BIO_ctrl, BIO_callback_ctrl, BIO_ptr_ctrl, BIO_int_ctrl, BIO_reset, BIO_seek, BIO_tell, BIO_flush, BIO_eof, BIO_set_close, BIO_get_close, BIO_pending, BIO_wpending, BIO_ctrl_pending, BIO_ctrl_wpending, BIO_get_info_callback, BIO_set_info_callback (3) - BIO control operations
BIO_f_base64 (3) - base64 BIO filter
BIO_f_buffer (3) - buffering BIO
BIO_f_cipher, BIO_set_cipher, BIO_get_cipher_status, BIO_get_cipher_ctx (3) - cipher BIO filter
BIO_f_md, BIO_set_md, BIO_get_md, BIO_get_md_ctx (3) - message digest BIO filter
BIO_f_null (3) - null filter
BIO_f_ssl, BIO_set_ssl, BIO_get_ssl, BIO_set_ssl_mode, BIO_set_ssl_renegotiate_bytes, BIO_get_num_renegotiates, BIO_set_ssl_renegotiate_timeout, BIO_new_ssl, BIO_new_ssl_connect, BIO_new_buffer_ssl_connect, BIO_ssl_copy_session_id, BIO_ssl_shutdown (3) - SSL BIO
BIO_find_type, BIO_next (3) - BIO chain traversal
BIO_new, BIO_set, BIO_free, BIO_vfree, BIO_free_all (3) - BIO allocation and freeing functions
BIO_push, BIO_pop (3) - add and remove BIOs from a chain.
BIO_read, BIO_write, BIO_gets, BIO_puts (3) - BIO I/O functions
BIO_s_accept, BIO_set_accept_port, BIO_get_accept_port, BIO_set_nbio_accept, BIO_set_accept_bios, BIO_set_bind_mode, BIO_get_bind_mode, BIO_do_accept (3) - accept BIO
BIO_s_bio, BIO_make_bio_pair, BIO_destroy_bio_pair, BIO_shutdown_wr, BIO_set_write_buf_size, BIO_get_write_buf_size, BIO_new_bio_pair, BIO_get_write_guarantee, BIO_ctrl_get_write_guarantee, BIO_get_read_request, BIO_ctrl_get_read_request, BIO_ctrl_reset_read_request (3) - BIO pair BIO
BIO_s_connect, BIO_set_conn_hostname, BIO_set_conn_port, BIO_set_conn_ip, BIO_set_conn_int_port, BIO_get_conn_hostname, BIO_get_conn_port, BIO_get_conn_ip, BIO_get_conn_int_port, BIO_set_nbio, BIO_do_connect (3) - connect BIO
BIO_s_fd, BIO_set_fd, BIO_get_fd, BIO_new_fd (3) - file descriptor BIO
BIO_s_file, BIO_new_file, BIO_new_fp, BIO_set_fp, BIO_get_fp, BIO_read_filename, BIO_write_filename, BIO_append_filename, BIO_rw_filename (3) - FILE bio
BIO_s_mem, BIO_set_mem_eof_return, BIO_get_mem_data, BIO_set_mem_buf, BIO_get_mem_ptr, BIO_new_mem_buf (3) - memory BIO
BIO_s_null (3) - null data sink
BIO_s_socket, BIO_new_socket (3) - socket BIO
BIO_set_callback, BIO_get_callback, BIO_set_callback_arg, BIO_get_callback_arg, BIO_debug_callback (3) - BIO callback functions
BIO_should_retry, BIO_should_read, BIO_should_write, BIO_should_io_special, BIO_retry_type, BIO_should_retry, BIO_get_retry_BIO, BIO_get_retry_reason (3) - BIO retry functions
PEM, PEM_read_bio_PrivateKey, PEM_read_PrivateKey, PEM_write_bio_PrivateKey, PEM_write_PrivateKey, PEM_write_bio_PKCS8PrivateKey, PEM_write_PKCS8PrivateKey, PEM_write_bio_PKCS8PrivateKey_nid, PEM_write_PKCS8PrivateKey_nid, PEM_read_bio_PUBKEY, PEM_read_PUBKEY, PEM_write_bio_PUBKEY, PEM_write_PUBKEY, PEM_read_bio_RSAPrivateKey, PEM_read_RSAPrivateKey, PEM_write_bio_RSAPrivateKey, PEM_write_RSAPrivateKey, PEM_read_bio_RSAPublicKey, PEM_read_RSAPublicKey, PEM_write_bio_RSAPublicKey, PEM_write_RSAPublicKey, PEM_read_bio_RSA_PUBKEY, PEM_read_RSA_PUBKEY, PEM_write_bio_RSA_PUBKEY, PEM_write_RSA_PUBKEY, PEM_read_bio_DSAPrivateKey, PEM_read_DSAPrivateKey, PEM_write_bio_DSAPrivateKey, PEM_write_DSAPrivateKey, PEM_read_bio_DSA_PUBKEY, PEM_read_DSA_PUBKEY, PEM_write_bio_DSA_PUBKEY, PEM_write_DSA_PUBKEY, PEM_read_bio_DSAparams, PEM_read_DSAparams, PEM_write_bio_DSAparams, PEM_write_DSAparams, PEM_read_bio_DHparams, PEM_read_DHparams, PEM_write_bio_DHparams, PEM_write_DHparams, PEM_read_bio_X509, PEM_read_X509, PEM_write_bio_X509, PEM_write_X509, PEM_read_bio_X509_AUX, PEM_read_X509_AUX, PEM_write_bio_X509_AUX, PEM_write_X509_AUX, PEM_read_bio_X509_REQ, PEM_read_X509_REQ, PEM_write_bio_X509_REQ, PEM_write_X509_REQ, PEM_write_bio_X509_REQ_NEW, PEM_write_X509_REQ_NEW, PEM_read_bio_X509_CRL, PEM_read_X509_CRL, PEM_write_bio_X509_CRL, PEM_write_X509_CRL, PEM_read_bio_PKCS7, PEM_read_PKCS7, PEM_write_bio_PKCS7, PEM_write_PKCS7, PEM_read_bio_NETSCAPE_CERT_SEQUENCE, PEM_read_NETSCAPE_CERT_SEQUENCE, PEM_write_bio_NETSCAPE_CERT_SEQUENCE, PEM_write_NETSCAPE_CERT_SEQUENCE (3) - PEM routines
SSL_get_rbio (3) - get BIO linked to an SSL object
SSL_set_bio (3) - connect the SSL object with a BIO
bio (3) - I/O abstraction
bio (4) - block I/O ioctl tunnel pseudo-device
bio_register, bio_unregister (9) - block I/O ioctl tunnelling interface
bioctl (8) - RAID management interface
bios (4/AMD64) - a driver for PC Firmware, aka BIOS
bios (4/i386) - a driver for PC Firmware, aka BIOS
biosboot (8/AMD64) - amd64-specific first-stage system bootstrap
biosboot (8/i386) - i386-specific first-stage system bootstrap
buffercache, bread, breadn, bwrite, bawrite, bdwrite, getblk, geteblk, incore, allocbuf, brelse, biodone, biowait (9) - buffer cache interfaces
d2i_PKCS8PrivateKey_bio, d2i_PKCS8PrivateKey_fp, i2d_PKCS8PrivateKey_bio, i2d_PKCS8PrivateKey_fp, i2d_PKCS8PrivateKey_nid_bio, i2d_PKCS8PrivateKey_nid_fp (3) - PKCS#8 format private key functions
d2i_X509, i2d_X509, d2i_X509_bio, d2i_X509_fp, i2d_X509_bio, i2d_X509_fp (3) - X509 encode and decode functions
d2i_X509_CRL, i2d_X509_CRL, d2i_X509_CRL_bio, d2i_509_CRL_fp, i2d_X509_CRL_bio, i2d_X509_CRL_fp (3) - PKCS#10 certificate request functions.
d2i_X509_REQ, i2d_X509_REQ, d2i_X509_REQ_bio, d2i_X509_REQ_fp, i2d_X509_REQ_bio, i2d_X509_REQ_fp (3) - PKCS#10 certificate request functions.
lh_stats, lh_node_stats, lh_node_usage_stats, lh_stats_bio, lh_node_stats_bio, lh_node_usage_stats_bio (3) - LHASH statistics
macobio (4/MacPPC) - introduction to Apple PowerPC onboard I/O bus support
mpbios (4/AMD64) - MP BIOS
mpbios (4/i386) - MP BIOS
obio (4/LANDISK) - landisk onboard I/O bus device
obio (4/Mac68k) - Mac68k onboard I/O bus device
obio (4/SOCPPC) - socppc onboard I/O bus device
ofobio (4/MVME68k) - MVME141 On-Board I/O
oosiop (4) - Symbios/NCR 53C700 SCSI driver
osiop (4) - Symbios/NCR 53C710 SCSI driver
pcibios (4/i386) - introduction to PCI BIOS support
siop (4) - LSI/Symbios Logic/NCR 53c8xx SCSI interface
Bio::Align::AlignI (3p) - An interface for describing sequence alignments.
Bio::Align::DNAStatistics (3p) - Calculate some statistics for a DNA alignment
Bio::Align::PairwiseStatistics (3p) - Base statistic object for Pairwise Alignments
Bio::Align::ProteinStatistics (3p) - Calculate Protein Alignment statistics (mostly distances)
Bio::Align::StatisticsI (3p) - Calculate some statistics for an alignment
Bio::Align::Utilities (3p) - A collection of utilities regarding converting and manipulating alignment objects
Bio::AlignIO (3p) - Handler for AlignIO Formats
Bio::AlignIO::Handler::GenericAlignHandler (3p) - Bio::HandlerI-based generic data handler class for alignment-based data
Bio::AlignIO::arp (3p) - ARP MSA Sequence input/output stream
Bio::AlignIO::bl2seq (3p) - bl2seq sequence input/output stream
Bio::AlignIO::clustalw (3p) - clustalw sequence input/output stream
Bio::AlignIO::emboss (3p) - Parse EMBOSS alignment output (from applications water and needle)
Bio::AlignIO::fasta (3p) - fasta MSA Sequence input/output stream
Bio::AlignIO::largemultifasta (3p) - Largemultifasta MSA Sequence input/output stream
Bio::AlignIO::maf (3p) - Multiple Alignment Format sequence input stream
Bio::AlignIO::mase (3p) - mase sequence input/output stream
Bio::AlignIO::mega (3p) - Parse and Create MEGA format data files
Bio::AlignIO::meme (3p) - meme sequence input/output stream
Bio::AlignIO::metafasta (3p) - Metafasta MSA Sequence input/output stream
Bio::AlignIO::msf (3p) - msf sequence input/output stream
Bio::AlignIO::nexus (3p) - NEXUS format sequence input/output stream
Bio::AlignIO::pfam (3p) - pfam sequence input/output stream
Bio::AlignIO::phylip (3p) - PHYLIP format sequence input/output stream
Bio::AlignIO::po (3p) - po MSA Sequence input/output stream
Bio::AlignIO::proda (3p) - proda sequence input/output stream
Bio::AlignIO::prodom (3p) - prodom sequence input/output stream
Bio::AlignIO::psi (3p) - Read/Write PSI-BLAST profile alignment files
Bio::AlignIO::selex (3p) - selex sequence input/output stream
Bio::AlignIO::stockholm (3p) - stockholm sequence input/output stream
Bio::AlignIO::xmfa (3p) - XMFA MSA Sequence input/output stream
Bio::AnalysisI (3p) - An interface to any (local or remote) analysis tool
Bio::AnalysisParserI (3p) - Generic analysis output parser interface
Bio::AnalysisResultI (3p) - Interface for analysis result objects
Bio::AnnotatableI (3p) - the base interface an annotatable object must implement
Bio::Annotation::AnnotationFactory (3p) - Instantiates a new Bio::AnnotationI (or derived class) through a factory
Bio::Annotation::Collection (3p) - Default Perl implementation of AnnotationCollectionI
Bio::Annotation::Comment (3p) - A comment object, holding text
Bio::Annotation::DBLink (3p) - untyped links between databases
Bio::Annotation::OntologyTerm (3p) - An ontology term adapted to AnnotationI
Bio::Annotation::Reference (3p) - Specialised DBLink object for Literature References
Bio::Annotation::Relation (3p) - Relationship (pairwise) with other objects SeqI and NodeI;
Bio::Annotation::SimpleValue (3p) - A simple scalar
Bio::Annotation::StructuredValue (3p) - A scalar with embedded structured information
Bio::Annotation::TagTree (3p) - AnnotationI with tree-like hierarchal key-value relationships ('structured tags') that can be represented as simple text.
Bio::Annotation::Target (3p) - Provides an object which represents a target (ie, a similarity hit) from one object to something in another database
Bio::Annotation::Tree (3p) - Provide a tree as an annotation to a Bio::AnnotatableI object
Bio::Annotation::TypeManager (3p) - Manages types for annotation collections
Bio::AnnotationCollectionI (3p) - Interface for annotation collections
Bio::AnnotationI (3p) - Annotation interface
Bio::Assembly::Contig (3p) - Perl module to hold and manipulate sequence assembly contigs.
Bio::Assembly::ContigAnalysis (3p) - Perform analysis on sequence assembly contigs.
Bio::Assembly::IO (3p) - Handler for Assembly::IO Formats
Bio::Assembly::IO::ace (3p) - module to load ACE files from various assembly programs
Bio::Assembly::IO::phrap (3p) - driver to load phrap.out files.
Bio::Assembly::IO::tigr (3p) - Driver to read and write assembly files in the TIGR Assembler v2 default format.
Bio::Assembly::Scaffold (3p) - Perl module to hold and manipulate sequence assembly data.
Bio::Assembly::ScaffoldI (3p) - Abstract Inteface of Sequence Assemblies
Bio::Assembly::Singlet (3p) - Perl module to hold and manipulate singlets from sequence assembly contigs.
Bio::Assembly::Tools::ContigSpectrum (3p) - create and manipulate contig spectra
Bio::Biblio (3p) - A Bibliographic Query Service module
Bio::Biblio::Article (3p) - Representation of a general article
Bio::Biblio::BiblioBase (3p) - An abstract base for other biblio classes
Bio::Biblio::Book (3p) - Representation of a book
Bio::Biblio::BookArticle (3p) - Representation of a book article
Bio::Biblio::IO (3p) - Handling the bibliographic references
Bio::Biblio::IO::medline2ref (3p) - A converter of a raw hash to MEDLINE citations
Bio::Biblio::IO::medlinexml (3p) - A converter of XML files with MEDLINE citations
Bio::Biblio::IO::pubmed2ref (3p) - A converter of a raw hash to PUBMED citations
Bio::Biblio::IO::pubmedxml (3p) - A converter of XML files with PUBMED citations
Bio::Biblio::Journal (3p) - Representation of a journal
Bio::Biblio::JournalArticle (3p) - Representation of a journal article
Bio::Biblio::MedlineArticle (3p) - Representation of a MEDLINE article
Bio::Biblio::MedlineBook (3p) - Representation of a MEDLINE book
Bio::Biblio::MedlineBookArticle (3p) - Representation of a MEDLINE book article
Bio::Biblio::MedlineJournal (3p) - Representation of a MEDLINE journal
Bio::Biblio::MedlineJournalArticle (3p) - Representation of a MEDLINE journal article
Bio::Biblio::Organisation (3p) - Representation of an organisation
Bio::Biblio::Patent (3p) - Representation of a patent
Bio::Biblio::Person (3p) - Representation of a person
Bio::Biblio::Proceeding (3p) - Representation of a conference proceeding
Bio::Biblio::Provider (3p) - Representation of a general provider
Bio::Biblio::PubmedArticle (3p) - Representation of a PUBMED article
Bio::Biblio::PubmedBookArticle (3p) - Representation of a PUBMED book article
Bio::Biblio::PubmedJournalArticle (3p) - Representation of a PUBMED journal article
Bio::Biblio::Ref (3p) - Representation of a bibliographic reference
Bio::Biblio::Service (3p) - Representation of a provider of type service
Bio::Biblio::TechReport (3p) - Representation of a technical report
Bio::Biblio::Thesis (3p) - Representation of thesis
Bio::Biblio::WebResource (3p) - Representation of a web resource
Bio::Cluster::ClusterFactory (3p) - Instantiates a new Bio::ClusterI (or derived class) through a factory
Bio::Cluster::FamilyI (3p) - Family Interface
Bio::Cluster::SequenceFamily (3p) - Sequence Family object
Bio::Cluster::UniGene (3p) - UniGene object
Bio::Cluster::UniGeneI (3p) - abstract interface of UniGene object
Bio::ClusterI (3p) - Cluster Interface
Bio::ClusterIO (3p) - Handler for Cluster Formats
Bio::ClusterIO::dbsnp (3p) - dbSNP input stream
Bio::ClusterIO::unigene (3p) - UniGene input stream
Bio::CodonUsage::IO (3p) - for reading and writing codon usage tables to file
Bio::CodonUsage::Table (3p) - for access to the Codon usage Database at http://www.kazusa.or.jp/codon.
Bio::Coordinate::Chain (3p) - Mapping locations through a chain of coordinate mappers
Bio::Coordinate::Collection (3p) - Noncontinuous match between two coordinate sets
Bio::Coordinate::ExtrapolatingPair (3p) - Continuous match between two coordinate sets
Bio::Coordinate::GeneMapper (3p) - transformations between gene related coordinate systems
Bio::Coordinate::Graph (3p) - Finds shortest path between nodes in a graph
Bio::Coordinate::MapperI (3p) - Interface describing coordinate mappers
Bio::Coordinate::Pair (3p) - Continuous match between two coordinate sets
Bio::Coordinate::Result (3p) - Results from coordinate transformation
Bio::Coordinate::Result::Gap (3p) - Another name for Bio::Location::Simple
Bio::Coordinate::Result::Match (3p) - Another name for Bio::Location::Simple
Bio::Coordinate::ResultI (3p) - Interface to identify coordinate mapper results
Bio::Coordinate::Utils (3p) - Additional methods to create Bio::Coordinate objects
Bio::DB::Ace (3p) - Database object interface to ACeDB servers
Bio::DB::Biblio::biofetch (3p) - A BioFetch-based access to a bibliographic citation retrieval
Bio::DB::Biblio::eutils (3p) - Access to PubMed's bibliographic query service
Bio::DB::Biblio::soap (3p) - A SOAP-based access to a bibliographic query service
Bio::DB::BiblioI (3p) - An interface to a Bibliographic Query Service
Bio::DB::BioFetch (3p) - Database object interface to BioFetch retrieval
Bio::DB::CUTG (3p) - for access to the Codon usage Database at http://www.kazusa.or.jp/codon.
Bio::DB::DBFetch (3p) - Database object for retrieving using the dbfetch script
Bio::DB::EMBL (3p) - Database object interface for EMBL entry retrieval
Bio::DB::EUtilities (3p) - webagent which interacts with and retrieves data from NCBI's eUtils
Bio::DB::EntrezGene (3p) - Database object interface to Entrez Gene
Bio::DB::Expression (3p) - DESCRIPTION of Object
Bio::DB::Expression::geo (3p) - *** DESCRIPTION of Class
Bio::DB::Failover (3p) - A Bio::DB::RandomAccessI compliant class which wraps a prioritized list of DBs
Bio::DB::Fasta (3p) -- Fast indexed access to a directory of fasta files
Bio::DB::FileCache (3p) - In file cache for BioSeq objects
Bio::DB::Flat (3p) - Interface for indexed flat files
Bio::DB::Flat::BDB (3p) - Interface for BioHackathon standard BDB-indexed flat file
Bio::DB::Flat::BDB::embl (3p) - embl adaptor for Open-bio standard BDB-indexed flat file
Bio::DB::Flat::BDB::fasta (3p) - fasta adaptor for Open-bio standard BDB-indexed flat file
Bio::DB::Flat::BDB::genbank (3p) - genbank adaptor for Open-bio standard BDB-indexed flat file
Bio::DB::Flat::BDB::swiss (3p) - swissprot adaptor for Open-bio standard BDB-indexed flat file
Bio::DB::Flat::BinarySearch (3p) - BinarySearch search indexing system for sequence files
Bio::DB::GFF (3p) -- Storage and retrieval of sequence annotation data
Bio::DB::GFF::Adaptor::ace (3p) -- ace interface (for multiple inheritance)
Bio::DB::GFF::Adaptor::berkeleydb (3p) -- Bio::DB::GFF database adaptor for in-memory databases
Bio::DB::GFF::Adaptor::berkeleydb::iterator (3p) - iterator for Bio::DB::GFF::Adaptor::berkeleydb
Bio::DB::GFF::Adaptor::biofetch (3p) -- Cache BioFetch objects in a Bio::DB::GFF database
Bio::DB::GFF::Adaptor::biofetch_oracle (3p) -- Cache BioFetch objects in a Bio::DB::GFF database
Bio::DB::GFF::Adaptor::dbi (3p) -- Database adaptor for DBI (SQL) databases
Bio::DB::GFF::Adaptor::dbi::caching_handle (3p) -- Cache for database handles
Bio::DB::GFF::Adaptor::dbi::iterator (3p) - iterator for Bio::DB::GFF::Adaptor::dbi
Bio::DB::GFF::Adaptor::dbi::mysql (3p) -- Database adaptor for a specific mysql schema
Bio::DB::GFF::Adaptor::dbi::mysqlace (3p) -- Unholy union between mysql GFF database and acedb database
Bio::DB::GFF::Adaptor::dbi::mysqlcmap (3p) -- Database adaptor for an integraded CMap/GBrowse mysql schema
Bio::DB::GFF::Adaptor::dbi::mysqlopt (3p) -- Deprecated database adaptor
Bio::DB::GFF::Adaptor::dbi::oracle (3p) -- Database adaptor for a specific oracle schema
Bio::DB::GFF::Adaptor::dbi::oracleace (3p) -- Unholy union between oracle GFF database and acedb database
Bio::DB::GFF::Adaptor::dbi::pg (3p) -- Database adaptor for a specific postgres schema
Bio::DB::GFF::Adaptor::dbi::pg_fts (3p) -- Database adaptor for a specific postgres schema with a TSearch2 implementation
Bio::DB::GFF::Adaptor::memory (3p) -- Bio::DB::GFF database adaptor for in-memory databases
Bio::DB::GFF::Adaptor::memory::feature_serializer (3p) - utility methods for serializing and deserializing GFF features
Bio::DB::GFF::Adaptor::memory::iterator (3p) - iterator for Bio::DB::GFF::Adaptor::memory
Bio::DB::GFF::Aggregator (3p) -- Aggregate GFF groups into composite features
Bio::DB::GFF::Aggregator::alignment (3p) -- Alignment aggregator
Bio::DB::GFF::Aggregator::clone (3p) -- Clone aggregator
Bio::DB::GFF::Aggregator::coding (3p) -- The Coding Region Aggregator
Bio::DB::GFF::Aggregator::gene (3p) -- Sequence Ontology Geene
Bio::DB::GFF::Aggregator::match (3p) -- Match aggregator
Bio::DB::GFF::Aggregator::none (3p) -- No aggregation
Bio::DB::GFF::Aggregator::orf (3p) -- An aggregator for orf regions
Bio::DB::GFF::Aggregator::processed_transcript (3p) -- Sequence Ontology Transcript
Bio::DB::GFF::Aggregator::so_transcript (3p) -- Sequence Ontology Transcript
Bio::DB::GFF::Aggregator::transcript (3p) -- Transcript aggregator
Bio::DB::GFF::Aggregator::ucsc_acembly (3p) -- UCSC acembly aggregator
Bio::DB::GFF::Aggregator::ucsc_ensgene (3p) -- UCSC ensGene aggregator
Bio::DB::GFF::Aggregator::ucsc_genscan (3p) -- UCSC genscan aggregator
Bio::DB::GFF::Aggregator::ucsc_refgene (3p) -- UCSC refGene aggregator
Bio::DB::GFF::Aggregator::ucsc_sanger22 (3p) -- UCSC sanger22 aggregator
Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo (3p) -- UCSC sanger22pseudo aggregator
Bio::DB::GFF::Aggregator::ucsc_softberry (3p) -- UCSC softberry aggregator
Bio::DB::GFF::Aggregator::ucsc_twinscan (3p) -- UCSC twinscan aggregator
Bio::DB::GFF::Aggregator::ucsc_unigene (3p) -- UCSC UniGene aggregator
Bio::DB::GFF::Featname (3p) -- The name of a feature
Bio::DB::GFF::Feature (3p) -- A relative segment identified by a feature type
Bio::DB::GFF::Homol (3p) -- A segment of DNA that is homologous to another
Bio::DB::GFF::RelSegment (3p) -- Sequence segment with relative coordinate support
Bio::DB::GFF::Segment (3p) -- Simple DNA segment object
Bio::DB::GFF::Typename (3p) -- The name of a feature type
Bio::DB::GFF::Util::Binning (3p) - binning utility for Bio::DB::GFF index
Bio::DB::GFF::Util::Rearrange (3p) - rearrange utility
Bio::DB::GenBank (3p) - Database object interface to GenBank
Bio::DB::GenPept (3p) - Database object interface to GenPept
Bio::DB::GenericWebAgent (3p) - helper base class for parameter-based remote server access and response retrieval.
Bio::DB::HIV (3p) - Database object interface to the Los Alamos HIV Sequence Database
Bio::DB::HIV::HIVQueryHelper (3p) - Routines and packages used by Bio::DB::HIV and Bio::DB::Query::HIVQuery
Bio::DB::InMemoryCache (3p) - Abstract interface for a sequence database
Bio::DB::LocationI (3p) - A RandomAccessI-like abstract interface for retrieving location data from a sequence database and returning Bio::LocationI objects
Bio::DB::MeSH (3p) - Term retrieval from a Web MeSH database
Bio::DB::NCBIHelper (3p) - A collection of routines useful for queries to NCBI databases.
Bio::DB::Qual (3p) -- Fast indexed access to a directory of quality files
Bio::DB::Query::GenBank (3p) - Build a GenBank Entrez Query
Bio::DB::Query::HIVQuery (3p) - Query interface to the Los Alamos HIV Sequence Database
Bio::DB::Query::WebQuery (3p) - Helper class for web-based sequence queryies
Bio::DB::QueryI (3p) - Object Interface to queryable sequence databases
Bio::DB::RandomAccessI (3p) - Abstract interface for a sequence database
Bio::DB::RefSeq (3p) - Database object interface for RefSeq retrieval
Bio::DB::ReferenceI (3p) - A RandomAccessI-like abstract interface for retrieving Reference data from a sequence database and returning Bio::Annotation::Reference objects
Bio::DB::Registry (3p) - Access to the Open Bio Database Access registry scheme
Bio::DB::SeqFeature (3p) -- Normalized feature for use with Bio::DB::SeqFeature::Store
Bio::DB::SeqFeature::NormalizedFeature (3p) -- Normalized feature for use with Bio::DB::SeqFeature::Store
Bio::DB::SeqFeature::NormalizedFeatureI (3p) -- Interface for normalized features
Bio::DB::SeqFeature::NormalizedTableFeatureI (3p) -- Interface for normalized features whose hierarchy is stored in a table
Bio::DB::SeqFeature::Segment (3p) -- Location-based access to genome annotation data
Bio::DB::SeqFeature::Store (3p) -- Storage and retrieval of sequence annotation data
Bio::DB::SeqFeature::Store::DBI::Iterator (3p) - utility methods for creating and iterating over SeqFeature records
Bio::DB::SeqFeature::Store::DBI::Pg (3p) -- Mysql implementation of Bio::DB::SeqFeature::Store
Bio::DB::SeqFeature::Store::DBI::SQLite (3p) -- SQLite implementation of Bio::DB::SeqFeature::Store
Bio::DB::SeqFeature::Store::DBI::mysql (3p) -- Mysql implementation of Bio::DB::SeqFeature::Store
Bio::DB::SeqFeature::Store::FeatureFileLoader (3p) -- feature file loader for Bio::DB::SeqFeature::Store
Bio::DB::SeqFeature::Store::GFF2Loader (3p) -- GFF2 file loader for Bio::DB::SeqFeature::Store
Bio::DB::SeqFeature::Store::GFF3Loader (3p) -- GFF3 file loader for Bio::DB::SeqFeature::Store
Bio::DB::SeqFeature::Store::LoadHelper (3p) -- Internal utility for Bio::DB::SeqFeature::Store
Bio::DB::SeqFeature::Store::Loader (3p) -- Loader
Bio::DB::SeqFeature::Store::bdb (3p) - fetch and store objects from a BerkeleyDB
Bio::DB::SeqFeature::Store::berkeleydb (3p) -- Storage and retrieval of sequence annotation data in Berkeleydb files
Bio::DB::SeqFeature::Store::berkeleydb3 (3p) -- Storage and retrieval of sequence annotation data in Berkeleydb files
Bio::DB::SeqFeature::Store::memory (3p) -- In-memory implementation of Bio::DB::SeqFeature::Store
Bio::DB::SeqHound (3p) - Database object interface to SeqHound
Bio::DB::SeqI (3p) - Abstract Interface for Sequence databases
Bio::DB::SeqVersion (3p) - front end to querying databases for identifier versions
Bio::DB::SeqVersion::gi (3p) - interface to NCBI Sequence Revision History page
Bio::DB::SwissProt (3p) - Database object interface to SwissProt retrieval
Bio::DB::TFBS (3p) - Access to a Transcription Factor Binding Site database
Bio::DB::TFBS::transfac_pro (3p) - An implementation of Bio::DB::TFBS which uses local flat files for transfac pro
Bio::DB::Taxonomy (3p) - Access to a taxonomy database
Bio::DB::Taxonomy::entrez (3p) - Taxonomy Entrez driver
Bio::DB::Taxonomy::flatfile (3p) - An implementation of Bio::DB::Taxonomy which uses local flat files
Bio::DB::Taxonomy::list (3p) - An implementation of Bio::DB::Taxonomy that accepts lists of words to build a database
Bio::DB::Universal (3p) - Artificial database that delegates to specific databases
Bio::DB::UpdateableSeqI (3p) - An interface for writing to a database of sequences.
Bio::DB::WebDBSeqI (3p) - Object Interface to generalize Web Databases for retrieving sequences
Bio::DBLinkContainerI (3p) - Abstract interface for any object wanting to use database cross references
Bio::Das::FeatureTypeI (3p) - Simple interface to Sequence Ontology feature types
Bio::Das::SegmentI (3p) - DAS-style access to a feature database
Bio::DasI (3p) - DAS-style access to a feature database
Bio::DescribableI (3p) - interface for objects with human readable names and descriptions
Bio::Event::EventGeneratorI (3p) - This interface describes the basic event generator class.
Bio::Event::EventHandlerI (3p) - An Event Handler Interface
Bio::Expression::Contact (3p) - DESCRIPTION of Object
Bio::Expression::DataSet (3p) - DESCRIPTION of Object
Bio::Expression::FeatureGroup (3p) - a set of DNA/RNA features. ISA Bio::Expression::FeatureI
Bio::Expression::FeatureGroup::FeatureGroupMas50 (3p) - utility class for Mas50 FeatureGroup
Bio::Expression::FeatureI (3p) - an interface class for DNA/RNA features
Bio::Expression::FeatureSet::FeatureSetMas50 (3p) - utility class for Mas50 FeatureSet
Bio::Expression::Platform (3p) - DESCRIPTION of Object
Bio::Expression::ProbeI (3p) - an interface class for DNA/RNA probes
Bio::Expression::Sample (3p) - DESCRIPTION of Object
Bio::Factory::AnalysisI (3p) - An interface to analysis tool factory
Bio::Factory::ApplicationFactoryI (3p) - Interface class for Application Factories
Bio::Factory::DriverFactory (3p) - Base class for factory classes loading drivers
Bio::Factory::FTLocationFactory (3p) - A FeatureTable Location Parser
Bio::Factory::LocationFactoryI (3p) - A factory interface for generating locations from a string
Bio::Factory::MapFactoryI (3p) - A Factory for getting markers
Bio::Factory::ObjectBuilderI (3p) - Interface for an object builder
Bio::Factory::ObjectFactory (3p) - Instantiates a new Bio::Root::RootI (or derived class) through a factory
Bio::Factory::ObjectFactoryI (3p) - A General object creator factory
Bio::Factory::SeqAnalysisParserFactory (3p) - class capable of creating SeqAnalysisParserI compliant parsers
Bio::Factory::SeqAnalysisParserFactoryI (3p) - interface describing objects capable of creating SeqAnalysisParserI compliant parsers
Bio::Factory::SequenceFactoryI (3p) - This interface allows for generic building of sequences in factories which create sequences (like SeqIO)
Bio::Factory::SequenceProcessorI (3p) - Interface for chained sequence processing algorithms
Bio::Factory::SequenceStreamI (3p) - Interface describing the basics of a Sequence Stream.
Bio::Factory::TreeFactoryI (3p) - Factory Interface for getting and writing trees from/to a data stream
Bio::FeatureHolderI (3p) - the base interface an object with features must implement
Bio::FeatureIO (3p) - Handler for FeatureIO
Bio::FeatureIO::bed (3p) - read/write features from UCSC BED format
Bio::FeatureIO::gff (3p) - read/write GFF feature files
Bio::FeatureIO::gtf (3p) - read write features in GTF format
Bio::FeatureIO::interpro (3p) - read features from InterPro XML
Bio::FeatureIO::ptt (3p) - read/write features in PTT format
Bio::FeatureIO::vecscreen_simple (3p) - read/write features from NCBI vecscreen -f 3 output
Bio::HandlerBaseI (3p) - Interface class for handler methods which interact with any event-driven parsers (drivers).
Bio::IdCollectionI (3p) - interface for objects with multiple identifiers
Bio::IdentifiableI (3p) - interface for objects with identifiers
Bio::Index::Abstract (3p) - Abstract interface for indexing a flat file
Bio::Index::AbstractSeq (3p) - base class for AbstractSeq
Bio::Index::Blast (3p) - Indexes Blast reports and supports retrieval based on query accession(s)
Bio::Index::BlastTable (3p) - Indexes tabular Blast reports (-m 9 format) and supports retrieval based on query accession(s)
Bio::Index::EMBL (3p) - Interface for indexing (multiple) EMBL/Swissprot .dat files (i.e. flat file EMBL/Swissprot format).
Bio::Index::Fasta (3p) - Interface for indexing (multiple) fasta files
Bio::Index::Fastq (3p) - Interface for indexing (multiple) fastq files
Bio::Index::GenBank (3p) - Interface for indexing one or more GenBank files (i.e. flat file GenBank format).
Bio::Index::Hmmer (3p) - indexes HMMER reports and supports retreival based on query
Bio::Index::Qual (3p) - Interface for indexing (multiple) fasta qual files
Bio::Index::Stockholm (3p) - 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 (3p) - Interface for indexing swisspfam files
Bio::Index::Swissprot (3p) - Interface for indexing one or more Swissprot files.
Bio::LiveSeq::AARange (3p) - AARange abstract class for LiveSeq
Bio::LiveSeq::Chain (3p) - DoubleChain DataStructure for Perl
Bio::LiveSeq::ChainI (3p) - Double linked chain data structure
Bio::LiveSeq::DNA (3p) - DNA object for LiveSeq
Bio::LiveSeq::Exon (3p) - Range abstract class for LiveSeq
Bio::LiveSeq::Gene (3p) - Range abstract class for LiveSeq
Bio::LiveSeq::IO::BioPerl (3p) - Loader for LiveSeq from EMBL entries with BioPerl
Bio::LiveSeq::IO::Loader (3p) - Parent Loader for LiveSeq
Bio::LiveSeq::Intron (3p) - Range abstract class for LiveSeq
Bio::LiveSeq::Mutation (3p) - Mutation event descriptor class
Bio::LiveSeq::Mutator (3p) - Package mutating LiveSequences
Bio::LiveSeq::Prim_Transcript (3p) - Prim_Transcript class for LiveSeq
Bio::LiveSeq::Range (3p) - Range abstract class for LiveSeq
Bio::LiveSeq::Repeat_Region (3p) - Repeat_Region class for LiveSeq
Bio::LiveSeq::Repeat_Unit (3p) - Repeat_Unit class for LiveSeq
Bio::LiveSeq::SeqI (3p) - Abstract sequence interface class for LiveSeq
Bio::LiveSeq::Transcript (3p) - Transcript class for LiveSeq
Bio::LiveSeq::Translation (3p) - Translation class for LiveSeq
Bio::LocatableSeq (3p) - 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 (3p) - Implementation of a Atomic Location on a Sequence
Bio::Location::AvWithinCoordPolicy (3p) - class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise
Bio::Location::CoordinatePolicyI (3p) - Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location
Bio::Location::Fuzzy (3p) - Implementation of a Location on a Sequence which has unclear start and/or end locations
Bio::Location::FuzzyLocationI (3p) - Abstract interface of a Location on a Sequence which has unclear start/end location
Bio::Location::NarrowestCoordPolicy (3p) - class implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range
Bio::Location::Simple (3p) - Implementation of a Simple Location on a Sequence
Bio::Location::Split (3p) - Implementation of a Location on a Sequence which has multiple locations (start/end points)
Bio::Location::SplitLocationI (3p) - Abstract interface of a Location on a Sequence which has multiple locations (start/end points)
Bio::Location::WidestCoordPolicy (3p) - class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable range
Bio::LocationI (3p) - Abstract interface of a Location on a Sequence
Bio::Map::Clone (3p) - An central map object representing a clone
Bio::Map::Contig (3p) - A MapI implementation handling the contigs of a Physical Map (such as FPC)
Bio::Map::CytoMap (3p) - A Bio::MapI compliant map implementation handling cytogenic bands
Bio::Map::CytoMarker (3p) - An object representing a marker.
Bio::Map::CytoPosition (3p) - Marker class with cytogenetic band storing attributes
Bio::Map::EntityI (3p) - An Entity Interface
Bio::Map::FPCMarker (3p) - An central map object representing a marker
Bio::Map::Gene (3p) - An gene modelled as a mappable element.
Bio::Map::GeneMap (3p) - A MapI implementation to represent the area around a gene
Bio::Map::GenePosition (3p) - A typed position, suitable for modelling the various regions of a gene.
Bio::Map::GeneRelative (3p) - Represents being relative to named sub-regions of a gene.
Bio::Map::LinkageMap (3p) - A representation of a genetic linkage map.
Bio::Map::LinkagePosition (3p) - Create a Position for a Marker that will be placed on a Bio::Map::LinkageMap
Bio::Map::MapI (3p) - Interface for describing Map objects in bioperl
Bio::Map::Mappable (3p) - An object representing a generic map element that can have multiple locations in several maps.
Bio::Map::MappableI (3p) - An object that can be placed in a map
Bio::Map::Marker (3p) - An central map object representing a generic marker that can have multiple location in several maps.
Bio::Map::MarkerI (3p) - Interface for basic marker functionality
Bio::Map::Microsatellite (3p) - An object representing a Microsatellite marker.
Bio::Map::OrderedPosition (3p) - 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 (3p) - 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 (3p) - A class for handling a Physical Map (such as FPC)
Bio::Map::Position (3p) - A single position of a Marker, or the range over which that marker lies, in a Map
Bio::Map::PositionHandler (3p) - A Position Handler Implementation
Bio::Map::PositionHandlerI (3p) - A Position Handler Interface
Bio::Map::PositionI (3p) - Abstracts the notion of a position having a value in the context of a marker and a Map
Bio::Map::PositionWithSequence (3p) - A position with a sequence.
Bio::Map::Prediction (3p) - An object representing the predictions of something that can have multiple locations in several maps.
Bio::Map::Relative (3p) - Represents what a Position's coordiantes are relative to.
Bio::Map::RelativeI (3p) - Interface for describing what a Position's coordiantes are relative to.
Bio::Map::SimpleMap (3p) - A MapI implementation handling the basics of a Map
Bio::Map::TranscriptionFactor (3p) - A transcription factor modelled as a mappable element
Bio::MapIO (3p) - A Map Factory object
Bio::MapIO::fpc (3p) - A FPC Map reader
Bio::MapIO::mapmaker (3p) - A Mapmaker Map reader
Bio::Matrix::Generic (3p) - A generic matrix implementation
Bio::Matrix::IO (3p) - A factory for Matrix parsing
Bio::Matrix::IO::mlagan (3p) - A parser for the mlagan substitution matrix
Bio::Matrix::IO::phylip (3p) - A parser for PHYLIP distance matricies
Bio::Matrix::IO::scoring (3p) - A parser for PAM/BLOSUM matricies
Bio::Matrix::MatrixI (3p) - An interface for describing a Matrix
Bio::Matrix::Mlagan (3p) - A generic matrix with mlagan fields
Bio::Matrix::PSM::IO (3p) - PSM parser
Bio::Matrix::PSM::IO::mast (3p) - PSM mast parser implementation
Bio::Matrix::PSM::IO::masta (3p) - motif fasta format parser
Bio::Matrix::PSM::IO::meme (3p) - PSM meme parser implementation
Bio::Matrix::PSM::IO::psiblast (3p) - PSM psiblast parser
Bio::Matrix::PSM::IO::transfac (3p) - PSM transfac parser
Bio::Matrix::PSM::InstanceSite (3p) - A PSM site occurance
Bio::Matrix::PSM::InstanceSiteI (3p) - InstanceSite interface, holds an instance of a PSM
Bio::Matrix::PSM::ProtMatrix (3p) - SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) with log-odds scoring information.
Bio::Matrix::PSM::ProtPsm (3p) - handle combination of site matricies
Bio::Matrix::PSM::Psm (3p) - handle combination of site matricies
Bio::Matrix::PSM::PsmHeader (3p) - PSM mast parser implementation
Bio::Matrix::PSM::PsmHeaderI (3p) - handles the header data from a PSM file
Bio::Matrix::PSM::PsmI (3p) - abstract interface to handler of site matricies
Bio::Matrix::PSM::SiteMatrix (3p) - SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds
Bio::Matrix::PSM::SiteMatrixI (3p) - SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds
Bio::Matrix::PhylipDist (3p) - A Phylip Distance Matrix object
Bio::Matrix::Scoring (3p) - Object which can hold scoring matrix information
Bio::MolEvol::CodonModel (3p) - Codon Evolution Models
Bio::Ontology::DocumentRegistry (3p) - Keep track of where to find ontologies. Allows lookups by name.
Bio::Ontology::GOterm (3p) - representation of GO terms
Bio::Ontology::InterProTerm (3p) - Implementation of InterProI term interface
Bio::Ontology::OBOEngine (3p) - An Ontology Engine for OBO style flat file format from the Gene Ontology Consortium
Bio::Ontology::OBOterm (3p) - representation of OBO terms
Bio::Ontology::Ontology (3p) - standard implementation of an Ontology
Bio::Ontology::OntologyEngineI (3p) - Interface a minimal Ontology implementation should satisfy
Bio::Ontology::OntologyI (3p) - Interface for an ontology implementation
Bio::Ontology::OntologyStore (3p) - A repository of ontologies
Bio::Ontology::Path (3p) - a path for an ontology term graph
Bio::Ontology::PathI (3p) - Interface for a path between ontology terms
Bio::Ontology::Relationship (3p) - a relationship for an ontology
Bio::Ontology::RelationshipFactory (3p) - Instantiates a new Bio::Ontology::RelationshipI (or derived class) through a factory
Bio::Ontology::RelationshipI (3p) - Interface for a relationship between ontology terms
Bio::Ontology::RelationshipType (3p) - a relationship type for an ontology
Bio::Ontology::SimpleGOEngine::GraphAdaptor (3p) - Graph adaptor for Bio::Ontology::SimpleGOEngine
Bio::Ontology::SimpleGOEngine::GraphAdaptor02 (3p) - Graph adaptor (v02.x) for Bio::Ontology::SimpleGOEngine
Bio::Ontology::SimpleOntologyEngine (3p) - Implementation of OntologyEngineI interface
Bio::Ontology::Term (3p) - implementation of the interface for ontology terms
Bio::Ontology::TermFactory (3p) - Instantiates a new Bio::Ontology::TermI (or derived class) through a factory
Bio::Ontology::TermI (3p) - interface for ontology terms
Bio::OntologyIO (3p) - Parser factory for Ontology formats
Bio::OntologyIO::Handlers::BaseSAXHandler (3p) - base class for SAX Handlers
Bio::OntologyIO::Handlers::InterProHandler (3p) - XML handler class for InterProParser
Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler (3p) - parse an InterPro XML file and persist the resulting terms to a Biosql database
Bio::OntologyIO::InterProParser (3p) - Parser for InterPro xml files.
Bio::OntologyIO::dagflat (3p) - a base class parser for GO flat-file type formats
Bio::OntologyIO::goflat (3p) - a parser for the Gene Ontology flat-file format
Bio::OntologyIO::obo (3p) - a parser for OBO flat-file format from Gene Ontology Consortium
Bio::OntologyIO::simplehierarchy (3p) - a base class parser for simple hierarchy-by-indentation type formats
Bio::OntologyIO::soflat (3p) - a parser for the Sequence Ontology flat-file format
Bio::ParameterBaseI (3p) - Simple interface class for any parameter-related data such as IDs, database name, program arguments, and other odds and ends.
Bio::Perl (3p) - Functional access to BioPerl for people who don't know objects
Bio::Phenotype::Correlate (3p) - Representation of a correlating phenotype in a given species
Bio::Phenotype::MeSH::Term (3p) - A MeSH term
Bio::Phenotype::MeSH::Twig (3p) - Context for a MeSH term
Bio::Phenotype::Measure (3p) - Representation of context/value(-range)/unit triplets
Bio::Phenotype::OMIM::MiniMIMentry (3p) - Representation of a Mini MIM entry
Bio::Phenotype::OMIM::OMIMentry (3p) - represents OMIM (Online Mendelian Inheritance in Man) database entries
Bio::Phenotype::OMIM::OMIMentryAllelicVariant (3p) - Representation of a allelic variant of the OMIM database
Bio::Phenotype::OMIM::OMIMparser (3p) - parser for the OMIM database
Bio::Phenotype::Phenotype (3p) - A class for modeling phenotypes
Bio::Phenotype::PhenotypeI (3p) - An interface for classes modeling phenotypes
Bio::PhyloNetwork (3p) - Module to compute with Phylogenetic Networks
Bio::PhyloNetwork::Factory (3p) - Module to sequentially generate Phylogenetic Networks
Bio::PhyloNetwork::FactoryX (3p) - Module to sequentially generate Phylogenetic Networks
Bio::PhyloNetwork::GraphViz (3p) - Interface between PhyloNetwork and GraphViz
Bio::PhyloNetwork::RandomFactory (3p) - Module to generate random Phylogenetic Networks
Bio::PhyloNetwork::TreeFactory (3p) - Module to sequentially generate Phylogenetic Trees
Bio::PhyloNetwork::TreeFactoryMulti (3p) - Module to sequentially generate Phylogenetic Trees
Bio::PhyloNetwork::TreeFactoryX (3p) - Module to sequentially generate Phylogenetic Trees
Bio::PhyloNetwork::muVector (3p) - Module to compute with vectors of arbitrary dimension
Bio::PopGen::Genotype (3p) - An implementation of GenotypeI which is just an allele container
Bio::PopGen::GenotypeI (3p) - A marker and alleles for a specific individual
Bio::PopGen::HtSNP.pm (3p) - Select htSNP from a haplotype set
Bio::PopGen::IO (3p) - Input individual,marker,allele information
Bio::PopGen::IO::csv (3p) -Extract individual allele data from a CSV parser
Bio::PopGen::IO::hapmap (3p) - A parser for HapMap output data
Bio::PopGen::IO::phase (3p) - A parser for Phase format data
Bio::PopGen::IO::prettybase (3p) - Extract individual allele data from PrettyBase format
Bio::PopGen::Individual (3p) - An implementation of an Individual who has Genotype or Sequence Results
Bio::PopGen::IndividualI (3p) - An individual who has Genotype or Sequence Results
Bio::PopGen::Marker (3p) - A genetic marker which one uses to generate genotypes
Bio::PopGen::MarkerI (3p) - A Population Genetic conceptual marker
Bio::PopGen::PopStats (3p) - A collection of methods for calculating statistics about a population or sets of populations
Bio::PopGen::Population (3p) - A population of individuals
Bio::PopGen::PopulationI (3p) - Interface for Populations
Bio::PopGen::Simulation::Coalescent (3p) - A Coalescent simulation factory
Bio::PopGen::Simulation::GeneticDrift (3p) - A simple genetic drift simulation
Bio::PopGen::Statistics (3p) - Population Genetics statistical tests
Bio::PopGen::TagHaplotype.pm (3p) - Haplotype tag object.
Bio::PopGen::Utilities (3p) - Utilities for working with PopGen data and objects
Bio::PrimarySeq (3p) - Bioperl lightweight Sequence Object
Bio::PrimarySeqI (3p) - Interface definition for a Bio::PrimarySeq
Bio::PullParserI (3p) - A base module for fast 'pull' parsing
Bio::Range (3p) - Pure perl RangeI implementation
Bio::RangeI (3p) - Range interface
Bio::Restriction::Analysis (3p) - cutting sequences with restriction enzymes
Bio::Restriction::Enzyme (3p) - A single restriction endonuclease (cuts DNA at specific locations)
Bio::Restriction::Enzyme::MultiCut (3p) - A single restriction endonuclease
Bio::Restriction::Enzyme::MultiSite (3p) - A single restriction endonuclease
Bio::Restriction::EnzymeCollection (3p) - Set of restriction endonucleases
Bio::Restriction::EnzymeI (3p) - Interface class for restriction endonuclease
Bio::Restriction::IO (3p) - Handler for sequence variation IO Formats
Bio::Restriction::IO::bairoch (3p) - bairoch enzyme set
Bio::Restriction::IO::base (3p) - base enzyme set
Bio::Restriction::IO::itype2 (3p) - itype2 enzyme set
Bio::Restriction::IO::prototype (3p) - prototype enzyme set
Bio::Restriction::IO::withrefm (3p) - withrefm enzyme set
Bio::Root::Build (3p) - A common Module::Build subclass base for BioPerl distributions
Bio::Root::Exception (3p) - Generic exception objects for Bioperl
Bio::Root::HTTPget (3p) - module for fallback HTTP get operations when LWP:: is unavailable
Bio::Root::IO (3p) - module providing several methods often needed when dealing with file IO
Bio::Root::Root (3p) - Hash-based implementation of Bio::Root::RootI
Bio::Root::RootI (3p) - Abstract interface to root object code
Bio::Root::Storable (3p) - object serialisation methods
Bio::Root::Test (3p) - A common base for all Bioperl test scripts.
Bio::Root::Test::Warn (3p) - Perl extension to test Bioperl methods for warnings
Bio::Root::Utilities (3p) - General-purpose utility module
Bio::Root::Version (3p) - provide global, distribution-level versioning
Bio::Search::BlastStatistics (3p) - An object for Blast statistics
Bio::Search::BlastUtils (3p) - Utility functions for Bio::Search:: BLAST objects
Bio::Search::DatabaseI (3p) - Interface for a database used in a sequence search
Bio::Search::GenericDatabase (3p) - Generic implementation of Bio::Search::DatabaseI
Bio::Search::GenericStatistics (3p) - An object for statistics
Bio::Search::HSP::BlastHSP (3p) - Bioperl BLAST High-Scoring Pair object
Bio::Search::HSP::BlastPullHSP (3p) - A parser and HSP object for BlastN hsps
Bio::Search::HSP::FastaHSP (3p) - HSP object for FASTA specific data
Bio::Search::HSP::GenericHSP (3p) - A "Generic" implementation of a High Scoring Pair
Bio::Search::HSP::HMMERHSP (3p) - A HSP object for HMMER results
Bio::Search::HSP::HSPFactory (3p) - A factory to create Bio::Search::HSP::HSPI objects
Bio::Search::HSP::HSPI (3p) - Interface for a High Scoring Pair in a similarity search result
Bio::Search::HSP::HmmpfamHSP (3p) - A parser and HSP object for hmmpfam hsps
Bio::Search::HSP::ModelHSP (3p) - A HSP object for model-based searches
Bio::Search::HSP::PSLHSP (3p) - A HSP for PSL output
Bio::Search::HSP::PsiBlastHSP (3p) - Bioperl BLAST High-Scoring Pair object
Bio::Search::HSP::PullHSPI (3p) - Bio::Search::HSP::HSPI interface for pull parsers.
Bio::Search::HSP::WABAHSP (3p) - HSP object suitable for describing WABA alignments
Bio::Search::Hit::BlastHit (3p) - Blast-specific subclass of Bio::Search::Hit::GenericHit
Bio::Search::Hit::BlastPullHit (3p) - A parser and hit object for BLASTN hits
Bio::Search::Hit::Fasta (3p) - Hit object specific for Fasta-generated hits
Bio::Search::Hit::GenericHit (3p) - A generic implementation of the Bio::Search::Hit::HitI interface
Bio::Search::Hit::HMMERHit (3p) - A Hit module for HMMER hits
Bio::Search::Hit::HitFactory (3p) - A factory to create Bio::Search::Hit::HitI objects
Bio::Search::Hit::HitI (3p) - Interface for a hit in a similarity search result
Bio::Search::Hit::HmmpfamHit (3p) - A parser and hit object for hmmpfam hits
Bio::Search::Hit::ModelHit (3p) - A model-based implementation of the Bio::Search::Hit::HitI interface
Bio::Search::Hit::PsiBlastHit (3p) - Bioperl BLAST Hit object
Bio::Search::Hit::PullHitI (3p) - Bio::Search::Hit::HitI interface for pull parsers.
Bio::Search::Iteration::GenericIteration (3p) - A generic implementation of the Bio::Search::Iteration::IterationI interface.
Bio::Search::Iteration::IterationI (3p) - Abstract interface to an iteration from an iterated search result, such as PSI-BLAST.
Bio::Search::Processor (3p) - DESCRIPTION of Object
Bio::Search::Result::BlastPullResult (3p) - A parser and result object for BLASTN results
Bio::Search::Result::BlastResult (3p) - Blast-specific subclass of Bio::Search::Result::GenericResult
Bio::Search::Result::CrossMatchResult (3p) - CrossMatch-specific subclass of Bio::Search::Result::GenericResult
Bio::Search::Result::GenericResult (3p) - Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results.
Bio::Search::Result::HMMERResult (3p) - A Result object for HMMER results
Bio::Search::Result::HmmpfamResult (3p) - A parser and result object for hmmpfam results
Bio::Search::Result::PullResultI (3p) - Bio::Search::Result::ResultI interface for 'pull' parsers
Bio::Search::Result::ResultFactory (3p) - A factory to create Bio::Search::Result::ResultI objects
Bio::Search::Result::ResultI (3p) - Abstract interface to Search Result objects
Bio::Search::Result::WABAResult (3p) - Result object for WABA alignment output
Bio::Search::SearchUtils (3p) - Utility functions for Bio::Search:: objects
Bio::Search::StatisticsI (3p) - A Base object for statistics
Bio::Search::Tiling::MapTileUtils (3p) - utilities for manipulating closed intervals for an HSP tiling algorithm
Bio::Search::Tiling::MapTiling (3p) - An implementation of an HSP tiling algorithm, with methods to obtain frequently-requested statistics
Bio::Search::Tiling::TilingI (3p) - Abstract interface for an HSP tiling module
Bio::SearchDist (3p) - A perl wrapper around Sean Eddy's histogram object
Bio::SearchIO (3p) - Driver for parsing Sequence Database Searches (BLAST, FASTA, ...)
Bio::SearchIO::EventHandlerI (3p) - An abstract Event Handler for Search Result parsing
Bio::SearchIO::FastHitEventBuilder (3p) - Event Handler for SearchIO events.
Bio::SearchIO::IteratedSearchResultEventBuilder (3p) - Event Handler for SearchIO events.
Bio::SearchIO::SearchResultEventBuilder (3p) - Event Handler for SearchIO events.
Bio::SearchIO::SearchWriterI (3p) - Interface for outputting parsed Search results
Bio::SearchIO::Writer::BSMLResultWriter (3p) - BSML output writer
Bio::SearchIO::Writer::GbrowseGFF (3p) - Interface for outputting parsed search results in Gbrowse GFF format
Bio::SearchIO::Writer::HSPTableWriter (3p) - Tab-delimited data for Bio::Search::HSP::HSPI objects
Bio::SearchIO::Writer::HTMLResultWriter (3p) - write a Bio::Search::ResultI in HTML
Bio::SearchIO::Writer::HitTableWriter (3p) - Tab-delimited data for Bio::Search::Hit::HitI objects
Bio::SearchIO::Writer::ResultTableWriter (3p) - Outputs tab-delimited data for each Bio::Search::Result::ResultI object.
Bio::SearchIO::Writer::TextResultWriter (3p) - Object to implement writing a Bio::Search::ResultI in Text.
Bio::SearchIO::XML::BlastHandler (3p) - XML Handler for NCBI Blast XML parsing.
Bio::SearchIO::XML::PsiBlastHandler (3p) - XML Handler for NCBI Blast PSIBLAST XML parsing.
Bio::SearchIO::axt (3p) - a parser for axt format reports
Bio::SearchIO::blast (3p) - Event generator for event based parsing of blast reports
Bio::SearchIO::blast_pull (3p) - A parser for BLAST output
Bio::SearchIO::blasttable (3p) - Driver module for SearchIO for parsing NCBI -m 8/9 format
Bio::SearchIO::blastxml (3p) - A SearchIO implementation of NCBI Blast XML parsing.
Bio::SearchIO::cross_match (3p) - CrossMatch-specific subclass of Bio::SearchIO
Bio::SearchIO::erpin (3p) - SearchIO-based ERPIN parser
Bio::SearchIO::exonerate (3p) - parser for Exonerate
Bio::SearchIO::fasta (3p) - A SearchIO parser for FASTA results
Bio::SearchIO::gmap_f9 (3p) - Event generator for parsing gmap reports (Z format)
Bio::SearchIO::hmmer (3p) - A parser for HMMER output (hmmpfam, hmmsearch)
Bio::SearchIO::hmmer_pull (3p) - A parser for HMMER output
Bio::SearchIO::infernal (3p) - SearchIO-based Infernal parser
Bio::SearchIO::megablast (3p) - a driver module for Bio::SearchIO to parse megablast reports (format 0)
Bio::SearchIO::psl (3p) - A parser for PSL output (UCSC)
Bio::SearchIO::rnamotif (3p) - SearchIO-based RNAMotif parser
Bio::SearchIO::sim4 (3p) - parser for Sim4 alignments
Bio::SearchIO::waba (3p) - SearchIO parser for Jim Kent WABA program alignment output
Bio::SearchIO::wise (3p) - Parsing of wise output as alignments
Bio::Seq (3p) - Sequence object, with features
Bio::Seq::BaseSeqProcessor (3p) - Base implementation for a SequenceProcessor
Bio::Seq::EncodedSeq (3p) - subtype of Bio::LocatableSeq to store DNA that encodes a protein
Bio::Seq::LargeLocatableSeq (3p) - LocatableSeq object that stores sequence as files in the tempdir
Bio::Seq::LargePrimarySeq (3p) - 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 (3p) - SeqI compliant object that stores sequence as files in /tmp
Bio::Seq::LargeSeqI (3p) - Interface class for sequences that cache their residues in a temporary file
Bio::Seq::Meta (3p) - Generic superclass for sequence objects with residue-based meta information
Bio::Seq::Meta::Array (3p) - array-based generic implementation of a sequence class with residue-based meta information
Bio::Seq::MetaI (3p) - Interface for sequence objects with residue-based meta information
Bio::Seq::PrimaryQual (3p) - Bioperl lightweight Quality Object
Bio::Seq::PrimedSeq (3p) - A representation of a sequence and two primers flanking a target region
Bio::Seq::QualI (3p) - Interface definition for a Bio::Seq::Qual
Bio::Seq::Quality (3p) - Implementation of sequence with residue quality and trace values
Bio::Seq::RichSeq (3p) - Module implementing a sequence created from a rich sequence database entry
Bio::Seq::RichSeqI (3p) - interface for sequences from rich data sources, mostly databases
Bio::Seq::SeqBuilder (3p) - Configurable object builder for sequence stream parsers
Bio::Seq::SeqFactory (3p) - Instantiates a new Bio::PrimarySeqI (or derived class) through a factory
Bio::Seq::SeqFastaSpeedFactory (3p) - Instantiates a new Bio::PrimarySeqI (or derived class) through a factory
Bio::Seq::SeqWithQuality (3p) - Bioperl object packaging a sequence with its quality. Deprecated class, use Bio::Seq::Quality instead!
Bio::Seq::SequenceTrace (3p) - Bioperl object packaging a sequence with its trace
Bio::Seq::TraceI (3p) - Interface definition for a Bio::Seq::Trace
Bio::SeqAnalysisParserI (3p) - Sequence analysis output parser interface
Bio::SeqEvolution::DNAPoint (3p) - evolve a sequence by point mutations
Bio::SeqEvolution::EvolutionI (3p) - the interface for evolving sequences
Bio::SeqEvolution::Factory (3p) - Factory object to instantiate sequence evolving classes
Bio::SeqFeature::Annotated (3p) - PLEASE PUT SOMETHING HERE
Bio::SeqFeature::AnnotationAdaptor (3p) - integrates SeqFeatureIs annotation
Bio::SeqFeature::Collection (3p) - 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 (3p) - An interface for a collection of SeqFeatureI objects.
Bio::SeqFeature::Computation (3p) - Computation SeqFeature
Bio::SeqFeature::FeaturePair (3p) - hold pair feature information e.g. blast hits
Bio::SeqFeature::Gene::Exon (3p) - a feature representing an exon
Bio::SeqFeature::Gene::ExonI (3p) - Interface for a feature representing an exon
Bio::SeqFeature::Gene::GeneStructure (3p) - A feature representing an arbitrarily complex structure of a gene
Bio::SeqFeature::Gene::GeneStructureI (3p) - A feature representing an arbitrarily complex structure of a gene
Bio::SeqFeature::Gene::Intron (3p) - An intron feature
Bio::SeqFeature::Gene::NC_Feature.pm (3p) - superclass for non-coding features
Bio::SeqFeature::Gene::Poly_A_site (3p) - poly A feature
Bio::SeqFeature::Gene::Promoter (3p) - Describes a promoter
Bio::SeqFeature::Gene::Transcript (3p) - A feature representing a transcript
Bio::SeqFeature::Gene::TranscriptI (3p) - Interface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site.
Bio::SeqFeature::Gene::UTR (3p) - A feature representing an untranslated region that is part of a transcriptional unit
Bio::SeqFeature::Generic (3p) - Generic SeqFeature
Bio::SeqFeature::Lite (3p) - Lightweight Bio::SeqFeatureI class
Bio::SeqFeature::PositionProxy (3p) - handle features when truncation/revcom sequences span a feature
Bio::SeqFeature::Primer (3p) - Primer Generic SeqFeature
Bio::SeqFeature::SiRNA::Oligo (3p) - Perl object for small inhibitory RNAs.
Bio::SeqFeature::SiRNA::Pair (3p) - Perl object for small inhibitory RNA (SiRNA) oligo pairs
Bio::SeqFeature::Similarity (3p) - A sequence feature based on similarity
Bio::SeqFeature::SimilarityPair (3p) - Sequence feature based on the similarity of two sequences.
Bio::SeqFeature::Tools::FeatureNamer (3p) - generates unique persistent names for features
Bio::SeqFeature::Tools::IDHandler (3p) - maps $seq_feature->primary_tag
Bio::SeqFeature::Tools::TypeMapper (3p) - maps $seq_feature->primary_tag
Bio::SeqFeature::Tools::Unflattener (3p) - turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy
Bio::SeqFeature::TypedSeqFeatureI (3p) - a strongly typed SeqFeature
Bio::SeqFeatureI (3p) - Abstract interface of a Sequence Feature
Bio::SeqI (3p) - [Developers] Abstract Interface of Sequence (with features)
Bio::SeqIO (3p) - Handler for SeqIO Formats
Bio::SeqIO::FTHelper (3p) - Helper class for Embl/Genbank feature tables
Bio::SeqIO::Handler::GenericRichSeqHandler (3p) - Bio::HandlerI-based data handler for GenBank/EMBL/UniProt (and other) sequence data
Bio::SeqIO::MultiFile (3p) - Treating a set of files as a single input stream
Bio::SeqIO::abi (3p) - abi trace sequence input/output stream
Bio::SeqIO::ace (3p) - ace sequence input/output stream
Bio::SeqIO::agave (3p) - AGAVE sequence output stream.
Bio::SeqIO::alf (3p) - alf trace sequence input/output stream
Bio::SeqIO::asciitree (3p) - asciitree sequence input/output stream
Bio::SeqIO::bsml (3p) - BSML sequence input/output stream
Bio::SeqIO::bsml_sax (3p) - BSML sequence input/output stream using SAX
Bio::SeqIO::chadoxml (3p) - chadoxml sequence output stream
Bio::SeqIO::chaos (3p) - chaos sequence input/output stream
Bio::SeqIO::chaosxml (3p) - chaosxml sequence input/output stream
Bio::SeqIO::ctf (3p) - ctf trace sequence input/output stream
Bio::SeqIO::embl (3p) - EMBL sequence input/output stream
Bio::SeqIO::embldriver (3p) - EMBL sequence input/output stream
Bio::SeqIO::entrezgene (3p) - Entrez Gene ASN1 parser
Bio::SeqIO::excel (3p) - sequence input/output stream from a MSExcel-formatted table
Bio::SeqIO::exp (3p) - exp trace sequence input/output stream
Bio::SeqIO::fasta (3p) - fasta sequence input/output stream
Bio::SeqIO::fastq (3p) - fastq sequence input/output stream
Bio::SeqIO::flybase_chadoxml (3p) - FlyBase variant of chadoxml with sequence output stream
Bio::SeqIO::game (3p) -- a class for parsing and writing game-XML
Bio::SeqIO::game::featHandler (3p) -- a class for handling feature elements
Bio::SeqIO::game::gameHandler (3p) -- PerlSAX handler for game-XML
Bio::SeqIO::game::gameSubs (3p) -- a base class for game-XML parsing
Bio::SeqIO::game::gameWriter (3p) -- a class for writing game-XML
Bio::SeqIO::game::seqHandler (3p) -- a class for handling game-XML sequences
Bio::SeqIO::gbdriver (3p) - GenBank handler-based push parser
Bio::SeqIO::gcg (3p) - GCG sequence input/output stream
Bio::SeqIO::genbank (3p) - GenBank sequence input/output stream
Bio::SeqIO::interpro (3p) - InterProScan XML input/output stream
Bio::SeqIO::kegg (3p) - KEGG sequence input/output stream
Bio::SeqIO::largefasta (3p) - method i/o on very large fasta sequence files
Bio::SeqIO::lasergene (3p) - Lasergene sequence file input/output stream
Bio::SeqIO::locuslink (3p) - LocusLink input/output stream
Bio::SeqIO::metafasta (3p) - metafasta sequence input/output stream
Bio::SeqIO::phd (3p) - .phd file input/output stream
Bio::SeqIO::pir (3p) - PIR sequence input/output stream
Bio::SeqIO::pln (3p) - pln trace sequence input/output stream
Bio::SeqIO::qual (3p) - .qual file input/output stream
Bio::SeqIO::raw (3p) - raw sequence file input/output stream
Bio::SeqIO::scf (3p) - .scf file input/output stream
Bio::SeqIO::strider (3p) - DNA strider sequence input/output stream
Bio::SeqIO::swiss (3p) - Swissprot sequence input/output stream
Bio::SeqIO::swissdriver (3p) - SwissProt/UniProt handler-based push parser
Bio::SeqIO::tab (3p) - nearly raw sequence file input/output stream. Reads/writes id"\et"sequence"\en"
Bio::SeqIO::table (3p) - sequence input/output stream from a delimited table
Bio::SeqIO::tigr (3p) - TIGR XML sequence input/output stream
Bio::SeqIO::tigrxml (3p) - Parse TIGR (new) XML
Bio::SeqIO::tinyseq (3p) - reading/writing sequences in NCBI TinySeq format
Bio::SeqIO::tinyseq::tinyseqHandler (3p) - XML event handlers to support NCBI TinySeq XML parsing
Bio::SeqIO::ztr (3p) - ztr trace sequence input/output stream
Bio::SeqUtils (3p) - Additional methods for PrimarySeq objects
Bio::SimpleAlign (3p) - Multiple alignments held as a set of sequences
Bio::SimpleAnalysisI (3p) - A simple interface to any (local or remote) analysis tool
Bio::Species (3p) - Generic species object
Bio::Structure::Atom (3p) - Bioperl structure Object, describes an Atom
Bio::Structure::Chain (3p) - Bioperl structure Object, describes a chain
Bio::Structure::Entry (3p) - Bioperl structure Object, describes the whole entry
Bio::Structure::IO (3p) - Handler for Structure Formats
Bio::Structure::IO::pdb (3p) - PDB input/output stream
Bio::Structure::Model (3p) - Bioperl structure Object, describes a Model
Bio::Structure::Residue (3p) - Bioperl structure Object, describes a Residue
Bio::Structure::SecStr::DSSP::Res (3p) - Module for parsing/accessing dssp output
Bio::Structure::SecStr::STRIDE::Res (3p) - Module for parsing/accessing stride output
Bio::Structure::StructureI (3p) - Abstract Interface for a Structure objects
Bio::Symbol::Alphabet (3p) - BSANE/BioCORBA compliant symbol list alphabet
Bio::Symbol::AlphabetI (3p) - A Symbol Alphabet
Bio::Symbol::DNAAlphabet (3p) - A ready made DNA alphabet
Bio::Symbol::ProteinAlphabet (3p) - A ready made Protein alphabet
Bio::Symbol::Symbol (3p) - A biological symbol
Bio::Symbol::SymbolI (3p) - Interface for a Symbol
Bio::Taxon (3p) - A node in a represented taxonomy
Bio::Taxonomy (3p) - representing Taxonomy.
Bio::Taxonomy::FactoryI (3p) - interface to define how to access NCBI Taxonoy
Bio::Taxonomy::Node (3p) - A node in a represented taxonomy
Bio::Taxonomy::Taxon (3p) - Generic Taxonomic Entity object
Bio::Taxonomy::Tree (3p) - An Organism Level Implementation of TreeI interface.
Bio::Tools::AlignFactory (3p) - Base object for alignment factories
Bio::Tools::Alignment::Consed (3p) - A module to work with objects from consed .ace files
Bio::Tools::Alignment::Trim (3p) - A kludge to do specialized trimming of sequence based on quality.
Bio::Tools::Analysis::DNA::ESEfinder (3p) - a wrapper around ESEfinder server
Bio::Tools::Analysis::Protein::Domcut (3p) - a wrapper around Domcut server
Bio::Tools::Analysis::Protein::ELM (3p) - a wrapper around the ELM server which predicts short functional motifs on amino acid sequences
Bio::Tools::Analysis::Protein::GOR4 (3p) - a wrapper around GOR4 protein secondary structure prediction server
Bio::Tools::Analysis::Protein::HNN (3p) - a wrapper around the HNN protein secondary structure prediction server
Bio::Tools::Analysis::Protein::Mitoprot (3p) - a wrapper around Mitoprot server
Bio::Tools::Analysis::Protein::NetPhos (3p) - a wrapper around NetPhos server
Bio::Tools::Analysis::Protein::Scansite (3p) - a wrapper around the Scansite server
Bio::Tools::Analysis::Protein::Sopma (3p) - a wrapper around the Sopma protein secondary structure prediction server
Bio::Tools::Analysis::SimpleAnalysisBase (3p) - abstract superclass for SimpleAnalysis implementations
Bio::Tools::AnalysisResult (3p) - Base class for analysis result objects and parsers
Bio::Tools::Blat (3p) - parser for Blat program
Bio::Tools::CodonTable (3p) - Codon table object
Bio::Tools::Coil (3p) - parser for Coil output
Bio::Tools::ECnumber (3p) - representation of EC numbers (Enzyme Classification)
Bio::Tools::EMBOSS::Palindrome (3p) - parse EMBOSS palindrome output
Bio::Tools::EPCR (3p) - Parse ePCR output and make features
Bio::Tools::ERPIN (3p) - a parser for ERPIN output
Bio::Tools::ESTScan (3p) - Results of one ESTScan run
Bio::Tools::EUtilities (3p) - NCBI eutil XML parsers
Bio::Tools::EUtilities::Cookie (3p) - lightweight implementation of HistoryI interface (not bound to filehandles, extraneous methods, etc).
Bio::Tools::EUtilities::EUtilDataI (3p) - eutil data object interface
Bio::Tools::EUtilities::EUtilParameters (3p) - Manipulation of NCBI eutil-based parameters for remote database requests.
Bio::Tools::EUtilities::History (3p) - lightweight implementation of HistoryI interface (not bound to filehandles, extraneous methods, etc).
Bio::Tools::EUtilities::HistoryI (3p) - simple extension of EUtilDataI interface class for classes which hold NCBI server history data
Bio::Tools::EUtilities::Info (3p) - interface class for storing einfo data
Bio::Tools::EUtilities::Info::FieldInfo (3p) - class for storing einfo field data
Bio::Tools::EUtilities::Info::LinkInfo (3p) - class for storing einfo link data
Bio::Tools::EUtilities::Link (3p) - general API for accessing data retrieved from elink queries
Bio::Tools::EUtilities::Link::LinkSet (3p) - class for EUtils LinkSets
Bio::Tools::EUtilities::Link::UrlLink (3p) - class for EUtils UrlLinks
Bio::Tools::EUtilities::Query (3p) - parse and collect esearch, epost, espell, egquery information
Bio::Tools::EUtilities::Query::GlobalQuery (3p) - container class for egquery data
Bio::Tools::EUtilities::Summary (3p) - class for handlign data output (XML) from esummary.
Bio::Tools::EUtilities::Summary::DocSum (3p) - data object for document summary data from esummary
Bio::Tools::EUtilities::Summary::Item (3p) - simple layered object for DocSum item data
Bio::Tools::EUtilities::Summary::ItemContainerI (3p) - 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 (3p) - Results of one Eponine run
Bio::Tools::Est2Genome (3p) - Parse est2genome output, makes simple Bio::SeqFeature::Generic objects
Bio::Tools::Fgenesh (3p) - parse results of one Fgenesh run
Bio::Tools::FootPrinter (3p) - write sequence features in FootPrinter format
Bio::Tools::GFF (3p) - A Bio::SeqAnalysisParserI compliant GFF format parser
Bio::Tools::Gel (3p) - Calculates relative electrophoretic migration distances
Bio::Tools::Geneid (3p) - Results of one geneid run
Bio::Tools::Genemark (3p) - Results of one Genemark run
Bio::Tools::Genewise (3p) - Results of one Genewise run
Bio::Tools::Genomewise (3p) - Results of one Genomewise run
Bio::Tools::Genscan (3p) - Results of one Genscan run
Bio::Tools::Glimmer (3p) - parser for Glimmer 2.X/3.X prokaryotic and GlimmerM/GlimmerHMM eukaryotic gene predictions
Bio::Tools::Grail (3p) - Results of one Grail run
Bio::Tools::GuessSeqFormat (3p) - Module for determining the sequence format of the contents of a file, a string, or through a filehandle.
Bio::Tools::HMMER::Domain (3p) - One particular domain hit from HMMER
Bio::Tools::HMMER::Results (3p) - Object representing HMMER output results
Bio::Tools::HMMER::Set (3p) - Set of identical domains from HMMER matches
Bio::Tools::Hmmpfam (3p) - Parser for Hmmpfam program
Bio::Tools::IUPAC (3p) - Generates unique Seq objects from an ambiguous Seq object
Bio::Tools::Infernal (3p) - A parser for Infernal output
Bio::Tools::Lucy (3p) - Object for analyzing the output from Lucy, a vector and quality trimming program from TIGR
Bio::Tools::MZEF (3p) - Results of one MZEF run
Bio::Tools::Match (3p) - Parses output from Transfac's match(TM)
Bio::Tools::OddCodes (3p) - Object holding alternative alphabet coding for one protein sequence
Bio::Tools::Phylo::Gerp (3p) - Parses output from GERP
Bio::Tools::Phylo::Gumby (3p) - Parses output from gumby
Bio::Tools::Phylo::Molphy (3p) - parser for Molphy output
Bio::Tools::Phylo::Molphy::Result (3p) - container for data parsed from a ProtML run
Bio::Tools::Phylo::PAML (3p) - Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00
Bio::Tools::Phylo::PAML::ModelResult (3p) - A container for NSSite Model Result from PAML
Bio::Tools::Phylo::PAML::Result (3p) - A PAML result set object
Bio::Tools::Phylo::Phylip::ProtDist (3p) - parser for ProtDist output
Bio::Tools::Prediction::Exon (3p) - A predicted exon feature
Bio::Tools::Prediction::Gene (3p) - a predicted gene structure feature
Bio::Tools::Primer3 (3p) - Create input for and work with the output from the program primer3
Bio::Tools::Primer::Assessor::Base (3p) - base class for common assessor things
Bio::Tools::Primer::AssessorI (3p) - interface for assessing primer pairs
Bio::Tools::Primer::Feature (3p) - position of a single primer
Bio::Tools::Primer::Pair (3p) - two primers on left and right side
Bio::Tools::Prints (3p) - Parser for FingerPRINTScanII program
Bio::Tools::Profile (3p) - parse Profile output
Bio::Tools::Promoterwise (3p) - parser for Promoterwise tab format output
Bio::Tools::PrositeScan (3p) - Parser for ps_scan result
Bio::Tools::Protparam (3p) - submit to and parse output from protparam ;
Bio::Tools::Pseudowise (3p) - Results of one Pseudowise run
Bio::Tools::QRNA (3p) - A Parser for qrna output
Bio::Tools::RNAMotif (3p) - A parser for RNAMotif output
Bio::Tools::RandomDistFunctions (3p) - A set of routines useful for generating random data in different distributions
Bio::Tools::RepeatMasker (3p) - a parser for RepeatMasker output
Bio::Tools::Run::GenericParameters (3p) - An object for the parameters used to run programs
Bio::Tools::Run::ParametersI (3p) - A Base object for the parameters used to run programs
Bio::Tools::Run::RemoteBlast (3p) - Object for remote execution of the NCBI Blast via HTTP
Bio::Tools::Run::StandAloneBlast (3p) - 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 (3p) - Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). With experimental support for NCBI rpsblast.
Bio::Tools::Run::StandAloneWUBlast (3p) - Object for the local execution of WU-Blast.
Bio::Tools::Run::WrapperBase (3p) - A Base object for wrappers around executables
Bio::Tools::Seg (3p) - parse "seg" output
Bio::Tools::SeqPattern (3p) - represent a sequence pattern or motif
Bio::Tools::SeqPattern::Backtranslate (3p) - (empty subject)
Bio::Tools::SeqStats (3p) - Object holding statistics for one particular sequence
Bio::Tools::SeqWords (3p) - Object holding n-mer statistics for a sequence
Bio::Tools::SiRNA::Ruleset::saigo (3p) - Perl object implementing the Saigo group's rules for designing small inhibitory RNAs
Bio::Tools::SiRNA::Ruleset::tuschl (3p) - Perl object implementing the tuschl group's rules for designing small inhibitory RNAs
Bio::Tools::Sigcleave (3p) - Bioperl object for sigcleave analysis
Bio::Tools::Signalp (3p) - parser for Signalp output
Bio::Tools::Signalp::ExtendedSignalp (3p) - enhanced parser for Signalp output
Bio::Tools::Sim4::Exon (3p) - A single exon determined by an alignment
Bio::Tools::Sim4::Results (3p) - Results of one Sim4 run
Bio::Tools::Spidey::Exon (3p) - A single exon determined by an alignment
Bio::Tools::Spidey::Results (3p) - Results of a Spidey run
Bio::Tools::TandemRepeatsFinder (3p) - a parser for Tandem Repeats Finder output
Bio::Tools::TargetP (3p) - Results of one TargetP run
Bio::Tools::Tmhmm (3p) - parse TMHMM output (TransMembrane HMM)
Bio::Tools::dpAlign (3p) - Perl extension to do pairwise dynamic programming sequence alignment
Bio::Tools::ipcress (3p) - Parse ipcress output and make features
Bio::Tools::isPcr (3p) - Parse isPcr output and make features
Bio::Tools::pICalculator (3p) - calculate the isoelectric point of a protein
Bio::Tools::pSW (3p) - pairwise Smith Waterman object
Bio::Tools::tRNAscanSE (3p) - A parser for tRNAscan-SE output
Bio::Tree::AlleleNode (3p) - A Node with Alleles attached
Bio::Tree::AnnotatableNode (3p) - A Tree Node with support for annotation
Bio::Tree::Compatible (3p) - Testing compatibility of phylogenetic trees with nested taxa.
Bio::Tree::DistanceFactory (3p) - Construct a tree using distance based methods
Bio::Tree::Draw::Cladogram (3p) - Drawing phylogenetic trees in Encapsulated PostScript (EPS) format.
Bio::Tree::Node (3p) - A Simple Tree Node
Bio::Tree::NodeI (3p) - Interface describing a Tree Node
Bio::Tree::NodeNHX (3p) - A Simple Tree Node with support for NHX tags
Bio::Tree::RandomFactory (3p) - TreeFactory for generating Random Trees
Bio::Tree::Statistics (3p) - Calculate certain statistics for a Tree
Bio::Tree::Tree (3p) - An Implementation of TreeI interface.
Bio::Tree::TreeFunctionsI (3p) - Decorated Interface implementing basic Tree exploration methods
Bio::Tree::TreeI (3p) - A Tree object suitable for lots of things, designed originally for Phylogenetic Trees.
Bio::TreeIO (3p) - Parser for Tree files
Bio::TreeIO::TreeEventBuilder (3p) - Build Bio::Tree::Tree's and Bio::Tree::Node's from Events
Bio::TreeIO::cluster (3p) - A TreeIO driver module for parsing Algorithm::Cluster::treecluster() output
Bio::TreeIO::lintree (3p) - Parser for lintree output trees
Bio::TreeIO::newick (3p) - TreeIO implementation for parsing Newick/New Hampshire/PHYLIP format.
Bio::TreeIO::nexus (3p) - A TreeIO driver module for parsing Nexus tree output from PAUP
Bio::TreeIO::nhx (3p) - TreeIO implementation for parsing Newick/New Hampshire eXtendend (NHX) format.
Bio::TreeIO::pag (3p) - Bio::TreeIO driver for Pagel format
Bio::TreeIO::phyloxml (3p) - TreeIO implementation for parsing PhyloXML format.
Bio::TreeIO::svggraph (3p) - A simple output format that converts a Tree object to an SVG output
Bio::TreeIO::tabtree (3p) - A simple output format which displays a tree as an ASCII drawing
Bio::UpdateableSeqI (3p) - Descendant of Bio::SeqI that allows updates
Bio::Variation::AAChange (3p) - Sequence change class for polypeptides
Bio::Variation::AAReverseMutate (3p) - point mutation and codon information from single amino acid changes
Bio::Variation::Allele (3p) - Sequence object with allele-specific attributes
Bio::Variation::DNAMutation (3p) - DNA level mutation class
Bio::Variation::IO (3p) - Handler for sequence variation IO Formats
Bio::Variation::IO::flat (3p) - flat file sequence variation input/output stream
Bio::Variation::IO::xml (3p) - XML sequence variation input/output stream
Bio::Variation::RNAChange (3p) - Sequence change class for RNA level
Bio::Variation::SNP (3p) - submitted SNP
Bio::Variation::SeqDiff (3p) - Container class for mutation/variant descriptions
Bio::Variation::VariantI (3p) - Sequence Change SeqFeature abstract class
Bio::WebAgent (3p) - A base class for Web (any protocol) access
HIVAnnotProcessor (3p) - Adds HIV-specific annotations to Bio::SeqIO streams
Win32::DBIODBC (3p) - Win32::ODBC emulation layer for the DBI
biblio.PLS (1) - bioperl client for accessing and querying a bibliographic repository.
biofetch_genbank_proxy.pl (1) - Caching BioFetch-compatible web proxy for GenBank
bioflat_index.pl (1) - index sequence files using Bio::DB::Flat
biogetseq (1) - sequence retrieval using OBDA registry
bp_fast_load_gff.pl (1) - Fast-load a Bio::DB::GFF database from GFF files.
bp_fetch.pl (1) - fetches sequences from bioperl indexed databases
bp_genbank2gff.pl (1) - Load a Bio::DB::GFF database from GENBANK files.
bp_load_gff.pl (1) - Load a Bio::DB::GFF database from GFF files.
bp_meta_gff.pl (1) - Get/set Bio::DB::GFF meta-data
bp_seqret (1) - bioperl implementation of sequence fetch from local db (like EMBOSS seqret)
bulk_load_gff.pl (1) - Bulk-load a Bio::DB::GFF database from GFF files.
generate_histogram.pl (1) -- Generate a histogram of Bio::DB::GFF features
hivq.PL (1) - an interactive command-line interface to Bio::DB::HIV and Bio::DB::Query::HIVQuery
seqconvert (1) - generic BioPerl sequence format converter
tree2pag (1) - convert Bio::TreeIO parseable format trees to pagel format