Result::BlastResult - Blast-specific subclass of Bio::Search::Result::GenericResult
• Bio::Search::Result::CrossMatchResult - CrossMatch-specific subclass of Bio::Search::Result::GenericResult
• Bio::Search::Result::GenericResult - Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results.
• Bio::Search::Result::HMMERResult - A Result object for HMMER results
• Bio::Search::Result::HmmpfamResult - A parser and result object for hmmpfam results
• Bio::Search::Result::PullResultI - Bio::Search::Result::ResultI interface for 'pull' parsers
• Bio::Search::Result::ResultFactory - A factory to create Bio::Search::Result::ResultI objects
• Bio::Search::Result::ResultI - Abstract interface to Search Result objects
• Bio::Search::Result::WABAResult - Result object for WABA alignment output
• Bio::Search::SearchUtils - Utility functions for Bio::Search:: objects
• Bio::Search::StatisticsI - A Base object for statistics
• Bio::Search::Tiling::MapTileUtils - utilities for manipulating closed intervals for an HSP tiling algorithm
• Bio::Search::Tiling::MapTiling - An implementation of an HSP tiling algorithm, with methods to obtain frequently-requested statistics
• Bio::Search::Tiling::TilingI - Abstract interface for an HSP tiling module
• Bio::SearchDist - A perl wrapper around Sean Eddy's histogram object
• Bio::SearchIO - Driver for parsing Sequence Database Searches (BLAST, FASTA, ...)
• Bio::SearchIO::EventHandlerI - An abstract Event Handler for Search Result parsing
• Bio::SearchIO::FastHitEventBuilder - Event Handler for SearchIO events.
• Bio::SearchIO::IteratedSearchResultEventBuilder - Event Handler for SearchIO events.
• Bio::SearchIO::SearchResultEventBuilder - Event Handler for SearchIO events.
• Bio::SearchIO::SearchWriterI - Interface for outputting parsed Search results
• Bio::SearchIO::Writer::BSMLResultWriter - BSML output writer
• Bio::SearchIO::Writer::GbrowseGFF - Interface for outputting parsed search results in Gbrowse GFF format
• Bio::SearchIO::Writer::HSPTableWriter - Tab-delimited data for Bio::Search::HSP::HSPI objects
• Bio::SearchIO::Writer::HTMLResultWriter - write a Bio::Search::ResultI in HTML
• Bio::SearchIO::Writer::HitTableWriter - Tab-delimited data for Bio::Search::Hit::HitI objects
• Bio::SearchIO::Writer::ResultTableWriter - Outputs tab-delimited data for each Bio::Search::Result::ResultI object.
• Bio::SearchIO::Writer::TextResultWriter - Object to implement writing a Bio::Search::ResultI in Text.
• Bio::SearchIO::XML::BlastHandler - XML Handler for NCBI Blast XML parsing.
• Bio::SearchIO::XML::PsiBlastHandler - XML Handler for NCBI Blast PSIBLAST XML parsing.
• Bio::SearchIO::axt - a parser for axt format reports
• Bio::SearchIO::blast - Event generator for event based parsing of blast reports
• Bio::SearchIO::blast_pull - A parser for BLAST output
• Bio::SearchIO::blasttable - Driver module for SearchIO for parsing NCBI -m 8/9 format
• Bio::SearchIO::blastxml - A SearchIO implementation of NCBI Blast XML parsing.
• Bio::SearchIO::cross_match - CrossMatch-specific subclass of Bio::SearchIO
• Bio::SearchIO::erpin - SearchIO-based ERPIN parser
• Bio::SearchIO::exonerate - parser for Exonerate
• Bio::SearchIO::fasta - A SearchIO parser for FASTA results
• Bio::SearchIO::gmap_f9 - Event generator for parsing gmap reports (Z format)
• Bio::SearchIO::hmmer - A parser for HMMER output (hmmpfam, hmmsearch)
• Bio::SearchIO::hmmer_pull - A parser for HMMER output
• Bio::SearchIO::infernal - SearchIO-based Infernal parser
• Bio::SearchIO::megablast - a driver module for Bio::SearchIO to parse megablast reports (format 0)
• Bio::SearchIO::psl - A parser for PSL output (UCSC)
• Bio::SearchIO::rnamotif - SearchIO-based RNAMotif parser
• Bio::SearchIO::sim4 - parser for Sim4 alignments
• Bio::SearchIO::waba - SearchIO parser for Jim Kent WABA program alignment output
• Bio::SearchIO::wise - Parsing of wise output as alignments
• Bio::Seq - Sequence object, with features
• Bio::Seq::BaseSeqProcessor - Base implementation for a SequenceProcessor
• Bio::Seq::EncodedSeq - subtype of Bio::LocatableSeq to store DNA that encodes a protein
• Bio::Seq::LargeLocatableSeq - LocatableSeq object that stores sequence as files in the tempdir
• 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
• Bio::Seq::LargeSeq - SeqI compliant object that stores sequence as files in /tmp
• Bio::Seq::LargeSeqI - Interface class for sequences that cache their residues in a temporary file
• Bio::Seq::Meta - Generic superclass for sequence objects with residue-based meta information
• Bio::Seq::Meta::Array - array-based generic implementation of a sequence class with residue-based meta information
• Bio::Seq::MetaI - Interface for sequence objects with residue-based meta information
• Bio::Seq::PrimaryQual - Bioperl lightweight Quality Object
• Bio::Seq::PrimedSeq - A representation of a sequence and two primers flanking a target region
• Bio::Seq::QualI - Interface definition for a Bio::Seq::Qual
• Bio::Seq::Quality - Implementation of sequence with residue quality and trace values
• Bio::Seq::RichSeq - Module implementing a sequence created from a rich sequence database entry
• Bio::Seq::RichSeqI - interface for sequences from rich data sources, mostly databases
• Bio::Seq::SeqBuilder - Configurable object builder for sequence stream parsers
• Bio::Seq::SeqFactory - Instantiates a new Bio::PrimarySeqI (or derived class) through a factory
• Bio::Seq::SeqFastaSpeedFactory - Instantiates a new Bio::PrimarySeqI (or derived class) through a factory
• Bio::Seq::SeqWithQuality - Bioperl object packaging a sequence with its quality. Deprecated class, use Bio::Seq::Quality instead!
• Bio::Seq::SequenceTrace - Bioperl object packaging a sequence with its trace
• Bio::Seq::TraceI - Interface definition for a Bio::Seq::Trace
• Bio::SeqAnalysisParserI - Sequence analysis output parser interface
• Bio::SeqEvolution::DNAPoint - evolve a sequence by point mutations
• Bio::SeqEvolution::EvolutionI - the interface for evolving sequences
• Bio::SeqEvolution::Factory - Factory object to instantiate sequence evolving classes
• Bio::SeqFeature::Annotated - PLEASE PUT SOMETHING HERE
• Bio::SeqFeature::AnnotationAdaptor - integrates SeqFeatureIs annotation
• 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.
• Bio::SeqFeature::CollectionI - An interface for a collection of SeqFeatureI objects.
• Bio::SeqFeature::Computation - Computation SeqFeature
• Bio::SeqFeature::FeaturePair - hold pair feature information e.g. blast hits
• Bio::SeqFeature::Gene::Exon - a feature representing an exon
• Bio::SeqFeature::Gene::ExonI - Interface for a feature representing an exon
• Bio::SeqFeature::Gene::GeneStructure - A feature representing an arbitrarily complex structure of a gene
• Bio::SeqFeature::Gene::GeneStructureI - A feature representing an arbitrarily complex structure of a gene
• Bio::SeqFeature::Gene::Intron - An intron feature
• Bio::SeqFeature::Gene::NC_Feature - superclass for non-coding features
• Bio::SeqFeature::Gene::Poly_A_site - poly A feature
• Bio::SeqFeature::Gene::Promoter - Describes a promoter
• Bio::SeqFeature::Gene::Transcript - A feature representing a transcript
• Bio::SeqFeature::Gene::TranscriptI - Interface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site.
• Bio::SeqFeature::Gene::UTR - A feature representing an untranslated region that is part of a transcriptional unit
• Bio::SeqFeature::Generic - Generic SeqFeature
• Bio::SeqFeature::Lite - Lightweight Bio::SeqFeatureI class
• Bio::SeqFeature::PositionProxy - handle features when truncation/revcom sequences span a feature
• Bio::SeqFeature::Primer - Primer Generic SeqFeature
• Bio::SeqFeature::SiRNA::Oligo - Perl object for small inhibitory RNAs.
• Bio::SeqFeature::SiRNA::Pair - Perl object for small inhibitory RNA (SiRNA) oligo pairs
• Bio::SeqFeature::Similarity - A sequence feature based on similarity
• Bio::SeqFeature::SimilarityPair - Sequence feature based on the similarity of two sequences.
• Bio::SeqFeature::Tools::FeatureNamer - generates unique persistent names for features
• Bio::SeqFeature::Tools::IDHandler - maps $seq_feature-gtprimary_tag
• Bio::SeqFeature::Tools::TypeMapper - maps $seq_feature-gtprimary_tag
• Bio::SeqFeature::Tools::Unflattener - turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy
• Bio::SeqFeature::TypedSeqFeatureI - a strongly typed SeqFeature
• Bio::SeqFeatureI - Abstract interface of a Sequence Feature
• Bio::SeqI - [Developers] Abstract Interface of Sequence (with features)
• Bio::SeqIO - Handler for SeqIO Formats
• Bio::SeqIO::FTHelper - Helper class for Embl/Genbank feature tables
• Bio::SeqIO::Handler::GenericRichSeqHandler - Bio::HandlerI-based data handler for GenBank/EMBL/UniProt (and other) sequence data
• Bio::SeqIO::MultiFile - Treating a set of files as a single input stream
• Bio::SeqIO::abi - abi trace sequence input/output stream
• Bio::SeqIO::ace - ace sequence input/output stream
• Bio::SeqIO::agave - AGAVE sequence output stream.
• Bio::SeqIO::alf - alf trace sequence input/output stream
• Bio::SeqIO::asciitree - asciitree sequence input/output stream
• Bio::SeqIO::bsml - BSML sequence input/output stream
• Bio::SeqIO::bsml_sax - BSML sequence input/output stream using SAX
• Bio::SeqIO::chadoxml - chadoxml sequence output stream
• Bio::SeqIO::chaos - chaos sequence input/output stream
• Bio::SeqIO::chaosxml - chaosxml sequence input/output stream
• Bio::SeqIO::ctf - ctf trace sequence input/output stream
• Bio::SeqIO::embl - EMBL sequence input/output stream
• Bio::SeqIO::embldriver - EMBL sequence input/output stream
• Bio::SeqIO::entrezgene - Entrez Gene ASN1 parser
• Bio::SeqIO::excel - sequence input/output stream from a MSExcel-formatted table
• Bio::SeqIO::exp - exp trace sequence input/output stream
• Bio::SeqIO::fasta - fasta sequence input/output stream
• Bio::SeqIO::fastq - fastq sequence input/output stream
• Bio::SeqIO::flybase_chadoxml - FlyBase variant of chadoxml with sequence output stream
• Bio::SeqIO::game - a class for parsing and writing game-XML
• Bio::SeqIO::game::featHandler - a class for handling feature elements
• Bio::SeqIO::game::gameHandler - PerlSAX handler for game-XML
• Bio::SeqIO::game::gameSubs - a base class for game-XML parsing
• Bio::SeqIO::game::gameWriter - a class for writing game-XML
• Bio::SeqIO::game::seqHandler - a class for handling game-XML sequences
• Bio::SeqIO::gbdriver - GenBank handler-based push parser
• Bio::SeqIO::gcg - GCG sequence input/output stream
• Bio::SeqIO::genbank - GenBank sequence input/output stream
• Bio::SeqIO::interpro - InterProScan XML input/output stream
• Bio::SeqIO::kegg - KEGG sequence input/output stream
• Bio::SeqIO::largefasta - method i/o on very large fasta sequence files
• Bio::SeqIO::lasergene - Lasergene sequence file input/output stream
• Bio::SeqIO::locuslink - LocusLink input/output stream
• Bio::SeqIO::metafasta - metafasta sequence input/output stream
• Bio::SeqIO::phd - .phd file input/output stream
• Bio::SeqIO::pir - PIR sequence input/output stream
• Bio::SeqIO::pln - pln trace sequence input/output stream
• Bio::SeqIO::qual - .qual file input/output stream
• Bio::SeqIO::raw - raw sequence file input/output stream
• Bio::SeqIO::scf - .scf file input/output stream
• Bio::SeqIO::strider - DNA strider sequence input/output stream
• Bio::SeqIO::swiss - Swissprot sequence input/output stream
• Bio::SeqIO::swissdriver - SwissProt/UniProt handler-based push parser
• Bio::SeqIO::tab - nearly raw sequence file input/output stream. Reads/writes id"\t"sequence"\n"
• Bio::SeqIO::table - sequence input/output stream from a delimited table
• Bio::SeqIO::tigr - TIGR XML sequence input/output stream
• Bio::SeqIO::tigrxml - Parse TIGR (new) XML
• Bio::SeqIO::tinyseq - reading/writing sequences in NCBI TinySeq format
• Bio::SeqIO::tinyseq::tinyseqHandler - XML event handlers to support NCBI TinySeq XML parsing
• Bio::SeqIO::ztr - ztr trace sequence input/output stream
• Bio::SeqUtils - Additional methods for PrimarySeq objects
• Bio::SimpleAlign - Multiple alignments held as a set of sequences
• Bio::SimpleAnalysisI - A simple interface to any (local or remote) analysis tool
• Bio::Species - Generic species object
• Bio::Structure::Atom - Bioperl structure Object, describes an Atom
• Bio::Structure::Chain - Bioperl structure Object, describes a chain
• Bio::Structure::Entry - Bioperl structure Object, describes the whole entry
• Bio::Structure::IO - Handler for Structure Formats
• Bio::Structure::IO::pdb - PDB input/output stream
• Bio::Structure::Model - Bioperl structure Object, describes a Model
• Bio::Structure::Residue - Bioperl structure Object, describes a Residue
• Bio::Structure::SecStr::DSSP::Res - Module for parsing/accessing dssp output
• Bio::Structure::SecStr::STRIDE::Res - Module for parsing/accessing stride output
• Bio::Structure::StructureI - Abstract Interface for a Structure objects
• Bio::Symbol::Alphabet - BSANE/BioCORBA compliant symbol list alphabet
• Bio::Symbol::AlphabetI - A Symbol Alphabet
• Bio::Symbol::DNAAlphabet - A ready made DNA alphabet
• Bio::Symbol::ProteinAlphabet - A ready made Protein alphabet
• Bio::Symbol::Symbol - A biological symbol
• Bio::Symbol::SymbolI - Interface for a Symbol
• Bio::Taxon - A node in a represented taxonomy
• Bio::Taxonomy - representing Taxonomy.
• Bio::Taxonomy::FactoryI - interface to define how to access NCBI Taxonoy
• Bio::Taxonomy::Node - A node in a represented taxonomy
• Bio::Taxonomy::Taxon - Generic Taxonomic Entity object
• Bio::Taxonomy::Tree - An Organism Level Implementation of TreeI interface.
• Bio::Tools::AlignFactory - Base object for alignment factories
• Bio::Tools::Alignment::Consed - A module to work with objects from consed .ace files
• Bio::Tools::Alignment::Trim - A kludge to do specialized trimming of sequence based on quality.
• Bio::Tools::Analysis::DNA::ESEfinder - a wrapper around ESEfinder server
• Bio::Tools::Analysis::Protein::Domcut - a wrapper around Domcut server
• Bio::Tools::Analysis::Protein::ELM - a wrapper around the ELM server which predicts short functional motifs on amino acid sequences
• Bio::Tools::Analysis::Protein::GOR4 - a wrapper around GOR4 protein secondary structure prediction server
• Bio::Tools::Analysis::Protein::HNN - a wrapper around the HNN protein secondary structure prediction server
• Bio::Tools::Analysis::Protein::Mitoprot - a wrapper around Mitoprot server
• Bio::Tools::Analysis::Protein::NetPhos - a wrapper around NetPhos server
• Bio::Tools::Analysis::Protein::Scansite - a wrapper around the Scansite server
• Bio::Tools::Analysis::Protein::Sopma - a wrapper around the Sopma protein secondary structure prediction server
• Bio::Tools::Analysis::SimpleAnalysisBase - abstract superclass for SimpleAnalysis implementations
• Bio::Tools::AnalysisResult - Base class for analysis result objects and parsers
• Bio::Tools::Blat - parser for Blat program
• Bio::Tools::CodonTable - Codon table object
• Bio::Tools::Coil - parser for Coil output
• Bio::Tools::ECnumber - representation of EC numbers (Enzyme Classification)
• Bio::Tools::EMBOSS::Palindrome - parse EMBOSS palindrome output
• Bio::Tools::EPCR - Parse ePCR output and make features
• Bio::Tools::ERPIN - a parser for ERPIN output
• Bio::Tools::ESTScan - Results of one ESTScan run
• Bio::Tools::EUtilities - NCBI eutil XML parsers
• Bio::Tools::EUtilities::History - lightweight implementation of HistoryI interface (not bound to filehandles, extraneous methods, etc).
• Bio::Tools::EUtilities::EUtilDataI - eutil data object interface
• Bio::Tools::EUtilities::EUtilParameters - Manipulation of NCBI eutil-based parameters for remote database requests.
• Bio::Tools::EUtilities::History - lightweight implementation of HistoryI interface (not bound to filehandles, extraneous methods, etc).
• Bio::Tools::EUtilities::HistoryI - simple extension of EUtilDataI interface class for classes which hold NCBI server history data
• Bio::Tools::EUtilities::Info - interface class for storing einfo data
• Bio::Tools::EUtilities::Info::FieldInfo - class for storing einfo field data
• Bio::Tools::EUtilities::Info::LinkInfo - class for storing einfo link data
• Bio::Tools::EUtilities::Link - general API for accessing data retrieved from elink queries
• Bio::Tools::EUtilities::Link::LinkSet - class for EUtils LinkSets
• Bio::Tools::EUtilities::Link::UrlLink - class for EUtils UrlLinks
• Bio::Tools::EUtilities::Query - parse and collect esearch, epost, espell, egquery information
• Bio::Tools::EUtilities::Query::GlobalQuery - container class for egquery data
• Bio::Tools::EUtilities::Summary - class for handlign data output (XML) from esummary.
• Bio::Tools::EUtilities::Summary::DocSum - data object for document summary data from esummary
• Bio::Tools::EUtilities::Summary::Item - simple layered object for DocSum item data
• Bio::Tools::EUtilities::Summary::ItemContainerI - abtract interface methods for accessing Item information from any Item-containing class. This pertains to either DocSums or to Items themselves (which can be layered)
• Bio::Tools::Eponine - Results of one Eponine run
• Bio::Tools::Est2Genome - Parse est2genome output, makes simple Bio::SeqFeature::Generic objects
• Bio::Tools::Fgenesh - parse results of one Fgenesh run
• Bio::Tools::FootPrinter - write sequence features in FootPrinter format
• Bio::Tools::GFF - A Bio::SeqAnalysisParserI compliant GFF format parser
• Bio::Tools::Gel - Calculates relative electrophoretic migration distances
• Bio::Tools::Geneid - Results of one geneid run
• Bio::Tools::Genemark - Results of one Genemark run
• Bio::Tools::Genewise - Results of one Genewise run
• Bio::Tools::Genomewise - Results of one Genomewise run
• Bio::Tools::Genscan - Results of one Genscan run
• Bio::Tools::Glimmer - parser for Glimmer 2.X/3.X prokaryotic and GlimmerM/GlimmerHMM eukaryotic gene predictions
• Bio::Tools::Grail - Results of one Grail run
• Bio::Tools::GuessSeqFormat - Module for determining the sequence format of the contents of a file, a string, or through a filehandle.
• Bio::Tools::HMMER::Domain - One particular domain hit from HMMER
• Bio::Tools::HMMER::Results - Object representing HMMER output results
• Bio::Tools::HMMER::Set - Set of identical domains from HMMER matches
• Bio::Tools::Hmmpfam - Parser for Hmmpfam program
• Bio::Tools::IUPAC - Generates unique Seq objects from an ambiguous Seq object
• Bio::Tools::Infernal - A parser for Infernal output
• Bio::Tools::Lucy - Object for analyzing the output from Lucy, a vector and quality trimming program from TIGR
• Bio::Tools::MZEF - Results of one MZEF run
• Bio::Tools::Match - Parses output from Transfac's match(TM)
• Bio::Tools::OddCodes - Object holding alternative alphabet coding for one protein sequence
• Bio::Tools::Phylo::Gerp - Parses output from GERP
• Bio::Tools::Phylo::Gumby - Parses output from gumby
• Bio::Tools::Phylo::Molphy - parser for Molphy output
• Bio::Tools::Phylo::Molphy::Result - container for data parsed from a ProtML run
• Bio::Tools::Phylo::PAML - Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00
• Bio::Tools::Phylo::PAML::ModelResult - A container for NSSite Model Result from PAML
• Bio::Tools::Phylo::PAML::Result - A PAML result set object
• Bio::Tools::Phylo::Phylip::ProtDist - parser for ProtDist output
• Bio::Tools::Prediction::Exon - A predicted exon feature
• Bio::Tools::Prediction::Gene - a predicted gene structure feature
• Bio::Tools::Primer::Assessor::Base - base class for common assessor things
• Bio::Tools::Primer::AssessorI - interface for assessing primer pairs
• Bio::Tools::Primer::Feature - position of a single primer
• Bio::Tools::Primer::Pair - two primers on left and right side
• Bio::Tools::Primer3 - Create input for and work with the output from the program primer3
• Bio::Tools::Prints - Parser for FingerPRINTScanII program
• Bio::Tools::Profile - parse Profile output
• Bio::Tools::Promoterwise - parser for Promoterwise tab format output
• Bio::Tools::PrositeScan - Parser for ps_scan result
• Bio::Tools::Protparam - submit to and parse output from protparam ;
• Bio::Tools::Pseudowise - Results of one Pseudowise run
• Bio::Tools::QRNA - A Parser for qrna output
• Bio::Tools::RNAMotif - A parser for RNAMotif output
• Bio::Tools::RandomDistFunctions - A set of routines useful for generating random data in different distributions
• Bio::Tools::RepeatMasker - a parser for RepeatMasker output
• Bio::Tools::Run::GenericParameters - An object for the parameters used to run programs
• Bio::Tools::Run::ParametersI - A Base object for the parameters used to run programs
• Bio::Tools::Run::RemoteBlast - Object for remote execution of the NCBI Blast via HTTP
• 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.
• Bio::Tools::Run::StandAloneNCBIBlast - Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). With experimental support for NCBI rpsblast.
• Bio::Tools::Run::StandAloneWUBlast - Object for the local execution of WU-Blast.
• Bio::Tools::Run::WrapperBase - A Base object for wrappers around executables
• Bio::Tools::Seg - parse seg output
• Bio::Tools::SeqPattern - represent a sequence pattern or motif
• Bio::Tools::SeqPattern::Backtranslate
• Bio::Tools::SeqStats - Object holding statistics for one particular sequence
• Bio::Tools::SeqWords - Object holding n-mer statistics for a sequence
• Bio::Tools::SiRNA - Perl object for designing small inhibitory RNAs.
• Bio::Tools::SiRNA::Ruleset::saigo - Perl object implementing the Saigo group's rules for designing small inhibitory RNAs
• Bio::Tools::SiRNA::Ruleset::tuschl - Perl object implementing the tuschl group's rules for designing small inhibitory RNAs
• Bio::Tools::Sigcleave - Bioperl object for sigcleave analysis
• Bio::Tools::Signalp - parser for Signalp output
• Bio::Tools::Signalp::ExtendedSignalp - enhanced parser for Signalp output
• Bio::Tools::Sim4::Exon - A single exon determined by an alignment
• Bio::Tools::Sim4::Results - Results of one Sim4 run
• Bio::Tools::Spidey::Exon - A single exon determined by an alignment
• Bio::Tools::Spidey::Results - Results of a Spidey run
• Bio::Tools::TandemRepeatsFinder - a parser for Tandem Repeats Finder output
• Bio::Tools::TargetP - Results of one TargetP run
• Bio::Tools::Tmhmm - parse TMHMM output (TransMembrane HMM)
• Bio::Tools::dpAlign - Perl extension to do pairwise dynamic programming sequence alignment
• Bio::Tools::ipcress - Parse ipcress output and make features
• Bio::Tools::isPcr - Parse isPcr output and make features
• Bio::Tools::pICalculator - calculate the isoelectric point of a protein
• Bio::Tools::pSW - pairwise Smith Waterman object
• Bio::Tools::tRNAscanSE - A parser for tRNAscan-SE output
• Bio::Tree::AlleleNode - A Node with Alleles attached
• Bio::Tree::AnnotatableNode - A Tree Node with support for annotation
• Bio::Tree::Compatible - Testing compatibility of phylogenetic trees with nested taxa.
• Bio::Tree::DistanceFactory - Construct a tree using distance based methods
• Bio::Tree::Draw::Cladogram - Drawing phylogenetic trees in Encapsulated PostScript (EPS) format.
• Bio::Tree::Node - A Simple Tree Node
• Bio::Tree::NodeI - Interface describing a Tree Node
• Bio::Tree::NodeNHX - A Simple Tree Node with support for NHX tags
• Bio::Tree::RandomFactory - TreeFactory for generating Random Trees
• Bio::Tree::Statistics - Calculate certain statistics for a Tree
• Bio::Tree::Tree - An Implementation of TreeI interface.
• Bio::Tree::TreeFunctionsI - Decorated Interface implementing basic Tree exploration methods
• Bio::Tree::TreeI - A Tree object suitable for lots of things, designed originally for Phylogenetic Trees.
• Bio::TreeIO - Parser for Tree files
• Bio::TreeIO::TreeEventBuilder - Build Bio::Tree::Tree's and Bio::Tree::Node's from Events
• Bio::TreeIO::cluster - A TreeIO driver module for parsing Algorithm::Cluster::treecluster() output
• Bio::TreeIO::lintree - Parser for lintree output trees
• Bio::TreeIO::newick - TreeIO implementation for parsing Newick/New Hampshire/PHYLIP format.
• Bio::TreeIO::nexus - A TreeIO driver module for parsing Nexus tree output from PAUP
• Bio::TreeIO::nhx - TreeIO implementation for parsing Newick/New Hampshire eXtendend (NHX) format.
• Bio::TreeIO::pag - Bio::TreeIO driver for Pagel format
• Bio::TreeIO::phyloxml - TreeIO implementation for parsing PhyloXML format.
• Bio::TreeIO::svggraph - A simple output format that converts a Tree object to an SVG output
• Bio::TreeIO::tabtree - A simple output format which displays a tree as an ASCII drawing
• Bio::UpdateableSeqI - Descendant of Bio::SeqI that allows updates
• Bio::Variation::AAChange - Sequence change class for polypeptides
• Bio::Variation::AAReverseMutate - point mutation and codon information from single amino acid changes
• Bio::Variation::Allele - Sequence object with allele-specific attributes
• Bio::Variation::DNAMutation - DNA level mutation class
• Bio::Variation::IO - Handler for sequence variation IO Formats
• Bio::Variation::IO::flat - flat file sequence variation input/output stream
• Bio::Variation::IO::xml - XML sequence variation input/output stream
• Bio::Variation::RNAChange - Sequence change class for RNA level
• Bio::Variation::SNP - submitted SNP
• Bio::Variation::SeqDiff - Container class for mutation/variant descriptions
• Bio::Variation::VariantI - Sequence Change SeqFeature abstract class
• Bio::WebAgent - A base class for Web (any protocol) access
• BioPerl - Perl Modules for Biology
• Deobfuscator - get BioPerl method and package information from a Berkeley DB
• Bio::PrimarySeq
• Bio::PrimarySeqI
• Bio::Seq
• Bio::SeqI
• TestInterface
• TestObject