Sendu Bala / bioperl-1.5.2_102

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::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	Multipla 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::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::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::SimpleValue	A simple scalar
Bio::Annotation::StructuredValue	A scalar with embedded structured information
Bio::Annotation::Target	Provides an object which represents a target (ie, a similarity hit) from one object to something in another database
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 phrap ACE files.
Bio::Assembly::IO::phrap	driver to load phrap.out files.
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::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::pdf	Fetch PDF for a PubMed ID
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	interface for handling web queries and data retrieval from Entrez Utilities at NCBI.
Bio::DB::EUtilities::Cookie	simple object to hold NCBI cookie information and descriptions
Bio::DB::EUtilities::ElinkData
Bio::DB::EUtilities::efetch	retrieval of records from a list of IDs or the user's environment.
Bio::DB::EUtilities::egquery	counts for a global query of Entrez databases
Bio::DB::EUtilities::einfo	NCBI database information
Bio::DB::EUtilities::elink	check for and retrieve external or related ID's from a list of one or more primary ID's, including relevancy scores.
Bio::DB::EUtilities::epost	posting IDs on the remote NCBI server for batch retrieval and chained queries
Bio::DB::EUtilities::esearch	Base interface class for handling web queries and data retrieval from Entrez Utilities from NCBI. You shouldn't use this class directly.
Bio::DB::EUtilities::esummary	retrieval of NCBI DocSum data from a list of primary IDs or a Cookie
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::BDB::swissprot	swissprot adaptor for Open-bio standard BDB-indexed flat file
Bio::DB::Flat::BinarySearch	BinarySearch search indexing system for sequence files
Bio::DB::GDB	Database object interface to GDB HTTP query
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
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::match	Match aggregator
Bio::DB::GFF::Aggregator::none	No aggregation
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::GenericWebDBI	abstract interface for parameter-based remote database access
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::Query::GenBank	Build a GenBank Entrez Query
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
Bio::DB::SeqFeature::Store::DBI::mysql	Mysql implementation of Bio::DB::SeqFeature::Store
Bio::DB::SeqFeature::Store::GFF3Loader	GFF3 file loader for Bio::DB::SeqFeature::Store
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::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::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::DB::XEMBL	Database object interface for XEMBL entry retrieval
Bio::DB::XEMBLService	SOAP service definition for XEMBL
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
Bio::Expression::FeatureI	an interface class for DNA/RNA features
Bio::Expression::FeatureSet::FeatureSetMas50
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::HitFactoryI	Interface for an object that builds Bio::Search::Hit::HitI objects
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::ResultFactoryI	Interface for an object that builds Bio::Search::Result::ResultI objects
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	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::Graph::Edge	encapsulation of an interaction between 2 Bio::Seq objects
Bio::Graph::IO	Class for reading /writing biological graph data.
Bio::Graph::IO::dip	class for parsing interaction data in dip format
Bio::Graph::IO::psi_xml	access and manipulate PSI XML graphs
Bio::Graph::ProteinGraph	a representation of a protein interaction graph.
Bio::Graph::SimpleGraph	create and manipulate undirected graphs
Bio::Graph::SimpleGraph::Traversal	graph traversal operations for Bio::Graph::SimpleGraph and Bio::Graph::Protein::Graph objects
Bio::Graphics	Generate GD images of Bio::Seq objects
Bio::Graphics::ConfiguratorI	A sectioned map of configuration options (a map of maps), with a default section. Intended to augment existing tag->value semantics (ie. of Bio::AnnotationCollectionI) for object-representation inform
Bio::Graphics::Feature	A simple feature object for use with Bio::Graphics::Panel
Bio::Graphics::FeatureBase	Base class for Bio::Graphics::Feature
Bio::Graphics::FeatureFile	A set of Bio::Graphics features, stored in a file
Bio::Graphics::FeatureFile::Iterator	Iterator across a Bio::Graphics::FeatureFile
Bio::Graphics::Glyph	Base class for Bio::Graphics::Glyph objects
Bio::Graphics::Glyph::Factory	Factory for Bio::Graphics::Glyph objects
Bio::Graphics::Glyph::alignment	The "alignment" glyph
Bio::Graphics::Glyph::anchored_arrow	The "anchored_arrow" glyph
Bio::Graphics::Glyph::arrow	the "arrow" glyph
Bio::Graphics::Glyph::box	The "box" glyph
Bio::Graphics::Glyph::broken_line	The "broken line" glyph
Bio::Graphics::Glyph::cds	The "cds" glyph
Bio::Graphics::Glyph::christmas_arrow	The "christmas arrow" glyph
Bio::Graphics::Glyph::crossbox	The "crossbox" glyph
Bio::Graphics::Glyph::dashed_line	The "dashed line" glyph
Bio::Graphics::Glyph::diamond	The "diamond" glyph
Bio::Graphics::Glyph::dna	The "dna" glyph
Bio::Graphics::Glyph::dot	The "dot" glyph
Bio::Graphics::Glyph::dumbbell	A glyph that draws a "dumbbell" with the same shapes on both ends.
Bio::Graphics::Glyph::ellipse	The "ellipse" glyph
Bio::Graphics::Glyph::ex	the "ex", or "crossed box" glyph
Bio::Graphics::Glyph::extending_arrow	The "extending arrow" glyph
Bio::Graphics::Glyph::flag	the "flag" glyph
Bio::Graphics::Glyph::gene	A GFF3-compatible gene glyph
Bio::Graphics::Glyph::generic	The "generic" glyph
Bio::Graphics::Glyph::graded_segments	The "graded_segments" glyph
Bio::Graphics::Glyph::group	The "group" glyph
Bio::Graphics::Glyph::heterogeneous_segments	The "heterogeneous_segments" glyph
Bio::Graphics::Glyph::image	A glyph that draws photographs & other images
Bio::Graphics::Glyph::lightning	The "lightning" glyph
Bio::Graphics::Glyph::line	The "line" glyph
Bio::Graphics::Glyph::merge_parts	a base class which suppors semantic zooming of scored alignment features
Bio::Graphics::Glyph::merged_alignment	The "merged_alignment" glyph
Bio::Graphics::Glyph::minmax	The minmax glyph
Bio::Graphics::Glyph::oval	The "oval" glyph
Bio::Graphics::Glyph::pentagram	The "pentagram" glyph
Bio::Graphics::Glyph::pinsertion	The "Drosophila P-element Insertion" glyph
Bio::Graphics::Glyph::primers	The "STS primers" glyph
Bio::Graphics::Glyph::processed_transcript	The sequence ontology transcript glyph
Bio::Graphics::Glyph::protein	The "protein" glyph
Bio::Graphics::Glyph::ragged_ends	The "ragged ends" glyph
Bio::Graphics::Glyph::redgreen_box	The "redgreen_box" glyph
Bio::Graphics::Glyph::redgreen_segment
Bio::Graphics::Glyph::repeating_shape	A glyph that draws the same shape repeatedly.
Bio::Graphics::Glyph::rndrect	The "round rect" glyph
Bio::Graphics::Glyph::ruler_arrow	glyph for drawing an arrow as ruler (5' and 3' are marked as label)
Bio::Graphics::Glyph::saw_teeth	The "saw teeth" glyph
Bio::Graphics::Glyph::segmented_keyglyph	The "segmented_keyglyph" glyph
Bio::Graphics::Glyph::segments	The "segments" glyph
Bio::Graphics::Glyph::so_transcript	The sequence ontology transcript glyph
Bio::Graphics::Glyph::span	The "span" glyph
Bio::Graphics::Glyph::splice_site	The "splice_site" glyph
Bio::Graphics::Glyph::text_in_box	The "text in box" glyph
Bio::Graphics::Glyph::three_letters	DAS-compatible package to use for drawing a line of groups of three letters
Bio::Graphics::Glyph::tic_tac_toe	The "tic-tac-toe" glyph
Bio::Graphics::Glyph::toomany	The "too many to show" glyph
Bio::Graphics::Glyph::track	The "track" glyph
Bio::Graphics::Glyph::transcript	The "transcript" glyph
Bio::Graphics::Glyph::transcript2	The "transcript2" glyph
Bio::Graphics::Glyph::translation	The "6-frame translation" glyph
Bio::Graphics::Glyph::triangle	The "triangle" glyph
Bio::Graphics::Glyph::two_bolts	The "two bolts" glyph
Bio::Graphics::Glyph::wave	The "wave" glyph
Bio::Graphics::Glyph::weighted_arrow	The "weighted arrow" glyph
Bio::Graphics::Glyph::whiskerplot	The whiskerplot glyph
Bio::Graphics::Glyph::xyplot	The xyplot glyph
Bio::Graphics::Panel	Generate GD images of Bio::Seq objects
Bio::Graphics::Pictogram	generate SVG output of Pictogram display for consensus motifs
Bio::Graphics::RendererI	A renderer for the Bio::Graphics class that renders Bio::SeqFeature::CollectionI objects onto Bio::Graphics::Panels using configuration information provided by a Bio::Graphics::ConfiguratorI.
Bio::Graphics::Util	non-object-oriented utilities used in Bio::Graphics modules
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::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::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 Sequence 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::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::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::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::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::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
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::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	a Ontology Engine for GO implementing OntologyEngineI
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::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::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	Select htSNP from a haplotype set
Bio::PopGen::IO	Input individual,marker,allele information
Bio::PopGen::IO::csv	Extract individual allele data from a CSV parser
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::withrefm	withrefm enzyme set
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::Version	provide global, distribution-level versioning	1.005002102
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::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::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::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::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::BlastResult	Blast-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::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::axt	a parser for axt format reports
Bio::SearchIO::blast	Event generator for event based parsing of blast reports
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::exonerate	parser for Exonerate
Bio::SearchIO::fasta	A SearchIO parser for FASTA results
Bio::SearchIO::hmmer	A parser for HMMER output (hmmpfam, hmmsearch)
Bio::SearchIO::hmmer_pull	A parser for HMMER output
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::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
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::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::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->primary_tag
Bio::SeqFeature::Tools::TypeMapper	maps $seq_feature->primary_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::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::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::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::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::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::BPbl2seq	Lightweight BLAST parser for pair-wise sequence alignment using the BLAST algorithm.
Bio::Tools::BPlite	Lightweight BLAST parser
Bio::Tools::BPlite::HSP	Blast report High Scoring Pair (HSP)
Bio::Tools::BPlite::Iteration	object for parsing single iteration of a PSIBLAST report
Bio::Tools::BPlite::Sbjct	A Blast Subject (database search Hit)
Bio::Tools::BPpsilite	Lightweight BLAST parser for (iterated) psiblast reports
Bio::Tools::Blat	parser for Blat program
Bio::Tools::CodonTable	Bioperl 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::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 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::HMM	Perl extension to perform Hidden Markov Model calculations
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::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::OddCodes	Object holding alternative alphabet coding for one protein sequence
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::Primer3	Create input for and work with the output from the program primer3
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::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::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::RestrictionEnzyme	Bioperl object for a restriction endonuclease (cuts DNA at specific locations)
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::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::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::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::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::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::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
Deobfuscator	get BioPerl method and package information from a Berkeley DB	0.0.2
ModuleBuildBioperl		1.005002101
TestInterface	A simple subclass of Interface
TestObject	An implementation of TestInterface

Bio::Graphics::Glyph::redgreen_segments	The "redgreen_segments" glyph
aacomp	amino acid composition of protein sequences
authors.pl	check modules and scripts for authors not in AUTHORS file
biblio-eutils-example.pl
biblio-soap-example.pl
biblio.PLS	bioperl client for accessing and querying a bibliographic repository.
biofetch_genbank_proxy.pl	Caching BioFetch-compatible web proxy for GenBank
bioflat_index.pl	index sequence files using Bio::DB::Flat
biogetseq	sequence retrieval using OBDA registry
bp_embl2picture.pl	Render a Genbank/EMBL sequence file graphically as a png image
bp_fast_load_gff.pl	Fast-load a Bio::DB::GFF database from GFF files.
bp_fetch.pl	fetches sequences from bioperl indexed databases
bp_genbank2gff.pl	Load a Bio::DB::GFF database from GENBANK files.
bp_genbank2gff3.pl	Genbank->gbrowse-friendly GFF3
bp_glyphs1-demo.pl	First demo of Bio::Graphics glyphs
bp_glyphs2-demo.pl	Second demo of Bio::Graphics glyphs
bp_index.pl	indexes files for use by bp_fetch.pl
bp_load_gff.pl	Load a Bio::DB::GFF database from GFF files.
bp_meta_gff.pl	Get/set Bio::DB::GFF meta-data
bp_mrtrans	implement a transformer of alignments from protein to mrna coordinates
bp_nrdb.PLS	a script to emulate Warren Gish's nrdb, make a unique sequence database from a set of input databases
bp_seqret	bioperl implementation of sequence fetch from local db (like EMBOSS seqret)
bpsreformat	convert sequence formats
bulk_load_gff.pl	Bulk-load a Bio::DB::GFF database from GFF files.
chaos_plot	a chaos plot from DNA and RNA sequences
check_NAMEs.pl	check NAME in module POD has fully qualified object name
check_URLs.pl	validate URLs located in module code and POD
classify_hits_kingdom	classify BLAST hits by taxonomic kingdom
composite_LD	i filename.prettybase.txt --sortbyld > outfile
dbfetch	generic CGI program to retrieve biological database entries in various formats and styles (using SRS)
dbsplit	script to split an input set of database(s) into smaller pieces
deob_detail.cgi	displays a web page of detailed information about a BioPerl method
deob_index.pl	extracts BioPerl documentation and indexes it in a database for easy retrieval
deob_interface.cgi	a WWW user interface to the BioPerl Deobfuscator
extract_feature_seq	extract the corresponding sequence for a specified feature type
extract_genes.pl	extract genomic sequences from NCBI files using BioPerl
fastm9_to_table	turn FASTA -m 9 output into NCBI -m 9 tabular output
feature_draw.pl	Render a Bio::Graphics Feature File
filter_search	filters searchio results, outputting a tab delimited summary
flanks	finding flanking sequences for a variant in a sequence position
frend.pl	Render a Bio::Graphics Feature File on the web
gccalc	GC content of nucleotide sequences
generate_histogram.pl	Generate a histogram of Bio::DB::GFF features
gff2ps	you will want to change this script
heterogeneity_test	a test for distinguishing between selection and population expansion.
hmmer_to_table	turn HMMER output into tabular format
local_taxonomydb_query	query a local TaxonomyDB for species or taxonid
longorf	perl script to find the longest ORF of a sequence
maintenance/version.pl
make_mrna_protein	Convert an input mRNA/cDNA sequence into protein
mask_by_search	mask sequence(s) based on its alignment results
modules.pl	information about modules in BioPerl core
mutate.pl	randomly mutagenize a single protein or DNA sequence
nexus2nh	convert nexus format trees (from PAUP* and MrBayes) to new hampshire
oligo_count	oligo count and frequency
pairwise_kaks	script to calculate pairwise Ka,Ks for a set of sequences
parse_hmmsearch	parse single/multiple HMMSEARCH results file(s) with different output options
pod.pl	check the POD documentation syntax in modules and scripts
process_gadfly.pl	Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser
process_sgd.pl	Massage SGD annotation flat files into a version suitable for the Generic Genome Browser
process_wormbase.pl	Massage WormBase GFF files into a version suitable for the Generic Genome Browser
query_entrez_taxa	query Entrez taxonomy database and print out information
remote_blast.pl	script for submitting jobs to a remote blast server (ncbi blast queue at this time)
rnai_finder.cgi
run_primer3.pl	run primer3 and parse its output
search2alnblocks	Turn SearchIO parseable reports(s) into a set of aligned blocks
search2bsml	Turn SearchIO parseable reports(s) into a BSML report
search2gff	Turn SearchIO parseable reports(s) into a GFF report
search2table	turn SearchIO parseable reports into tab delimited format like NCBI's -m 9
search2tribe	Turn SearchIO parseable reports(s) into TRIBE matrix
search_overview	Render a SearchIO parser report into a simple overview graphic
seq_length.pl	lists the number of bases and number of sequences in specified sequence database files
seqconvert	generic BioPerl sequence format converter
split_seq	splits a sequence into equal sized chunks with an optional overlapping range
symlink_script.pl	install script to create symbolic links
symlink_scripts.pl	install script to create symbolic links
taxid4species:	Simple script which returns the NCBI Taxanomic id for a requested species
taxonomy2tree	Building a taxonomic tree based on the full lineages of a set of species names
translate_seq	translates a sequence
tree2pag	convert Bio::TreeIO parseable format trees to pagel format
tree_from_seqsearch	builds a phylogenetic tree based on a sequence search (FastA,BLAST,HMMER)
unflatten_seq	unflatten a genbank or genbank-style feature file into a nested SeqFeature hierarchy
waba2gff3.pl	convert waba output into GFF3 suitable for Gbrowse

bioperl-1.5.2_102

Modules

Documentation

Other Files