Christopher Fields > BioPerl

BioPerl

This Release BioPerl-1.6.923  [Download] [Browse 17 Dec 2013
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License The Perl 5 License (Artistic 1 & GPL 1)
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Modules

Bio::Align::AlignI An interface for describing sequence alignments.      
Bio::Align::DNAStatistics Calculate some statistics for a DNA alignment      
Bio::Align::Graphics Graphic Rendering of Bio::Align::AlignI Objects      
Bio::Align::PairwiseStatistics Base statistic object for Pairwise Alignments      
Bio::Align::ProteinStatistics Calculate Protein Alignment statistics (mostly distances)      
Bio::Align::StatisticsI Calculate some statistics for an alignment      
Bio::Align::Utilities A collection of utilities regarding converting and manipulating alignment objects      
Bio::AlignIO Handler for AlignIO Formats      
Bio::AlignIO::Handler::GenericAlignHandler Bio::HandlerI-based generic data handler class for alignment-based data      
Bio::AlignIO::arp ARP MSA Sequence input/output stream      
Bio::AlignIO::bl2seq bl2seq sequence input/output stream      
Bio::AlignIO::clustalw clustalw sequence input/output stream      
Bio::AlignIO::emboss Parse EMBOSS alignment output (from applications water and needle)      
Bio::AlignIO::fasta fasta MSA Sequence input/output stream      
Bio::AlignIO::largemultifasta Largemultifasta MSA Sequence input/output stream      
Bio::AlignIO::maf Multiple Alignment Format sequence input stream      
Bio::AlignIO::mase mase sequence input/output stream      
Bio::AlignIO::mega Parse and Create MEGA format data files      
Bio::AlignIO::meme meme sequence input/output stream      
Bio::AlignIO::metafasta Metafasta MSA Sequence input/output stream      
Bio::AlignIO::msf msf sequence input/output stream      
Bio::AlignIO::nexml NeXML format sequence alignment input/output stream driver      
Bio::AlignIO::nexus NEXUS format sequence input/output stream      
Bio::AlignIO::pfam pfam sequence input/output stream      
Bio::AlignIO::phylip PHYLIP format sequence input/output stream      
Bio::AlignIO::po po MSA Sequence input/output stream      
Bio::AlignIO::proda proda sequence input/output stream      
Bio::AlignIO::prodom prodom sequence input/output stream      
Bio::AlignIO::psi Read/Write PSI-BLAST profile alignment files      
Bio::AlignIO::selex selex sequence input/output stream      
Bio::AlignIO::stockholm stockholm sequence input/output stream      
Bio::AlignIO::xmfa XMFA MSA Sequence input/output stream      
Bio::AnalysisI An interface to any (local or remote) analysis tool      
Bio::AnalysisParserI Generic analysis output parser interface      
Bio::AnalysisResultI Interface for analysis result objects      
Bio::AnnotatableI the base interface an annotatable object must implement      
Bio::Annotation::AnnotationFactory Instantiates a new Bio::AnnotationI (or derived class) through a factory      
Bio::Annotation::Collection Default Perl implementation of AnnotationCollectionI      
Bio::Annotation::Comment A comment object, holding text      
Bio::Annotation::DBLink untyped links between databases      
Bio::Annotation::OntologyTerm An ontology term adapted to AnnotationI      
Bio::Annotation::Reference Specialised DBLink object for Literature References      
Bio::Annotation::Relation Relationship (pairwise) with other objects SeqI and NodeI;      
Bio::Annotation::SimpleValue A simple scalar      
Bio::Annotation::StructuredValue A scalar with embedded structured information      
Bio::Annotation::TagTree AnnotationI with tree-like hierarchal key-value relationships ('structured tags') that can be represented as simple text.      
Bio::Annotation::Target Provides an object which represents a target (ie, a similarity hit) from one object to something in another database      
Bio::Annotation::Tree Provide a tree as an annotation to a Bio::AnnotatableI object      
Bio::Annotation::TypeManager Manages types for annotation collections      
Bio::AnnotationCollectionI Interface for annotation collections      
Bio::AnnotationI Annotation interface      
Bio::Assembly::Contig Perl module to hold and manipulate sequence assembly contigs.      
Bio::Assembly::ContigAnalysis Perform analysis on sequence assembly contigs.      
Bio::Assembly::IO Handler for Assembly::IO Formats      
Bio::Assembly::IO::ace module to load ACE files from various assembly programs      
Bio::Assembly::IO::bowtie An IO module for assemblies in Bowtie format *BETA*      
Bio::Assembly::IO::maq Driver to read assembly files in maq format *BETA*      
Bio::Assembly::IO::phrap driver to load phrap.out files.      
Bio::Assembly::IO::sam An IO module for assemblies in Sam format *BETA*      
Bio::Assembly::IO::tigr Driver to read and write assembly files in the TIGR Assembler v2 default format.      
Bio::Assembly::Scaffold Perl module to hold and manipulate sequence assembly data.      
Bio::Assembly::ScaffoldI Abstract Inteface of Sequence Assemblies      
Bio::Assembly::Singlet Perl module to hold and manipulate singlets from sequence assembly contigs.      
Bio::Assembly::Tools::ContigSpectrum create and manipulate contig spectra      
Bio::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::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::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 fasta files      
Bio::DB::FileCache In file cache for BioSeq objects      
Bio::DB::Flat Interface for indexed flat files      
Bio::DB::Flat::BDB Interface for BioHackathon standard BDB-indexed flat file      
Bio::DB::Flat::BDB::embl embl adaptor for Open-bio standard BDB-indexed flat file      
Bio::DB::Flat::BDB::fasta fasta adaptor for Open-bio standard BDB-indexed flat file      
Bio::DB::Flat::BDB::genbank genbank adaptor for Open-bio standard BDB-indexed flat file      
Bio::DB::Flat::BDB::swiss swissprot adaptor for Open-bio standard BDB-indexed flat file      
Bio::DB::Flat::BinarySearch BinarySearch search indexing system for sequence files      
Bio::DB::GFF Storage and retrieval of sequence annotation data      
Bio::DB::GFF::Adaptor::ace ace interface (for multiple inheritance)      
Bio::DB::GFF::Adaptor::berkeleydb Bio::DB::GFF database adaptor for in-memory databases      
Bio::DB::GFF::Adaptor::berkeleydb::iterator iterator for Bio::DB::GFF::Adaptor::berkeleydb      
Bio::DB::GFF::Adaptor::biofetch Cache BioFetch objects in a Bio::DB::GFF database      
Bio::DB::GFF::Adaptor::biofetch_oracle Cache BioFetch objects in a Bio::DB::GFF database      
Bio::DB::GFF::Adaptor::dbi Database adaptor for DBI (SQL) databases      
Bio::DB::GFF::Adaptor::dbi::caching_handle Cache for database handles      
Bio::DB::GFF::Adaptor::dbi::iterator iterator for Bio::DB::GFF::Adaptor::dbi      
Bio::DB::GFF::Adaptor::dbi::mysql Database adaptor for a specific mysql schema      
Bio::DB::GFF::Adaptor::dbi::mysqlace Unholy union between mysql GFF database and acedb database      
Bio::DB::GFF::Adaptor::dbi::mysqlcmap Database adaptor for an integraded CMap/GBrowse mysql schema      
Bio::DB::GFF::Adaptor::dbi::mysqlopt Deprecated database adaptor      
Bio::DB::GFF::Adaptor::dbi::oracle Database adaptor for a specific oracle schema      
Bio::DB::GFF::Adaptor::dbi::oracleace Unholy union between oracle GFF database and acedb database      
Bio::DB::GFF::Adaptor::dbi::pg Database adaptor for a specific postgres schema      
Bio::DB::GFF::Adaptor::dbi::pg_fts Database adaptor for a specific postgres schema with a TSearch2 implementation      
Bio::DB::GFF::Adaptor::memory Bio::DB::GFF database adaptor for in-memory databases      
Bio::DB::GFF::Adaptor::memory::feature_serializer utility methods for serializing and deserializing GFF features      
Bio::DB::GFF::Adaptor::memory::iterator iterator for Bio::DB::GFF::Adaptor::memory      
Bio::DB::GFF::Aggregator Aggregate GFF groups into composite features      
Bio::DB::GFF::Aggregator::alignment Alignment aggregator      
Bio::DB::GFF::Aggregator::clone Clone aggregator      
Bio::DB::GFF::Aggregator::coding The Coding Region Aggregator      
Bio::DB::GFF::Aggregator::gene Sequence Ontology Geene      
Bio::DB::GFF::Aggregator::match Match aggregator      
Bio::DB::GFF::Aggregator::none No aggregation      
Bio::DB::GFF::Aggregator::orf An aggregator for orf regions      
Bio::DB::GFF::Aggregator::processed_transcript Sequence Ontology Transcript      
Bio::DB::GFF::Aggregator::so_transcript Sequence Ontology Transcript      
Bio::DB::GFF::Aggregator::transcript Transcript aggregator      
Bio::DB::GFF::Aggregator::ucsc_acembly UCSC acembly aggregator      
Bio::DB::GFF::Aggregator::ucsc_ensgene UCSC ensGene aggregator      
Bio::DB::GFF::Aggregator::ucsc_genscan UCSC genscan aggregator      
Bio::DB::GFF::Aggregator::ucsc_refgene UCSC refGene aggregator      
Bio::DB::GFF::Aggregator::ucsc_sanger22 UCSC sanger22 aggregator      
Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo UCSC sanger22pseudo aggregator      
Bio::DB::GFF::Aggregator::ucsc_softberry UCSC softberry aggregator      
Bio::DB::GFF::Aggregator::ucsc_twinscan UCSC twinscan aggregator      
Bio::DB::GFF::Aggregator::ucsc_unigene UCSC UniGene aggregator      
Bio::DB::GFF::Featname The name of a feature      
Bio::DB::GFF::Feature A relative segment identified by a feature type      
Bio::DB::GFF::Homol A segment of DNA that is homologous to another      
Bio::DB::GFF::RelSegment Sequence segment with relative coordinate support      
Bio::DB::GFF::Segment Simple DNA segment object      
Bio::DB::GFF::Typename The name of a feature type      
Bio::DB::GFF::Util::Binning binning utility for Bio::DB::GFF index      
Bio::DB::GFF::Util::Rearrange rearrange utility      
Bio::DB::GenBank Database object interface to GenBank      
Bio::DB::GenPept Database object interface to GenPept      
Bio::DB::GenericWebAgent helper base class for parameter-based remote server access and response retrieval.      
Bio::DB::HIV Database object interface to the Los Alamos HIV Sequence Database      
Bio::DB::HIV::HIVAnnotProcessor Adds HIV-specific annotations to Bio::SeqIO streams      
Bio::DB::HIV::HIVQueryHelper Routines and packages used by Bio::DB::HIV and Bio::DB::Query::HIVQuery      
Bio::DB::InMemoryCache Abstract interface for a sequence database      
Bio::DB::IndexedBase Base class for modules using indexed sequence files      
Bio::DB::LocationI A RandomAccessI-like abstract interface for retrieving location data from a sequence database and returning Bio::LocationI objects      
Bio::DB::MeSH Term retrieval from a Web MeSH database      
Bio::DB::NCBIHelper A collection of routines useful for queries to NCBI databases.      
Bio::DB::Qual Fast indexed access to quality files      
Bio::DB::Query::GenBank Build a GenBank Entrez Query      
Bio::DB::Query::HIVQuery Query interface to the Los Alamos HIV Sequence Database      
Bio::DB::Query::WebQuery Helper class for web-based sequence queryies      
Bio::DB::QueryI Object Interface to queryable sequence databases      
Bio::DB::RandomAccessI Abstract interface for a sequence database      
Bio::DB::RefSeq Database object interface for RefSeq retrieval      
Bio::DB::ReferenceI A RandomAccessI-like abstract interface for retrieving Reference data from a sequence database and returning Bio::Annotation::Reference objects      
Bio::DB::Registry Access to the Open Bio Database Access registry scheme      
Bio::DB::SeqFeature Normalized feature for use with Bio::DB::SeqFeature::Store      
Bio::DB::SeqFeature::NormalizedFeature Normalized feature for use with Bio::DB::SeqFeature::Store      
Bio::DB::SeqFeature::NormalizedFeatureI Interface for normalized features      
Bio::DB::SeqFeature::NormalizedTableFeatureI Interface for normalized features whose hierarchy is stored in a table      
Bio::DB::SeqFeature::Segment Location-based access to genome annotation data      
Bio::DB::SeqFeature::Store Storage and retrieval of sequence annotation data      
Bio::DB::SeqFeature::Store::DBI::Iterator utility methods for creating and iterating over SeqFeature records      
Bio::DB::SeqFeature::Store::DBI::Pg PostgreSQL implementation of Bio::DB::SeqFeature::Store      
Bio::DB::SeqFeature::Store::DBI::SQLite SQLite implementation of Bio::DB::SeqFeature::Store      
Bio::DB::SeqFeature::Store::DBI::mysql Mysql implementation of Bio::DB::SeqFeature::Store      
Bio::DB::SeqFeature::Store::FeatureFileLoader feature file loader for Bio::DB::SeqFeature::Store      
Bio::DB::SeqFeature::Store::GFF2Loader GFF2 file loader for Bio::DB::SeqFeature::Store      
Bio::DB::SeqFeature::Store::GFF3Loader GFF3 file loader for Bio::DB::SeqFeature::Store      
Bio::DB::SeqFeature::Store::LoadHelper Internal utility for Bio::DB::SeqFeature::Store     1.10
Bio::DB::SeqFeature::Store::Loader Loader      
Bio::DB::SeqFeature::Store::bdb fetch and store objects from a BerkeleyDB      
Bio::DB::SeqFeature::Store::berkeleydb Storage and retrieval of sequence annotation data in Berkeleydb files      
Bio::DB::SeqFeature::Store::berkeleydb3 Storage and retrieval of sequence annotation data in Berkeleydb files      
Bio::DB::SeqFeature::Store::memory In-memory implementation of Bio::DB::SeqFeature::Store      
Bio::DB::SeqHound Database object interface to SeqHound      
Bio::DB::SeqI Abstract Interface for Sequence databases      
Bio::DB::SeqVersion front end to querying databases for identifier versions      
Bio::DB::SeqVersion::gi interface to NCBI Sequence Revision History page      
Bio::DB::SwissProt Database object interface to SwissProt retrieval      
Bio::DB::TFBS Access to a Transcription Factor Binding Site database      
Bio::DB::TFBS::transfac_pro An implementation of Bio::DB::TFBS which uses local flat files for transfac pro      
Bio::DB::Taxonomy Access to a taxonomy database      
Bio::DB::Taxonomy::entrez Taxonomy Entrez driver      
Bio::DB::Taxonomy::flatfile Use the NCBI taxonomy from local indexed flat files      
Bio::DB::Taxonomy::greengenes Use the Greengenes taxonomy      
Bio::DB::Taxonomy::list An implementation of Bio::DB::Taxonomy that accepts lists of words to build a database      
Bio::DB::Taxonomy::silva Use the Silva taxonomy      
Bio::DB::Universal Artificial database that delegates to specific databases      
Bio::DB::UpdateableSeqI An interface for writing to a database of sequences.      
Bio::DB::WebDBSeqI Object Interface to generalize Web Databases for retrieving sequences      
Bio::DBLinkContainerI Abstract interface for any object wanting to use database cross references      
Bio::Das::FeatureTypeI Simple interface to Sequence Ontology feature types      
Bio::Das::SegmentI DAS-style access to a feature database      
Bio::DasI DAS-style access to a feature database      
Bio::DescribableI interface for objects with human readable names and descriptions      
Bio::Draw::Pictogram generate SVG output of Pictogram display for consensus motifs      
Bio::Event::EventGeneratorI This interface describes the basic event generator class.      
Bio::Event::EventHandlerI An Event Handler Interface      
Bio::Factory::AnalysisI An interface to analysis tool factory      
Bio::Factory::ApplicationFactoryI Interface class for Application Factories      
Bio::Factory::DriverFactory Base class for factory classes loading drivers      
Bio::Factory::FTLocationFactory A FeatureTable Location Parser      
Bio::Factory::LocationFactoryI A factory interface for generating locations from a string      
Bio::Factory::MapFactoryI A Factory for getting markers      
Bio::Factory::ObjectBuilderI Interface for an object builder      
Bio::Factory::ObjectFactory Instantiates a new Bio::Root::RootI (or derived class) through a factory      
Bio::Factory::ObjectFactoryI A General object creator factory      
Bio::Factory::SeqAnalysisParserFactory class capable of creating SeqAnalysisParserI compliant parsers      
Bio::Factory::SeqAnalysisParserFactoryI interface describing objects capable of creating SeqAnalysisParserI compliant parsers      
Bio::Factory::SequenceFactoryI This interface allows for generic building of sequences in factories which create sequences (like SeqIO)      
Bio::Factory::SequenceProcessorI Interface for chained sequence processing algorithms      
Bio::Factory::SequenceStreamI Interface describing the basics of a Sequence Stream.      
Bio::Factory::TreeFactoryI Factory Interface for getting and writing trees from/to a data stream      
Bio::FeatureHolderI the base interface an object with features must implement      
Bio::HandlerBaseI Interface class for handler methods which interact with any event-driven parsers (drivers).      
Bio::IdCollectionI interface for objects with multiple identifiers      
Bio::IdentifiableI interface for objects with identifiers      
Bio::Index::Abstract Abstract interface for indexing a flat file      
Bio::Index::AbstractSeq base class for AbstractSeq      
Bio::Index::Blast Indexes Blast reports and supports retrieval based on query accession(s)      
Bio::Index::BlastTable Indexes tabular Blast reports (-m 8 or -m 9 format) and supports retrieval based on query accession(s)      
Bio::Index::EMBL Interface for indexing (multiple) EMBL/Swissprot .dat files (i.e. flat file EMBL/Swissprot format).      
Bio::Index::Fasta Interface for indexing (multiple) fasta files      
Bio::Index::Fastq Interface for indexing (multiple) fastq files      
Bio::Index::GenBank Interface for indexing one or more GenBank files (i.e. flat file GenBank format).      
Bio::Index::Hmmer indexes HMMER reports and supports retreival based on query      
Bio::Index::Qual Interface for indexing (multiple) fasta qual files      
Bio::Index::Stockholm      
Bio::Index::SwissPfam Interface for indexing swisspfam files      
Bio::Index::Swissprot Interface for indexing one or more Swissprot files.      
Bio::LiveSeq::AARange AARange abstract class for LiveSeq      
Bio::LiveSeq::Chain DoubleChain DataStructure for Perl      
Bio::LiveSeq::ChainI Double linked chain data structure      
Bio::LiveSeq::DNA DNA object for LiveSeq      
Bio::LiveSeq::Exon Range abstract class for LiveSeq      
Bio::LiveSeq::Gene Range abstract class for LiveSeq      
Bio::LiveSeq::IO::BioPerl Loader for LiveSeq from EMBL entries with BioPerl      
Bio::LiveSeq::IO::Loader Parent Loader for LiveSeq      
Bio::LiveSeq::Intron Range abstract class for LiveSeq      
Bio::LiveSeq::Mutation Mutation event descriptor class      
Bio::LiveSeq::Mutator Package mutating LiveSequences      
Bio::LiveSeq::Prim_Transcript Prim_Transcript class for LiveSeq      
Bio::LiveSeq::Range Range abstract class for LiveSeq      
Bio::LiveSeq::Repeat_Region Repeat_Region class for LiveSeq      
Bio::LiveSeq::Repeat_Unit Repeat_Unit class for LiveSeq      
Bio::LiveSeq::SeqI Abstract sequence interface class for LiveSeq      
Bio::LiveSeq::Transcript Transcript class for LiveSeq      
Bio::LiveSeq::Translation Translation class for LiveSeq      
Bio::LocatableSeq A Bio::PrimarySeq object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq.      
Bio::Location::Atomic Implementation of a Atomic Location on a Sequence      
Bio::Location::AvWithinCoordPolicy class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise      
Bio::Location::CoordinatePolicyI Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location      
Bio::Location::Fuzzy Implementation of a Location on a Sequence which has unclear start and/or end locations      
Bio::Location::FuzzyLocationI Abstract interface of a Location on a Sequence which has unclear start/end location      
Bio::Location::NarrowestCoordPolicy class implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range      
Bio::Location::Simple Implementation of a Simple Location on a Sequence      
Bio::Location::Split Implementation of a Location on a Sequence which has multiple locations (start/end points)      
Bio::Location::SplitLocationI Abstract interface of a Location on a Sequence which has multiple locations (start/end points)      
Bio::Location::WidestCoordPolicy class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable range      
Bio::LocationI Abstract interface of a Location on a Sequence      
Bio::Map::Clone An central map object representing a clone      
Bio::Map::Contig A MapI implementation handling the contigs of a Physical Map (such as FPC)      
Bio::Map::CytoMap A Bio::MapI compliant map implementation handling cytogenic bands      
Bio::Map::CytoMarker An object representing a marker.      
Bio::Map::CytoPosition Marker class with cytogenetic band storing attributes      
Bio::Map::EntityI An Entity Interface      
Bio::Map::FPCMarker An central map object representing a marker      
Bio::Map::Gene An gene modelled as a mappable element.      
Bio::Map::GeneMap A MapI implementation to represent the area around a gene      
Bio::Map::GenePosition A typed position, suitable for modelling the various regions of a gene.      
Bio::Map::GeneRelative Represents being relative to named sub-regions of a gene.      
Bio::Map::LinkageMap A representation of a genetic linkage map.      
Bio::Map::LinkagePosition Create a Position for a Marker that will be placed on a Bio::Map::LinkageMap      
Bio::Map::MapI Interface for describing Map objects in bioperl      
Bio::Map::Mappable An object representing a generic map element that can have multiple locations in several maps.      
Bio::Map::MappableI An object that can be placed in a map      
Bio::Map::Marker An central map object representing a generic marker that can have multiple location in several maps.      
Bio::Map::MarkerI Interface for basic marker functionality      
Bio::Map::Microsatellite An object representing a Microsatellite marker.      
Bio::Map::OrderedPosition Abstracts the notion of a member of an ordered list of markers. Each marker is a certain distance from the one in the ordered list before it.      
Bio::Map::OrderedPositionWithDistance Abstracts the notion of a member of an ordered list of markers. Each marker is a certain distance from the one in the ordered list before it.      
Bio::Map::Physical A class for handling a Physical Map (such as FPC)      
Bio::Map::Position A single position of a Marker, or the range over which that marker lies, in a Map      
Bio::Map::PositionHandler A Position Handler Implementation      
Bio::Map::PositionHandlerI A Position Handler Interface      
Bio::Map::PositionI Abstracts the notion of a position having a value in the context of a marker and a Map      
Bio::Map::PositionWithSequence A position with a sequence.      
Bio::Map::Prediction An object representing the predictions of something that can have multiple locations in several maps.      
Bio::Map::Relative Represents what a Position's coordiantes are relative to.      
Bio::Map::RelativeI Interface for describing what a Position's coordiantes are relative to.      
Bio::Map::SimpleMap A MapI implementation handling the basics of a Map      
Bio::Map::TranscriptionFactor A transcription factor modelled as a mappable element      
Bio::MapIO A Map Factory object      
Bio::MapIO::fpc A FPC Map reader      
Bio::MapIO::mapmaker A Mapmaker Map reader      
Bio::Matrix::Generic A generic matrix implementation      
Bio::Matrix::IO A factory for Matrix parsing      
Bio::Matrix::IO::mlagan A parser for the mlagan substitution matrix      
Bio::Matrix::IO::phylip A parser for PHYLIP distance matricies      
Bio::Matrix::IO::scoring A parser for PAM/BLOSUM matricies      
Bio::Matrix::MatrixI An interface for describing a Matrix      
Bio::Matrix::Mlagan A generic matrix with mlagan fields      
Bio::Matrix::PSM::IO PSM parser      
Bio::Matrix::PSM::IO::mast PSM mast parser implementation      
Bio::Matrix::PSM::IO::masta motif fasta format parser      
Bio::Matrix::PSM::IO::meme PSM meme parser implementation      
Bio::Matrix::PSM::IO::psiblast PSM psiblast parser      
Bio::Matrix::PSM::IO::transfac PSM transfac parser      
Bio::Matrix::PSM::InstanceSite A PSM site occurance      
Bio::Matrix::PSM::InstanceSiteI InstanceSite interface, holds an instance of a PSM      
Bio::Matrix::PSM::ProtMatrix SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) with log-odds scoring information.      
Bio::Matrix::PSM::ProtPsm handle combination of site matricies      
Bio::Matrix::PSM::Psm handle combination of site matricies      
Bio::Matrix::PSM::PsmHeader PSM mast parser implementation      
Bio::Matrix::PSM::PsmHeaderI handles the header data from a PSM file      
Bio::Matrix::PSM::PsmI abstract interface to handler of site matricies      
Bio::Matrix::PSM::SiteMatrix SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds      
Bio::Matrix::PSM::SiteMatrixI SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds      
Bio::Matrix::PhylipDist A Phylip Distance Matrix object      
Bio::Matrix::Scoring Object which can hold scoring matrix information      
Bio::MolEvol::CodonModel Codon Evolution Models      
Bio::Nexml::Factory A factory module for creating BioPerl and Bio::Phylo objects from/to nexml documents      
Bio::NexmlIO stream handler for NeXML documents      
Bio::Ontology::DocumentRegistry Keep track of where to find ontologies. Allows lookups by name.      
Bio::Ontology::GOterm representation of GO terms      
Bio::Ontology::InterProTerm Implementation of InterProI term interface      
Bio::Ontology::OBOEngine An Ontology Engine for OBO style flat file format from the Gene Ontology Consortium      
Bio::Ontology::OBOterm representation of OBO terms      
Bio::Ontology::Ontology standard implementation of an Ontology      
Bio::Ontology::OntologyEngineI Interface a minimal Ontology implementation should satisfy      
Bio::Ontology::OntologyI Interface for an ontology implementation      
Bio::Ontology::OntologyStore A repository of ontologies      
Bio::Ontology::Path a path for an ontology term graph      
Bio::Ontology::PathI Interface for a path between ontology terms      
Bio::Ontology::Relationship a relationship for an ontology      
Bio::Ontology::RelationshipFactory Instantiates a new Bio::Ontology::RelationshipI (or derived class) through a factory      
Bio::Ontology::RelationshipI Interface for a relationship between ontology terms      
Bio::Ontology::RelationshipType a relationship type for an ontology      
Bio::Ontology::SimpleGOEngine::GraphAdaptor Graph adaptor for Bio::Ontology::SimpleGOEngine      
Bio::Ontology::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 base class for SAX Handlers      
Bio::OntologyIO::Handlers::InterProHandler XML handler class for InterProParser      
Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler parse an InterPro XML file and persist the resulting terms to a Biosql database      
Bio::OntologyIO::InterProParser Parser for InterPro xml files.      
Bio::OntologyIO::dagflat a base class parser for GO flat-file type formats      
Bio::OntologyIO::goflat a parser for the Gene Ontology flat-file format      
Bio::OntologyIO::obo a parser for OBO flat-file format from Gene Ontology Consortium      
Bio::OntologyIO::simplehierarchy a base class parser for simple hierarchy-by-indentation type formats      
Bio::OntologyIO::soflat a parser for the Sequence Ontology flat-file format      
Bio::ParameterBaseI Simple interface class for any parameter-related data such as IDs, database name, program arguments, and other odds and ends.      
Bio::Perl Functional access to BioPerl for people who don't know objects      
Bio::Phenotype::Correlate Representation of a correlating phenotype in a given species      
Bio::Phenotype::MeSH::Term A MeSH term      
Bio::Phenotype::MeSH::Twig Context for a MeSH term      
Bio::Phenotype::Measure Representation of context/value(-range)/unit triplets      
Bio::Phenotype::OMIM::MiniMIMentry Representation of a Mini MIM entry      
Bio::Phenotype::OMIM::OMIMentry represents OMIM (Online Mendelian Inheritance in Man) database entries      
Bio::Phenotype::OMIM::OMIMentryAllelicVariant Representation of a allelic variant of the OMIM database      
Bio::Phenotype::OMIM::OMIMparser parser for the OMIM database      
Bio::Phenotype::Phenotype A class for modeling phenotypes      
Bio::Phenotype::PhenotypeI An interface for classes modeling phenotypes      
Bio::PhyloNetwork Module to compute with Phylogenetic Networks      
Bio::PhyloNetwork::Factory Module to sequentially generate Phylogenetic Networks      
Bio::PhyloNetwork::FactoryX Module to sequentially generate Phylogenetic Networks      
Bio::PhyloNetwork::GraphViz Interface between PhyloNetwork and GraphViz      
Bio::PhyloNetwork::RandomFactory Module to generate random Phylogenetic Networks      
Bio::PhyloNetwork::TreeFactory Module to sequentially generate Phylogenetic Trees      
Bio::PhyloNetwork::TreeFactoryMulti Module to sequentially generate Phylogenetic Trees      
Bio::PhyloNetwork::TreeFactoryX Module to sequentially generate Phylogenetic Trees      
Bio::PhyloNetwork::muVector Module to compute with vectors of arbitrary dimension      
Bio::PopGen::Genotype An implementation of GenotypeI which is just an allele container      
Bio::PopGen::GenotypeI A marker and alleles for a specific individual      
Bio::PopGen::HtSNP 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::prototype prototype enzyme set      
Bio::Restriction::IO::withrefm withrefm enzyme set      
Bio::Root::Build A common Module::Build subclass base for BioPerl distributions     1.006923
Bio::Root::Exception Generic exception objects for Bioperl      
Bio::Root::HTTPget module for fallback HTTP get operations when LWP:: is unavailable      
Bio::Root::IO module providing several methods often needed when dealing with file IO      
Bio::Root::Root Hash-based implementation of Bio::Root::RootI      
Bio::Root::RootI Abstract interface to root object code      
Bio::Root::Storable object serialisation methods      
Bio::Root::Test A common base for all Bioperl test scripts.      
Bio::Root::Utilities General-purpose utility module      
Bio::Root::Version provide global, distribution-level versioning     1.006923
Bio::Search::BlastStatistics An object for Blast statistics      
Bio::Search::BlastUtils Utility functions for Bio::Search:: BLAST objects      
Bio::Search::DatabaseI Interface for a database used in a sequence search      
Bio::Search::GenericDatabase Generic implementation of Bio::Search::DatabaseI      
Bio::Search::GenericStatistics An object for statistics      
Bio::Search::HSP::BlastHSP Bioperl BLAST High-Scoring Pair object      
Bio::Search::HSP::BlastPullHSP A parser and HSP object for BlastN hsps      
Bio::Search::HSP::FastaHSP HSP object for FASTA specific data      
Bio::Search::HSP::GenericHSP A "Generic" implementation of a High Scoring Pair      
Bio::Search::HSP::HMMERHSP A HSP object for HMMER results      
Bio::Search::HSP::HSPFactory A factory to create Bio::Search::HSP::HSPI objects      
Bio::Search::HSP::HSPI Interface for a High Scoring Pair in a similarity search result      
Bio::Search::HSP::HmmpfamHSP A parser and HSP object for hmmpfam hsps      
Bio::Search::HSP::ModelHSP A HSP object for model-based searches      
Bio::Search::HSP::PSLHSP A HSP for PSL output      
Bio::Search::HSP::PsiBlastHSP Bioperl BLAST High-Scoring Pair object      
Bio::Search::HSP::PullHSPI Bio::Search::HSP::HSPI interface for pull parsers.      
Bio::Search::HSP::WABAHSP HSP object suitable for describing WABA alignments      
Bio::Search::Hit::BlastHit Blast-specific subclass of Bio::Search::Hit::GenericHit      
Bio::Search::Hit::BlastPullHit A parser and hit object for BLASTN hits      
Bio::Search::Hit::Fasta Hit object specific for Fasta-generated hits      
Bio::Search::Hit::GenericHit A generic implementation of the Bio::Search::Hit::HitI interface      
Bio::Search::Hit::HMMERHit A Hit module for HMMER hits      
Bio::Search::Hit::HitFactory A factory to create Bio::Search::Hit::HitI objects      
Bio::Search::Hit::HitI Interface for a hit in a similarity search result      
Bio::Search::Hit::HmmpfamHit A parser and hit object for hmmpfam hits      
Bio::Search::Hit::ModelHit A model-based implementation of the Bio::Search::Hit::HitI interface      
Bio::Search::Hit::PsiBlastHit Bioperl BLAST Hit object      
Bio::Search::Hit::PullHitI Bio::Search::Hit::HitI interface for pull parsers.      
Bio::Search::Hit::hmmer3Hit DESCRIPTION of Object      
Bio::Search::Iteration::GenericIteration A generic implementation of the Bio::Search::Iteration::IterationI interface.      
Bio::Search::Iteration::IterationI Abstract interface to an iteration from an iterated search result, such as PSI-BLAST.      
Bio::Search::Processor DESCRIPTION of Object      
Bio::Search::Result::BlastPullResult A parser and result object for BLASTN results      
Bio::Search::Result::BlastResult Blast-specific subclass of Bio::Search::Result::GenericResult      
Bio::Search::Result::CrossMatchResult CrossMatch-specific subclass of Bio::Search::Result::GenericResult      
Bio::Search::Result::GenericResult Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results.      
Bio::Search::Result::HMMERResult A Result object for HMMER results      
Bio::Search::Result::HmmpfamResult A parser and result object for hmmpfam results      
Bio::Search::Result::PullResultI Bio::Search::Result::ResultI interface for 'pull' parsers      
Bio::Search::Result::ResultFactory A factory to create Bio::Search::Result::ResultI objects      
Bio::Search::Result::ResultI Abstract interface to Search Result objects      
Bio::Search::Result::WABAResult Result object for WABA alignment output      
Bio::Search::Result::hmmer3Result DESCRIPTION of Object      
Bio::Search::SearchUtils Utility functions for Bio::Search:: objects      
Bio::Search::StatisticsI A Base object for statistics      
Bio::Search::Tiling::MapTileUtils utilities for manipulating closed intervals for an HSP tiling algorithm      
Bio::Search::Tiling::MapTiling An implementation of an HSP tiling algorithm, with methods to obtain frequently-requested statistics      
Bio::Search::Tiling::TilingI Abstract interface for an HSP tiling module      
Bio::SearchDist A perl wrapper around Sean Eddy's histogram object      
Bio::SearchIO Driver for parsing Sequence Database Searches (BLAST, FASTA, ...)      
Bio::SearchIO::EventHandlerI An abstract Event Handler for Search Result parsing      
Bio::SearchIO::FastHitEventBuilder Event Handler for SearchIO events.      
Bio::SearchIO::IteratedSearchResultEventBuilder Event Handler for SearchIO events.      
Bio::SearchIO::SearchResultEventBuilder Event Handler for SearchIO events.      
Bio::SearchIO::SearchWriterI Interface for outputting parsed Search results      
Bio::SearchIO::Writer::BSMLResultWriter BSML output writer      
Bio::SearchIO::Writer::GbrowseGFF Interface for outputting parsed search results in Gbrowse GFF format      
Bio::SearchIO::Writer::HSPTableWriter Tab-delimited data for Bio::Search::HSP::HSPI objects      
Bio::SearchIO::Writer::HTMLResultWriter write a Bio::Search::ResultI in HTML      
Bio::SearchIO::Writer::HitTableWriter Tab-delimited data for Bio::Search::Hit::HitI objects      
Bio::SearchIO::Writer::ResultTableWriter Outputs tab-delimited data for each Bio::Search::Result::ResultI object.      
Bio::SearchIO::Writer::TextResultWriter Object to implement writing a Bio::Search::ResultI in Text.      
Bio::SearchIO::XML::BlastHandler XML Handler for NCBI Blast XML parsing.      
Bio::SearchIO::XML::PsiBlastHandler XML Handler for NCBI Blast PSIBLAST XML parsing.      
Bio::SearchIO::axt a parser for axt format reports      
Bio::SearchIO::blast Event generator for event based parsing of blast reports      
Bio::SearchIO::blast_pull A parser for BLAST output      
Bio::SearchIO::blasttable Driver module for SearchIO for parsing NCBI -m 8/9 format      
Bio::SearchIO::blastxml A SearchIO implementation of NCBI Blast XML parsing.      
Bio::SearchIO::cross_match CrossMatch-specific subclass of Bio::SearchIO      
Bio::SearchIO::erpin SearchIO-based ERPIN parser      
Bio::SearchIO::exonerate parser for Exonerate      
Bio::SearchIO::fasta A SearchIO parser for FASTA results      
Bio::SearchIO::gmap_f9 Event generator for parsing gmap reports (Z format)      
Bio::SearchIO::hmmer A parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam)      
Bio::SearchIO::hmmer2 A parser for HMMER output (hmmpfam, hmmsearch)      
Bio::SearchIO::hmmer3      
Bio::SearchIO::hmmer_pull A parser for HMMER output      
Bio::SearchIO::infernal SearchIO-based Infernal parser      
Bio::SearchIO::megablast a driver module for Bio::SearchIO to parse megablast reports (format 0)      
Bio::SearchIO::psl A parser for PSL output (UCSC)      
Bio::SearchIO::rnamotif SearchIO-based RNAMotif parser      
Bio::SearchIO::sim4 parser for Sim4 alignments      
Bio::SearchIO::waba SearchIO parser for Jim Kent WABA program alignment output      
Bio::SearchIO::wise Parsing of wise output as alignments      
Bio::Seq Sequence object, with features      
Bio::Seq::BaseSeqProcessor Base implementation for a SequenceProcessor      
Bio::Seq::EncodedSeq subtype of Bio::LocatableSeq to store DNA that encodes a protein      
Bio::Seq::LargeLocatableSeq LocatableSeq object that stores sequence as files in the tempdir      
Bio::Seq::LargePrimarySeq PrimarySeq object that stores sequence as files in the tempdir (as found by File::Temp) or the default method in Bio::Root::Root      
Bio::Seq::LargeSeq SeqI compliant object that stores sequence as files in /tmp      
Bio::Seq::LargeSeqI Interface class for sequences that cache their residues in a temporary file      
Bio::Seq::Meta Generic superclass for sequence objects with residue-based meta information      
Bio::Seq::Meta::Array array-based generic implementation of a sequence class with residue-based meta information      
Bio::Seq::MetaI Interface for sequence objects with residue-based meta information      
Bio::Seq::PrimaryQual Bioperl lightweight Quality Object      
Bio::Seq::PrimedSeq A sequence and a pair of primers matching on it      
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 Instantiation of generic Bio::PrimarySeqI (or derived) objects through a factory      
Bio::Seq::SeqFastaSpeedFactory Rapid creation of Bio::Seq objects through a factory      
Bio::Seq::SeqWithQuality Bioperl object packaging a sequence with its quality. Deprecated class, use Bio::Seq::Quality instead!      
Bio::Seq::SequenceTrace Bioperl object packaging a sequence with its trace      
Bio::Seq::SimulatedRead Read with sequencing errors taken from a reference sequence      
Bio::Seq::TraceI Interface definition for a Bio::Seq::Trace      
Bio::SeqAnalysisParserI Sequence analysis output parser interface      
Bio::SeqEvolution::DNAPoint evolve a sequence by point mutations      
Bio::SeqEvolution::EvolutionI the interface for evolving sequences      
Bio::SeqEvolution::Factory Factory object to instantiate sequence evolving classes      
Bio::SeqFeature::Amplicon Amplicon feature      
Bio::SeqFeature::AnnotationAdaptor integrates SeqFeatureIs annotation      
Bio::SeqFeature::Collection A container class for SeqFeatures suitable for performing operations such as finding features within a range, that match a certain feature type, etc.      
Bio::SeqFeature::CollectionI An interface for a collection of SeqFeatureI objects.      
Bio::SeqFeature::Computation Computation SeqFeature      
Bio::SeqFeature::FeaturePair hold pair feature information e.g. blast hits      
Bio::SeqFeature::Gene::Exon a feature representing an exon      
Bio::SeqFeature::Gene::ExonI Interface for a feature representing an exon      
Bio::SeqFeature::Gene::GeneStructure A feature representing an arbitrarily complex structure of a gene      
Bio::SeqFeature::Gene::GeneStructureI A feature representing an arbitrarily complex structure of a gene      
Bio::SeqFeature::Gene::Intron An intron feature      
Bio::SeqFeature::Gene::NC_Feature superclass for non-coding features      
Bio::SeqFeature::Gene::Poly_A_site poly A feature      
Bio::SeqFeature::Gene::Promoter Describes a promoter      
Bio::SeqFeature::Gene::Transcript A feature representing a transcript      
Bio::SeqFeature::Gene::TranscriptI Interface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site.      
Bio::SeqFeature::Gene::UTR A feature representing an untranslated region that is part of a transcriptional unit      
Bio::SeqFeature::Generic Generic SeqFeature      
Bio::SeqFeature::Lite Lightweight Bio::SeqFeatureI class      
Bio::SeqFeature::PositionProxy handle features when truncation/revcom sequences span a feature      
Bio::SeqFeature::Primer Primer Generic SeqFeature      
Bio::SeqFeature::SiRNA::Oligo Perl object for small inhibitory RNAs.      
Bio::SeqFeature::SiRNA::Pair Perl object for small inhibitory RNA (SiRNA) oligo pairs      
Bio::SeqFeature::Similarity A sequence feature based on similarity      
Bio::SeqFeature::SimilarityPair Sequence feature based on the similarity of two sequences.      
Bio::SeqFeature::SubSeq Feature representing a subsequence      
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::Handler::GenericRichSeqHandler Bio::HandlerI-based data handler for GenBank/EMBL/UniProt (and other) sequence data      
Bio::SeqIO::MultiFile Treating a set of files as a single input stream      
Bio::SeqIO::abi abi trace sequence input/output stream      
Bio::SeqIO::ace ace sequence input/output stream      
Bio::SeqIO::agave AGAVE sequence output stream.      
Bio::SeqIO::alf alf trace sequence input/output stream      
Bio::SeqIO::asciitree asciitree sequence input/output stream      
Bio::SeqIO::bsml BSML sequence input/output stream      
Bio::SeqIO::bsml_sax BSML sequence input/output stream using SAX      
Bio::SeqIO::chadoxml chadoxml sequence output stream      
Bio::SeqIO::chaos chaos sequence input/output stream      
Bio::SeqIO::chaosxml chaosxml sequence input/output stream      
Bio::SeqIO::ctf ctf trace sequence input/output stream      
Bio::SeqIO::embl EMBL sequence input/output stream      
Bio::SeqIO::embldriver EMBL sequence input/output stream      
Bio::SeqIO::entrezgene Entrez Gene ASN1 parser      
Bio::SeqIO::excel sequence input/output stream from a MSExcel-formatted table      
Bio::SeqIO::exp exp trace sequence input/output stream      
Bio::SeqIO::fasta fasta sequence input/output stream      
Bio::SeqIO::fastq fastq sequence input/output stream      
Bio::SeqIO::flybase_chadoxml FlyBase variant of chadoxml with sequence output stream      
Bio::SeqIO::game a class for parsing and writing game-XML      
Bio::SeqIO::game::featHandler a class for handling feature elements      
Bio::SeqIO::game::gameHandler PerlSAX handler for game-XML      
Bio::SeqIO::game::gameSubs a base class for game-XML parsing      
Bio::SeqIO::game::gameWriter a class for writing game-XML      
Bio::SeqIO::game::seqHandler a class for handling game-XML sequences      
Bio::SeqIO::gbdriver GenBank handler-based push parser      
Bio::SeqIO::gbxml GenBank sequence input/output stream using SAX      
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::mbsout input stream for output by Teshima et al.'s mbs.      
Bio::SeqIO::metafasta metafasta sequence input/output stream      
Bio::SeqIO::msout input stream for output by Hudson's ms      
Bio::SeqIO::nexml NeXML 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::seqxml SeqXML sequence input/output stream      
Bio::SeqIO::strider DNA strider sequence input/output stream      
Bio::SeqIO::swiss Swissprot sequence input/output stream      
Bio::SeqIO::swissdriver SwissProt/UniProt handler-based push parser      
Bio::SeqIO::tab nearly raw sequence file input/output stream. Reads/writes id"\t"sequence"\n"      
Bio::SeqIO::table sequence input/output stream from a delimited table      
Bio::SeqIO::tigr TIGR XML sequence input/output stream      
Bio::SeqIO::tigrxml Parse TIGR (new) XML      
Bio::SeqIO::tinyseq reading/writing sequences in NCBI TinySeq format      
Bio::SeqIO::tinyseq::tinyseqHandler XML event handlers to support NCBI TinySeq XML parsing      
Bio::SeqIO::ztr ztr trace sequence input/output stream      
Bio::SeqUtils Additional methods for PrimarySeq objects      
Bio::SimpleAlign Multiple alignments held as a set of sequences      
Bio::SimpleAnalysisI A simple interface to any (local or remote) analysis tool      
Bio::Species Generic species object.      
Bio::Structure::Atom Bioperl structure Object, describes an Atom      
Bio::Structure::Chain Bioperl structure Object, describes a chain      
Bio::Structure::Entry Bioperl structure Object, describes the whole entry      
Bio::Structure::IO Handler for Structure Formats      
Bio::Structure::IO::pdb PDB input/output stream      
Bio::Structure::Model Bioperl structure Object, describes a Model      
Bio::Structure::Residue Bioperl structure Object, describes a Residue      
Bio::Structure::SecStr::DSSP::Res Module for parsing/accessing dssp output      
Bio::Structure::SecStr::STRIDE::Res Module for parsing/accessing stride output      
Bio::Structure::StructureI Abstract Interface for a Structure objects      
Bio::Symbol::Alphabet BSANE/BioCORBA compliant symbol list alphabet      
Bio::Symbol::AlphabetI A Symbol Alphabet      
Bio::Symbol::DNAAlphabet A ready made DNA alphabet      
Bio::Symbol::ProteinAlphabet A ready made Protein alphabet      
Bio::Symbol::Symbol A biological symbol      
Bio::Symbol::SymbolI Interface for a Symbol      
Bio::Taxon A node in a represented taxonomy      
Bio::Taxonomy representing Taxonomy.      
Bio::Taxonomy::FactoryI interface to define how to access NCBI Taxonoy      
Bio::Taxonomy::Node A node in a represented taxonomy      
Bio::Taxonomy::Taxon Generic Taxonomic Entity object      
Bio::Taxonomy::Tree An Organism Level Implementation of TreeI interface.      
Bio::Tools::AlignFactory Base object for alignment factories      
Bio::Tools::Alignment::Consed A module to work with objects from consed .ace files      
Bio::Tools::Alignment::Trim A kludge to do specialized trimming of sequence based on quality.      
Bio::Tools::AmpliconSearch Find amplicons in a template using degenerate PCR primers      
Bio::Tools::Analysis::DNA::ESEfinder a wrapper around ESEfinder server      
Bio::Tools::Analysis::Protein::Domcut a wrapper around Domcut server      
Bio::Tools::Analysis::Protein::ELM a wrapper around the ELM server which predicts short functional motifs on amino acid sequences      
Bio::Tools::Analysis::Protein::GOR4 a wrapper around GOR4 protein secondary structure prediction server      
Bio::Tools::Analysis::Protein::HNN a wrapper around the HNN protein secondary structure prediction server      
Bio::Tools::Analysis::Protein::Mitoprot a wrapper around Mitoprot server      
Bio::Tools::Analysis::Protein::NetPhos a wrapper around NetPhos server      
Bio::Tools::Analysis::Protein::Scansite a wrapper around the Scansite server      
Bio::Tools::Analysis::Protein::Sopma a wrapper around the Sopma protein secondary structure prediction server      
Bio::Tools::Analysis::SimpleAnalysisBase abstract superclass for SimpleAnalysis implementations      
Bio::Tools::AnalysisResult Base class for analysis result objects and parsers      
Bio::Tools::Blat parser for Blat program      
Bio::Tools::CodonTable Codon table object      
Bio::Tools::Coil parser for Coil output      
Bio::Tools::ECnumber representation of EC numbers (Enzyme Classification)      
Bio::Tools::EMBOSS::Palindrome parse EMBOSS palindrome output      
Bio::Tools::EPCR Parse ePCR output and make features      
Bio::Tools::ERPIN a parser for ERPIN output      
Bio::Tools::ESTScan Results of one ESTScan run      
Bio::Tools::Eponine Results of one Eponine run      
Bio::Tools::Est2Genome Parse est2genome output, makes simple Bio::SeqFeature::Generic objects      
Bio::Tools::Fgenesh parse results of one Fgenesh run      
Bio::Tools::FootPrinter write sequence features in FootPrinter format      
Bio::Tools::GFF A Bio::SeqAnalysisParserI compliant GFF format parser      
Bio::Tools::Gel Calculates relative electrophoretic migration distances      
Bio::Tools::Geneid Results of one geneid run      
Bio::Tools::Genemark Results of one Genemark run      
Bio::Tools::Genewise Results of one Genewise run      
Bio::Tools::Genomewise Results of one Genomewise run      
Bio::Tools::Genscan Results of one Genscan run      
Bio::Tools::Glimmer parser for Glimmer 2.X/3.X prokaryotic and GlimmerM/GlimmerHMM eukaryotic gene predictions      
Bio::Tools::Grail Results of one Grail run      
Bio::Tools::GuessSeqFormat Module for determining the sequence format of the contents of a file, a string, or through a filehandle.      
Bio::Tools::HMMER::Domain One particular domain hit from HMMER      
Bio::Tools::HMMER::Results Object representing HMMER output results      
Bio::Tools::HMMER::Set Set of identical domains from HMMER matches      
Bio::Tools::Hmmpfam Parser for Hmmpfam program      
Bio::Tools::IUPAC Generates unique sequence objects or regular expressions from an ambiguous IUPAC sequence      
Bio::Tools::Infernal A parser for Infernal output      
Bio::Tools::Lucy Object for analyzing the output from Lucy, a vector and quality trimming program from TIGR      
Bio::Tools::MZEF Results of one MZEF run      
Bio::Tools::Match Parses output from Transfac's match(TM)      
Bio::Tools::OddCodes Object holding alternative alphabet coding for one protein sequence      
Bio::Tools::Phylo::Gerp Parses output from GERP      
Bio::Tools::Phylo::Gumby Parses output from gumby      
Bio::Tools::Phylo::Molphy parser for Molphy output      
Bio::Tools::Phylo::Molphy::Result container for data parsed from a ProtML run      
Bio::Tools::Phylo::PAML Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00      
Bio::Tools::Phylo::PAML::Codeml Parses output from the PAML program codeml.      
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::Protparam submit to and parse output from protparam ;      
Bio::Tools::Pseudowise Results of one Pseudowise run      
Bio::Tools::QRNA A Parser for qrna output      
Bio::Tools::RNAMotif A parser for RNAMotif output      
Bio::Tools::RandomDistFunctions A set of routines useful for generating random data in different distributions      
Bio::Tools::RepeatMasker a parser for RepeatMasker output      
Bio::Tools::Run::GenericParameters An object for the parameters used to run programs      
Bio::Tools::Run::ParametersI A Base object for the parameters used to run programs      
Bio::Tools::Run::RemoteBlast Object for remote execution of the NCBI Blast via HTTP      
Bio::Tools::Run::StandAloneBlast Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). There is experimental support for WU-Blast and NCBI rpsblast.      
Bio::Tools::Run::StandAloneNCBIBlast Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). With experimental support for NCBI rpsblast.      
Bio::Tools::Run::StandAloneWUBlast Object for the local execution of WU-Blast.      
Bio::Tools::Run::WrapperBase A Base object for wrappers around executables      
Bio::Tools::Seg parse seg output      
Bio::Tools::SeqPattern represent a sequence pattern or motif      
Bio::Tools::SeqPattern::Backtranslate      
Bio::Tools::SeqStats Object holding statistics for one particular sequence      
Bio::Tools::SeqWords Object holding n-mer statistics for a sequence      
Bio::Tools::SiRNA Perl object for designing small inhibitory RNAs.      
Bio::Tools::SiRNA::Ruleset::saigo Perl object implementing the Saigo group's rules for designing small inhibitory RNAs      
Bio::Tools::SiRNA::Ruleset::tuschl Perl object implementing the tuschl group's rules for designing small inhibitory RNAs      
Bio::Tools::Sigcleave Bioperl object for sigcleave analysis      
Bio::Tools::Signalp parser for Signalp output      
Bio::Tools::Signalp::ExtendedSignalp enhanced parser for Signalp output      
Bio::Tools::Sim4::Exon A single exon determined by an alignment      
Bio::Tools::Sim4::Results Results of one Sim4 run      
Bio::Tools::Spidey::Exon A single exon determined by an alignment      
Bio::Tools::Spidey::Results Results of a Spidey run      
Bio::Tools::TandemRepeatsFinder a parser for Tandem Repeats Finder output      
Bio::Tools::TargetP Results of one TargetP run      
Bio::Tools::Tmhmm parse TMHMM output (TransMembrane HMM)      
Bio::Tools::dpAlign Perl extension to do pairwise dynamic programming sequence alignment      
Bio::Tools::ipcress Parse ipcress output and make features      
Bio::Tools::isPcr Parse isPcr output and make features      
Bio::Tools::pICalculator calculate the isoelectric point of a protein      
Bio::Tools::pSW pairwise Smith Waterman object      
Bio::Tools::tRNAscanSE A parser for tRNAscan-SE output      
Bio::Tree::AlleleNode A Node with Alleles attached      
Bio::Tree::AnnotatableNode A Tree Node with support for annotation      
Bio::Tree::Compatible Testing compatibility of phylogenetic trees with nested taxa.      
Bio::Tree::DistanceFactory Construct a tree using distance based methods      
Bio::Tree::Draw::Cladogram Drawing phylogenetic trees in Encapsulated PostScript (EPS) format.      
Bio::Tree::Node A Simple Tree Node      
Bio::Tree::NodeI Interface describing a Tree Node      
Bio::Tree::NodeNHX A Simple Tree Node with support for NHX tags      
Bio::Tree::RandomFactory TreeFactory for generating Random Trees      
Bio::Tree::Statistics Calculate certain statistics for a Tree      
Bio::Tree::Tree An implementation of the 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::NewickParser      
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      
Bio::TreeIO::nexml A TreeIO driver module for parsing NeXML tree files      
Bio::TreeIO::nexus A TreeIO driver module for parsing Nexus tree output from PAUP      
Bio::TreeIO::nhx TreeIO implementation for parsing Newick/New Hampshire eXtendend (NHX) format.      
Bio::TreeIO::pag Bio::TreeIO driver for Pagel format      
Bio::TreeIO::phyloxml TreeIO implementation for parsing PhyloXML format.      
Bio::TreeIO::svggraph A simple output format that converts a Tree object to an SVG output      
Bio::TreeIO::tabtree A simple output format which displays a tree as an ASCII drawing      
Bio::UpdateableSeqI Descendant of Bio::SeqI that allows updates      
Bio::Variation::AAChange Sequence change class for polypeptides      
Bio::Variation::AAReverseMutate point mutation and codon information from single amino acid changes      
Bio::Variation::Allele Sequence object with allele-specific attributes      
Bio::Variation::DNAMutation DNA level mutation class      
Bio::Variation::IO Handler for sequence variation IO Formats      
Bio::Variation::IO::flat flat file sequence variation input/output stream      
Bio::Variation::IO::xml XML sequence variation input/output stream      
Bio::Variation::RNAChange Sequence change class for RNA level      
Bio::Variation::SNP submitted SNP      
Bio::Variation::SeqDiff Container class for mutation/variant descriptions      
Bio::Variation::VariantI Sequence Change SeqFeature abstract class      
Bio::WebAgent A base class for Web (any protocol) access      
BioPerl Perl Modules for Biology      
Deobfuscator get BioPerl method and package information from a Berkeley DB     0.0.3
TestInterface A simple subclass of Interface      
TestObject An implementation of TestInterface      

Documentation

*bp_seqcut.pl*  
*bp_seqpart.pl* Takes one or more sequence files and splits them into a number of load balanced files.  
Bio::Tools::Run::WrapperBase::CommandExts Extensions to WrapperBase for handling programs with commands *ALPHA*  
Module which implements a newick string parser as a finite state machine which enables it to parse the full Newick specification.  
[[%ask1]] DESCRIPTION of Object  
authors.pl check modules and scripts for authors not in AUTHORS file  
bp_aacomp amino acid composition of protein sequences  
bp_biofetch_genbank_proxy.pl Caching BioFetch-compatible web proxy for GenBank  
bp_bioflat_index.pl index sequence files using Bio::DB::Flat  
bp_biogetseq sequence retrieval using OBDA registry  
bp_bulk_load_gff.pl Bulk-load a Bio::DB::GFF database from GFF files.  
bp_chaos_plot a chaos plot from DNA and RNA sequences  
bp_classify_hits_kingdom classify BLAST hits by taxonomic kingdom  
bp_composite_LD i filename.prettybase.txt --sortbyld > outfile  
bp_dbsplit script to split an input set of database(s) into smaller pieces  
bp_download_query_genbank script to query Genbank and retrieve records  
bp_extract_feature_seq extract the corresponding sequence for a specified feature type  
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_filter_search filters searchio results, outputting a tab delimited summary  
bp_flanks finding flanking sequences for a variant in a sequence position  
bp_gccalc GC content of nucleotide sequences  
bp_genbank2gff.pl Load a Bio::DB::GFF database from GENBANK files.  
bp_genbank2gff3.pl Genbank->gbrowse-friendly GFF3  
bp_generate_histogram.pl Generate a histogram of Bio::DB::GFF features  
bp_heterogeneity_test a test for distinguishing between selection and population expansion.  
bp_hivq.PL an interactive command-line interface to Bio::DB::HIV and Bio::DB::Query::HIVQuery  
bp_hmmer_to_table turn HMMER output into tabular format  
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_local_taxonomydb_query query a local TaxonomyDB for species or taxonid  
bp_make_mrna_protein Convert an input mRNA/cDNA sequence into protein  
bp_mask_by_search mask sequence(s) based on its alignment results  
bp_meta_gff.pl Get/set Bio::DB::GFF meta-data  
bp_mrtrans implement a transformer of alignments from protein to mrna coordinates  
bp_mutate.pl randomly mutagenize a single protein or DNA sequence  
bp_netinstall.pl  
bp_nexus2nh convert nexus format trees (from PAUP* and MrBayes) to new hampshire  
bp_nrdb.PLS a script to emulate Warren Gish's nrdb, make a unique sequence database from a set of input databases  
bp_oligo_count oligo count and frequency  
bp_pairwise_kaks script to calculate pairwise Ka,Ks for a set of sequences  
bp_parse_hmmsearch parse single/multiple HMMSEARCH results file(s) with different output options  
bp_process_gadfly.pl Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser  
bp_process_sgd.pl Massage SGD annotation flat files into a version suitable for the Generic Genome Browser  
bp_process_wormbase.pl Massage WormBase GFF files into a version suitable for the Generic Genome Browser  
bp_query_entrez_taxa query Entrez taxonomy database and print out information  
bp_remote_blast.pl script for submitting jobs to a remote blast server (ncbi blast queue at this time)  
bp_revtrans-motif Reverse translate a Profam-like protein motif  
bp_search2alnblocks Turn SearchIO parseable reports(s) into a set of aligned blocks  
bp_search2gff  
bp_search2table turn SearchIO parseable reports into tab delimited format like NCBI's -m 9  
bp_search2tribe Turn SearchIO parseable reports(s) into TRIBE matrix  
bp_seq_length.pl lists the number of bases and number of sequences in specified sequence database files  
bp_seqconvert generic BioPerl sequence format converter  
bp_seqfeature_load.pl Load GFF into a SeqFeature database  
bp_seqret bioperl implementation of sequence fetch from local db (like EMBOSS seqret)  
bp_seqretsplit split a sequence (or stream) into a single file per sequence  
bp_split_seq splits a sequence into equal sized chunks with an optional overlapping range  
bp_taxid4species simple script which returns the NCBI Taxonomic id for a requested species  
bp_taxonomy2tree Building a taxonomic tree based on the full lineages of a set of species names  
bp_translate_seq translates a sequence  
bp_tree2pag convert Bio::TreeIO parseable format trees to pagel format  
bp_unflatten_seq unflatten a genbank or genbank-style feature file into a nested SeqFeature hierarchy  
bpsreformat convert sequence formats  
check_NAMEs.pl check NAME in module POD has fully qualified object name  
check_URLs.pl validate URLs located in module code and POD  
cvs2cl_by_file.pl convert cvs log messages to changelogs  
dbfetch generic CGI program to retrieve biological database entries in various formats and styles (using SRS)  
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  
dependencies.pl check modules and scripts for dependencies not in core  
deprecated.pl Check modules and scripts for use of deprecated modules and methods, indicates presence in a file to STDERR. Optionally accepts new modules and adds them to a newly formatted deprecation file.  
examples/align/FastAlign.pl  
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  
find_mod_deps.pl inspect only hard-coded dependencies of sets of perl files  
gff2ps you will want to change this script  
longorf.pl perl script to find the longest ORF of a sequence  
maintenance/version.pl  
modules.pl information about modules in BioPerl core  
pod.pl check the POD documentation syntax in modules and scripts  
reverse-translate.pl  
rnai_finder.cgi  
run_primer3.pl run primer3 and parse its output  
search2bsml Turn SearchIO parseable reports(s) into a BSML report  
symlink_script.pl install script to create symbolic links  
tree_from_seqsearch builds a phylogenetic tree based on a sequence search (FastA,BLAST,HMMER)  
waba2gff3.pl convert waba output into GFF3 suitable for Gbrowse  

Other Files

Bio/LiveSeq/IO/README
Bio/Symbol/README.Symbol
Bio/Tools/Run/README
Bio/Variation/README
README.md
doc/Deobfuscator/README
doc/Deobfuscator/cgi-bin/deob_help.html
doc/README
examples/root/README
ide/bioperl-mode/README
maintenance/README
models/README
scripts/Bio-DB-GFF/README
scripts/README
scripts/das/README
scripts/searchio/README
scripts/utilities/README