Christopher Fields > BioPerl-1.6.901

BioPerl-1.6.901

This Release BioPerl-1.6.901  [Download] [Browse 18 May 2011
Latest Release BioPerl-1.6.924  [Download] [Browse 10 Jul 2014
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License The Perl 5 License (Artistic 1 & GPL 1)
Special Files
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Build.PL
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INSTALL
LICENSE
MANIFEST
META.json
README

Modules

Bio::Align::AlignI An interface for describing sequence alignments.     1.006901
Bio::Align::DNAStatistics Calculate some statistics for a DNA alignment     1.006901
Bio::Align::Graphics Graphic Rendering of Bio::Align::AlignI Objects     1.006901
Bio::Align::PairwiseStatistics Base statistic object for Pairwise Alignments     1.006901
Bio::Align::ProteinStatistics Calculate Protein Alignment statistics (mostly distances)     1.006901
Bio::Align::StatisticsI Calculate some statistics for an alignment     1.006901
Bio::Align::Utilities A collection of utilities regarding converting and manipulating alignment objects     1.006901
Bio::AlignIO Handler for AlignIO Formats     1.006901
Bio::AlignIO::Handler::GenericAlignHandler Bio::HandlerI-based generic data handler class for alignment-based data     1.006901
Bio::AlignIO::arp ARP MSA Sequence input/output stream     1.006901
Bio::AlignIO::bl2seq bl2seq sequence input/output stream     1.006901
Bio::AlignIO::clustalw clustalw sequence input/output stream     1.006901
Bio::AlignIO::emboss Parse EMBOSS alignment output (from applications water and needle)     1.006901
Bio::AlignIO::fasta fasta MSA Sequence input/output stream     1.006901
Bio::AlignIO::largemultifasta Largemultifasta MSA Sequence input/output stream     1.006901
Bio::AlignIO::maf Multiple Alignment Format sequence input stream     1.006901
Bio::AlignIO::mase mase sequence input/output stream     1.006901
Bio::AlignIO::mega Parse and Create MEGA format data files     1.006901
Bio::AlignIO::meme meme sequence input/output stream     1.006901
Bio::AlignIO::metafasta Metafasta MSA Sequence input/output stream     1.006901
Bio::AlignIO::msf msf sequence input/output stream     1.006901
Bio::AlignIO::nexml NeXML format sequence alignment input/output stream driver     1.006901
Bio::AlignIO::nexus NEXUS format sequence input/output stream     1.006901
Bio::AlignIO::pfam pfam sequence input/output stream     1.006901
Bio::AlignIO::phylip PHYLIP format sequence input/output stream     1.006901
Bio::AlignIO::po po MSA Sequence input/output stream     1.006901
Bio::AlignIO::proda proda sequence input/output stream     1.006901
Bio::AlignIO::prodom prodom sequence input/output stream     1.006901
Bio::AlignIO::psi Read/Write PSI-BLAST profile alignment files     1.006901
Bio::AlignIO::selex selex sequence input/output stream     1.006901
Bio::AlignIO::stockholm stockholm sequence input/output stream     1.006901
Bio::AlignIO::xmfa XMFA MSA Sequence input/output stream     1.006901
Bio::AnalysisI An interface to any (local or remote) analysis tool     1.006901
Bio::AnalysisI::JobI     1.006901
Bio::AnalysisParserI Generic analysis output parser interface     1.006901
Bio::AnalysisResultI Interface for analysis result objects     1.006901
Bio::AnnotatableI the base interface an annotatable object must implement     1.006901
Bio::Annotation::AnnotationFactory Instantiates a new Bio::AnnotationI (or derived class) through a factory     1.006901
Bio::Annotation::Collection Default Perl implementation of AnnotationCollectionI     1.006901
Bio::Annotation::Comment A comment object, holding text     1.006901
Bio::Annotation::DBLink untyped links between databases     1.006901
Bio::Annotation::OntologyTerm An ontology term adapted to AnnotationI     1.006901
Bio::Annotation::Reference Specialised DBLink object for Literature References     1.006901
Bio::Annotation::Relation Relationship (pairwise) with other objects SeqI and NodeI;     1.006901
Bio::Annotation::SimpleValue A simple scalar     1.006901
Bio::Annotation::StructuredValue A scalar with embedded structured information     1.006901
Bio::Annotation::TagTree AnnotationI with tree-like hierarchal key-value relationships ('structured tags') that can be represented as simple text.     1.006901
Bio::Annotation::Target Provides an object which represents a target (ie, a similarity hit) from one object to something in another database     1.006901
Bio::Annotation::Tree Provide a tree as an annotation to a Bio::AnnotatableI object     1.006901
Bio::Annotation::TypeManager Manages types for annotation collections     1.006901
Bio::AnnotationCollectionI Interface for annotation collections     1.006901
Bio::AnnotationI Annotation interface     1.006901
Bio::Assembly::Contig Perl module to hold and manipulate sequence assembly contigs.     1.006901
Bio::Assembly::ContigAnalysis Perform analysis on sequence assembly contigs.     1.006901
Bio::Assembly::IO Handler for Assembly::IO Formats     1.006901
Bio::Assembly::IO::ace module to load ACE files from various assembly programs     1.006901
Bio::Assembly::IO::bowtie An IO module for assemblies in Bowtie format *BETA*     1.006901
Bio::Assembly::IO::maq Driver to read assembly files in maq format *BETA*     1.006901
Bio::Assembly::IO::phrap driver to load phrap.out files.     1.006901
Bio::Assembly::IO::sam An IO module for assemblies in Sam format *BETA*     1.006901
Bio::Assembly::IO::tigr Driver to read and write assembly files in the TIGR Assembler v2 default format.     1.006901
Bio::Assembly::Scaffold Perl module to hold and manipulate sequence assembly data.     1.006901
Bio::Assembly::ScaffoldI Abstract Inteface of Sequence Assemblies     1.006901
Bio::Assembly::Singlet Perl module to hold and manipulate singlets from sequence assembly contigs.     1.006901
Bio::Assembly::Tools::ContigSpectrum create and manipulate contig spectra     1.006901
Bio::Biblio A Bibliographic Query Service module     1.006901
Bio::Biblio::Article Representation of a general article     1.006901
Bio::Biblio::BiblioBase An abstract base for other biblio classes     1.006901
Bio::Biblio::Book Representation of a book     1.006901
Bio::Biblio::BookArticle Representation of a book article     1.006901
Bio::Biblio::IO Handling the bibliographic references     1.006901
Bio::Biblio::IO::medline2ref A converter of a raw hash to MEDLINE citations     1.006901
Bio::Biblio::IO::medlinexml A converter of XML files with MEDLINE citations     1.006901
Bio::Biblio::IO::pubmed2ref A converter of a raw hash to PUBMED citations     1.006901
Bio::Biblio::IO::pubmedxml A converter of XML files with PUBMED citations     1.006901
Bio::Biblio::Journal Representation of a journal     1.006901
Bio::Biblio::JournalArticle Representation of a journal article     1.006901
Bio::Biblio::MedlineArticle Representation of a MEDLINE article     1.006901
Bio::Biblio::MedlineBook Representation of a MEDLINE book     1.006901
Bio::Biblio::MedlineBookArticle Representation of a MEDLINE book article     1.006901
Bio::Biblio::MedlineJournal Representation of a MEDLINE journal     1.006901
Bio::Biblio::MedlineJournalArticle Representation of a MEDLINE journal article     1.006901
Bio::Biblio::Organisation Representation of an organisation     1.006901
Bio::Biblio::Patent Representation of a patent     1.006901
Bio::Biblio::Person Representation of a person     1.006901
Bio::Biblio::Proceeding Representation of a conference proceeding     1.006901
Bio::Biblio::Provider Representation of a general provider     1.006901
Bio::Biblio::PubmedArticle Representation of a PUBMED article     1.006901
Bio::Biblio::PubmedBookArticle Representation of a PUBMED book article     1.006901
Bio::Biblio::PubmedJournalArticle Representation of a PUBMED journal article     1.006901
Bio::Biblio::Ref Representation of a bibliographic reference     1.006901
Bio::Biblio::Service Representation of a provider of type service     1.006901
Bio::Biblio::TechReport Representation of a technical report     1.006901
Bio::Biblio::Thesis Representation of thesis     1.006901
Bio::Biblio::WebResource Representation of a web resource     1.006901
Bio::Cluster::ClusterFactory Instantiates a new Bio::ClusterI (or derived class) through a factory     1.006901
Bio::Cluster::FamilyI Family Interface     1.006901
Bio::Cluster::SequenceFamily Sequence Family object     1.006901
Bio::Cluster::UniGene UniGene object     1.006901
Bio::Cluster::UniGeneI abstract interface of UniGene object     1.006901
Bio::ClusterI Cluster Interface     1.006901
Bio::ClusterIO Handler for Cluster Formats     1.006901
Bio::ClusterIO::dbsnp dbSNP input stream     1.006901
Bio::ClusterIO::unigene UniGene input stream     1.006901
Bio::CodonUsage::IO for reading and writing codon usage tables to file     1.006901
Bio::CodonUsage::Table for access to the Codon usage Database at http://www.kazusa.or.jp/codon.     1.006901
Bio::Coordinate::Chain Mapping locations through a chain of coordinate mappers     1.006901
Bio::Coordinate::Collection Noncontinuous match between two coordinate sets     1.006901
Bio::Coordinate::ExtrapolatingPair Continuous match between two coordinate sets     1.006901
Bio::Coordinate::GeneMapper transformations between gene related coordinate systems     1.006901
Bio::Coordinate::Graph Finds shortest path between nodes in a graph     1.006901
Bio::Coordinate::MapperI Interface describing coordinate mappers     1.006901
Bio::Coordinate::Pair Continuous match between two coordinate sets     1.006901
Bio::Coordinate::Result Results from coordinate transformation     1.006901
Bio::Coordinate::Result::Gap Another name for Bio::Location::Simple     1.006901
Bio::Coordinate::Result::Match Another name for Bio::Location::Simple     1.006901
Bio::Coordinate::ResultI Interface to identify coordinate mapper results     1.006901
Bio::Coordinate::Utils Additional methods to create Bio::Coordinate objects     1.006901
Bio::DB::Ace Database object interface to ACeDB servers     1.006901
Bio::DB::Biblio::biofetch A BioFetch-based access to a bibliographic citation retrieval     1.006901
Bio::DB::Biblio::eutils Access to PubMed's bibliographic query service     1.006901
Bio::DB::Biblio::soap A SOAP-based access to a bibliographic query service     1.006901
Bio::DB::BiblioI An interface to a Bibliographic Query Service     1.006901
Bio::DB::BioFetch Database object interface to BioFetch retrieval     1.006901
Bio::DB::CUTG for access to the Codon usage Database at http://www.kazusa.or.jp/codon.     1.006901
Bio::DB::DBFetch Database object for retrieving using the dbfetch script     1.006901
Bio::DB::EMBL Database object interface for EMBL entry retrieval     1.006901
Bio::DB::EUtilities webagent which interacts with and retrieves data from NCBI's eUtils     1.006901
Bio::DB::EntrezGene Database object interface to Entrez Gene     1.006901
Bio::DB::Expression DESCRIPTION of Object     1.006901
Bio::DB::Expression::geo *** DESCRIPTION of Class     1.006901
Bio::DB::Failover A Bio::DB::RandomAccessI compliant class which wraps a prioritized list of DBs     1.006901
Bio::DB::Fasta Fast indexed access to a directory of fasta files     1.006901
Bio::DB::Fasta::Stream     1.006901
Bio::DB::Fasta::Subdir     1.006901
Bio::DB::FileCache In file cache for BioSeq objects     1.006901
Bio::DB::Flat Interface for indexed flat files     1.006901
Bio::DB::Flat::BDB Interface for BioHackathon standard BDB-indexed flat file     1.006901
Bio::DB::Flat::BDB::embl embl adaptor for Open-bio standard BDB-indexed flat file     1.006901
Bio::DB::Flat::BDB::fasta fasta adaptor for Open-bio standard BDB-indexed flat file     1.006901
Bio::DB::Flat::BDB::genbank genbank adaptor for Open-bio standard BDB-indexed flat file     1.006901
Bio::DB::Flat::BDB::swiss swissprot adaptor for Open-bio standard BDB-indexed flat file     1.006901
Bio::DB::Flat::BinarySearch BinarySearch search indexing system for sequence files     1.006901
Bio::DB::GFF Storage and retrieval of sequence annotation data     1.006901
Bio::DB::GFF::Adaptor::ace ace interface (for multiple inheritance)     1.006901
Bio::DB::GFF::Adaptor::berkeleydb Bio::DB::GFF database adaptor for in-memory databases     1.006901
Bio::DB::GFF::Adaptor::berkeleydb::iterator iterator for Bio::DB::GFF::Adaptor::berkeleydb     1.006901
Bio::DB::GFF::Adaptor::biofetch Cache BioFetch objects in a Bio::DB::GFF database     1.006901
Bio::DB::GFF::Adaptor::biofetch_oracle Cache BioFetch objects in a Bio::DB::GFF database     1.006901
Bio::DB::GFF::Adaptor::dbi Database adaptor for DBI (SQL) databases     1.006901
Bio::DB::GFF::Adaptor::dbi::caching_handle Cache for database handles     1.006901
Bio::DB::GFF::Adaptor::dbi::faux_dbh     1.006901
Bio::DB::GFF::Adaptor::dbi::iterator iterator for Bio::DB::GFF::Adaptor::dbi     1.006901
Bio::DB::GFF::Adaptor::dbi::mysql Database adaptor for a specific mysql schema     1.006901
Bio::DB::GFF::Adaptor::dbi::mysqlace Unholy union between mysql GFF database and acedb database     1.006901
Bio::DB::GFF::Adaptor::dbi::mysqlcmap Database adaptor for an integraded CMap/GBrowse mysql schema     1.006901
Bio::DB::GFF::Adaptor::dbi::mysqlopt Deprecated database adaptor     1.006901
Bio::DB::GFF::Adaptor::dbi::oracle Database adaptor for a specific oracle schema     1.006901
Bio::DB::GFF::Adaptor::dbi::oracleace Unholy union between oracle GFF database and acedb database     1.006901
Bio::DB::GFF::Adaptor::dbi::pg Database adaptor for a specific postgres schema     1.006901
Bio::DB::GFF::Adaptor::dbi::pg_fts Database adaptor for a specific postgres schema with a TSearch2 implementation     1.006901
Bio::DB::GFF::Adaptor::memory Bio::DB::GFF database adaptor for in-memory databases     1.006901
Bio::DB::GFF::Adaptor::memory::feature_serializer utility methods for serializing and deserializing GFF features     1.006901
Bio::DB::GFF::Adaptor::memory::iterator iterator for Bio::DB::GFF::Adaptor::memory     1.006901
Bio::DB::GFF::Aggregator Aggregate GFF groups into composite features     1.006901
Bio::DB::GFF::Aggregator::alignment Alignment aggregator     1.006901
Bio::DB::GFF::Aggregator::clone Clone aggregator     1.006901
Bio::DB::GFF::Aggregator::coding The Coding Region Aggregator     1.006901
Bio::DB::GFF::Aggregator::gene Sequence Ontology Geene     1.006901
Bio::DB::GFF::Aggregator::match Match aggregator     1.006901
Bio::DB::GFF::Aggregator::none No aggregation     1.006901
Bio::DB::GFF::Aggregator::orf An aggregator for orf regions     1.006901
Bio::DB::GFF::Aggregator::processed_transcript Sequence Ontology Transcript     1.006901
Bio::DB::GFF::Aggregator::so_transcript Sequence Ontology Transcript     1.006901
Bio::DB::GFF::Aggregator::transcript Transcript aggregator     1.006901
Bio::DB::GFF::Aggregator::ucsc_acembly UCSC acembly aggregator     1.006901
Bio::DB::GFF::Aggregator::ucsc_ensgene UCSC ensGene aggregator     1.006901
Bio::DB::GFF::Aggregator::ucsc_genscan UCSC genscan aggregator     1.006901
Bio::DB::GFF::Aggregator::ucsc_refgene UCSC refGene aggregator     1.006901
Bio::DB::GFF::Aggregator::ucsc_sanger22 UCSC sanger22 aggregator     1.006901
Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo UCSC sanger22pseudo aggregator     1.006901
Bio::DB::GFF::Aggregator::ucsc_softberry UCSC softberry aggregator     1.006901
Bio::DB::GFF::Aggregator::ucsc_twinscan UCSC twinscan aggregator     1.006901
Bio::DB::GFF::Aggregator::ucsc_unigene UCSC UniGene aggregator     1.006901
Bio::DB::GFF::Featname The name of a feature     1.006901
Bio::DB::GFF::Feature A relative segment identified by a feature type     1.006901
Bio::DB::GFF::FeatureIterator     1.006901
Bio::DB::GFF::Homol A segment of DNA that is homologous to another     1.006901
Bio::DB::GFF::ID_Iterator     1.006901
Bio::DB::GFF::RelSegment Sequence segment with relative coordinate support     1.006901
Bio::DB::GFF::Segment Simple DNA segment object     1.006901
Bio::DB::GFF::Typename The name of a feature type     1.006901
Bio::DB::GFF::Util::Binning binning utility for Bio::DB::GFF index     1.006901
Bio::DB::GFF::Util::Rearrange rearrange utility     1.006901
Bio::DB::GenBank Database object interface to GenBank     1.006901
Bio::DB::GenPept Database object interface to GenPept     1.006901
Bio::DB::GenericWebAgent helper base class for parameter-based remote server access and response retrieval.     1.006901
Bio::DB::HIV Database object interface to the Los Alamos HIV Sequence Database     1.006901
Bio::DB::HIV::HIVAnnotProcessor Adds HIV-specific annotations to Bio::SeqIO streams     1.006901
Bio::DB::HIV::HIVQueryHelper Routines and packages used by Bio::DB::HIV and Bio::DB::Query::HIVQuery     1.006901
Bio::DB::InMemoryCache Abstract interface for a sequence database     1.006901
Bio::DB::LocationI A RandomAccessI-like abstract interface for retrieving location data from a sequence database and returning Bio::LocationI objects     1.006901
Bio::DB::MeSH Term retrieval from a Web MeSH database     1.006901
Bio::DB::NCBIHelper A collection of routines useful for queries to NCBI databases.     1.006901
Bio::DB::Qual Fast indexed access to a directory of quality files     1.006901
Bio::DB::Qual::Stream     1.006901
Bio::DB::Query::GenBank Build a GenBank Entrez Query     1.006901
Bio::DB::Query::HIVQuery Query interface to the Los Alamos HIV Sequence Database     1.006901
Bio::DB::Query::WebQuery Helper class for web-based sequence queryies     1.006901
Bio::DB::QueryI Object Interface to queryable sequence databases     1.006901
Bio::DB::RandomAccessI Abstract interface for a sequence database     1.006901
Bio::DB::RefSeq Database object interface for RefSeq retrieval     1.006901
Bio::DB::ReferenceI A RandomAccessI-like abstract interface for retrieving Reference data from a sequence database and returning Bio::Annotation::Reference objects     1.006901
Bio::DB::Registry Access to the Open Bio Database Access registry scheme     1.006901
Bio::DB::SeqFeature Normalized feature for use with Bio::DB::SeqFeature::Store     1.006901
Bio::DB::SeqFeature::NormalizedFeature Normalized feature for use with Bio::DB::SeqFeature::Store     1.006901
Bio::DB::SeqFeature::NormalizedFeatureI Interface for normalized features     1.006901
Bio::DB::SeqFeature::NormalizedTableFeatureI Interface for normalized features whose hierarchy is stored in a table     1.006901
Bio::DB::SeqFeature::Segment Location-based access to genome annotation data     1.006901
Bio::DB::SeqFeature::Store Storage and retrieval of sequence annotation data     1.006901
Bio::DB::SeqFeature::Store::DBI::Iterator utility methods for creating and iterating over SeqFeature records     1.006901
Bio::DB::SeqFeature::Store::DBI::Pg PostgreSQL implementation of Bio::DB::SeqFeature::Store     1.006901
Bio::DB::SeqFeature::Store::DBI::SQLite SQLite implementation of Bio::DB::SeqFeature::Store     1.006901
Bio::DB::SeqFeature::Store::DBI::mysql Mysql implementation of Bio::DB::SeqFeature::Store     1.006901
Bio::DB::SeqFeature::Store::FeatureFileLoader feature file loader for Bio::DB::SeqFeature::Store     1.006901
Bio::DB::SeqFeature::Store::FeatureIterator     1.006901
Bio::DB::SeqFeature::Store::GFF2Loader GFF2 file loader for Bio::DB::SeqFeature::Store     1.006901
Bio::DB::SeqFeature::Store::GFF3Loader GFF3 file loader for Bio::DB::SeqFeature::Store     1.006901
Bio::DB::SeqFeature::Store::LoadHelper Internal utility for Bio::DB::SeqFeature::Store     1.006901
Bio::DB::SeqFeature::Store::Loader Loader     1.006901
Bio::DB::SeqFeature::Store::bdb fetch and store objects from a BerkeleyDB     1.006901
Bio::DB::SeqFeature::Store::berkeleydb Storage and retrieval of sequence annotation data in Berkeleydb files     1.006901
Bio::DB::SeqFeature::Store::berkeleydb3 Storage and retrieval of sequence annotation data in Berkeleydb files     1.006901
Bio::DB::SeqFeature::Store::berkeleydb::Iterator     1.006901
Bio::DB::SeqFeature::Store::memory In-memory implementation of Bio::DB::SeqFeature::Store     1.006901
Bio::DB::SeqFeature::Store::memory::Iterator     1.006901
Bio::DB::SeqHound Database object interface to SeqHound     1.006901
Bio::DB::SeqI Abstract Interface for Sequence databases     1.006901
Bio::DB::SeqVersion front end to querying databases for identifier versions     1.006901
Bio::DB::SeqVersion::gi interface to NCBI Sequence Revision History page     1.006901
Bio::DB::SwissProt Database object interface to SwissProt retrieval     1.006901
Bio::DB::TFBS Access to a Transcription Factor Binding Site database     1.006901
Bio::DB::TFBS::transfac_pro An implementation of Bio::DB::TFBS which uses local flat files for transfac pro     1.006901
Bio::DB::Taxonomy Access to a taxonomy database     1.006901
Bio::DB::Taxonomy::entrez Taxonomy Entrez driver     1.006901
Bio::DB::Taxonomy::flatfile An implementation of Bio::DB::Taxonomy which uses local flat files     1.006901
Bio::DB::Taxonomy::list An implementation of Bio::DB::Taxonomy that accepts lists of words to build a database     1.006901
Bio::DB::Universal Artificial database that delegates to specific databases     1.006901
Bio::DB::UpdateableSeqI An interface for writing to a database of sequences.     1.006901
Bio::DB::WebDBSeqI Object Interface to generalize Web Databases for retrieving sequences     1.006901
Bio::DBLinkContainerI Abstract interface for any object wanting to use database cross references     1.006901
Bio::Das::FeatureTypeI Simple interface to Sequence Ontology feature types     1.006901
Bio::Das::SegmentI DAS-style access to a feature database     1.006901
Bio::DasI DAS-style access to a feature database     1.006901
Bio::DescribableI interface for objects with human readable names and descriptions     1.006901
Bio::Draw::Pictogram generate SVG output of Pictogram display for consensus motifs     1.006901
Bio::Event::EventGeneratorI This interface describes the basic event generator class.     1.006901
Bio::Event::EventHandlerI An Event Handler Interface     1.006901
Bio::Factory::AnalysisI An interface to analysis tool factory     1.006901
Bio::Factory::ApplicationFactoryI Interface class for Application Factories     1.006901
Bio::Factory::DriverFactory Base class for factory classes loading drivers     1.006901
Bio::Factory::FTLocationFactory A FeatureTable Location Parser     1.006901
Bio::Factory::LocationFactoryI A factory interface for generating locations from a string     1.006901
Bio::Factory::MapFactoryI A Factory for getting markers     1.006901
Bio::Factory::ObjectBuilderI Interface for an object builder     1.006901
Bio::Factory::ObjectFactory Instantiates a new Bio::Root::RootI (or derived class) through a factory     1.006901
Bio::Factory::ObjectFactoryI A General object creator factory     1.006901
Bio::Factory::SeqAnalysisParserFactory class capable of creating SeqAnalysisParserI compliant parsers     1.006901
Bio::Factory::SeqAnalysisParserFactoryI interface describing objects capable of creating SeqAnalysisParserI compliant parsers     1.006901
Bio::Factory::SequenceFactoryI This interface allows for generic building of sequences in factories which create sequences (like SeqIO)     1.006901
Bio::Factory::SequenceProcessorI Interface for chained sequence processing algorithms     1.006901
Bio::Factory::SequenceStreamI Interface describing the basics of a Sequence Stream.     1.006901
Bio::Factory::TreeFactoryI Factory Interface for getting and writing trees from/to a data stream     1.006901
Bio::FeatureHolderI the base interface an object with features must implement     1.006901
Bio::FeatureIO Handler for FeatureIO     1.006901
Bio::FeatureIO::bed read/write features from UCSC BED format     1.006901
Bio::FeatureIO::gff read/write GFF feature files     1.006901
Bio::FeatureIO::gtf read write features in GTF format     1.006901
Bio::FeatureIO::interpro read features from InterPro XML     1.006901
Bio::FeatureIO::ptt read/write features in PTT format     1.006901
Bio::FeatureIO::vecscreen_simple read/write features from NCBI vecscreen -f 3 output     1.006901
Bio::HandlerBaseI Interface class for handler methods which interact with any event-driven parsers (drivers).     1.006901
Bio::IdCollectionI interface for objects with multiple identifiers     1.006901
Bio::IdentifiableI interface for objects with identifiers     1.006901
Bio::Index::Abstract Abstract interface for indexing a flat file     1.006901
Bio::Index::AbstractSeq base class for AbstractSeq     1.006901
Bio::Index::Blast Indexes Blast reports and supports retrieval based on query accession(s)     1.006901
Bio::Index::BlastTable Indexes tabular Blast reports (-m 8 or -m 9 format) and supports retrieval based on query accession(s)     1.006901
Bio::Index::EMBL Interface for indexing (multiple) EMBL/Swissprot .dat files (i.e. flat file EMBL/Swissprot format).     1.006901
Bio::Index::Fasta Interface for indexing (multiple) fasta files     1.006901
Bio::Index::Fastq Interface for indexing (multiple) fastq files     1.006901
Bio::Index::GenBank Interface for indexing one or more GenBank files (i.e. flat file GenBank format).     1.006901
Bio::Index::Hmmer indexes HMMER reports and supports retreival based on query     1.006901
Bio::Index::Qual Interface for indexing (multiple) fasta qual files     1.006901
Bio::Index::Stockholm Indexes Stockholm format alignments (such as those from Pfam and Rfam. Retrieves raw stream data using the ID or a Bio::SimpleAlign (via Bio::AlignIO)     1.006901
Bio::Index::SwissPfam Interface for indexing swisspfam files     1.006901
Bio::Index::Swissprot Interface for indexing one or more Swissprot files.     1.006901
Bio::LiveSeq::AARange AARange abstract class for LiveSeq     1.006901
Bio::LiveSeq::Chain DoubleChain DataStructure for Perl     1.006901
Bio::LiveSeq::ChainI Double linked chain data structure     1.006901
Bio::LiveSeq::DNA DNA object for LiveSeq     1.006901
Bio::LiveSeq::Exon Range abstract class for LiveSeq     1.006901
Bio::LiveSeq::Gene Range abstract class for LiveSeq     1.006901
Bio::LiveSeq::IO::BioPerl Loader for LiveSeq from EMBL entries with BioPerl     1.006901
Bio::LiveSeq::IO::Loader Parent Loader for LiveSeq     1.006901
Bio::LiveSeq::Intron Range abstract class for LiveSeq     1.006901
Bio::LiveSeq::Mutation Mutation event descriptor class     1.006901
Bio::LiveSeq::Mutator Package mutating LiveSequences     1.006901
Bio::LiveSeq::Prim_Transcript Prim_Transcript class for LiveSeq     1.006901
Bio::LiveSeq::Range Range abstract class for LiveSeq     1.006901
Bio::LiveSeq::Repeat_Region Repeat_Region class for LiveSeq     1.006901
Bio::LiveSeq::Repeat_Unit Repeat_Unit class for LiveSeq     1.006901
Bio::LiveSeq::SeqI Abstract sequence interface class for LiveSeq     1.006901
Bio::LiveSeq::Transcript Transcript class for LiveSeq     1.006901
Bio::LiveSeq::Translation Translation class for LiveSeq     1.006901
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.     1.006901
Bio::Location::Atomic Implementation of a Atomic Location on a Sequence     1.006901
Bio::Location::AvWithinCoordPolicy class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise     1.006901
Bio::Location::CoordinatePolicyI Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location     1.006901
Bio::Location::Fuzzy Implementation of a Location on a Sequence which has unclear start and/or end locations     1.006901
Bio::Location::FuzzyLocationI Abstract interface of a Location on a Sequence which has unclear start/end location     1.006901
Bio::Location::NarrowestCoordPolicy class implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range     1.006901
Bio::Location::Simple Implementation of a Simple Location on a Sequence     1.006901
Bio::Location::Split Implementation of a Location on a Sequence which has multiple locations (start/end points)     1.006901
Bio::Location::SplitLocationI Abstract interface of a Location on a Sequence which has multiple locations (start/end points)     1.006901
Bio::Location::WidestCoordPolicy class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable range     1.006901
Bio::LocationI Abstract interface of a Location on a Sequence     1.006901
Bio::Map::Clone An central map object representing a clone     1.006901
Bio::Map::Contig A MapI implementation handling the contigs of a Physical Map (such as FPC)     1.006901
Bio::Map::CytoMap A Bio::MapI compliant map implementation handling cytogenic bands     1.006901
Bio::Map::CytoMarker An object representing a marker.     1.006901
Bio::Map::CytoPosition Marker class with cytogenetic band storing attributes     1.006901
Bio::Map::EntityI An Entity Interface     1.006901
Bio::Map::FPCMarker An central map object representing a marker     1.006901
Bio::Map::Gene An gene modelled as a mappable element.     1.006901
Bio::Map::GeneMap A MapI implementation to represent the area around a gene     1.006901
Bio::Map::GenePosition A typed position, suitable for modelling the various regions of a gene.     1.006901
Bio::Map::GeneRelative Represents being relative to named sub-regions of a gene.     1.006901
Bio::Map::LinkageMap A representation of a genetic linkage map.     1.006901
Bio::Map::LinkagePosition Create a Position for a Marker that will be placed on a Bio::Map::LinkageMap     1.006901
Bio::Map::MapI Interface for describing Map objects in bioperl     1.006901
Bio::Map::Mappable An object representing a generic map element that can have multiple locations in several maps.     1.006901
Bio::Map::MappableI An object that can be placed in a map     1.006901
Bio::Map::Marker An central map object representing a generic marker that can have multiple location in several maps.     1.006901
Bio::Map::MarkerI Interface for basic marker functionality     1.006901
Bio::Map::Microsatellite An object representing a Microsatellite marker.     1.006901
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.     1.006901
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.     1.006901
Bio::Map::Physical A class for handling a Physical Map (such as FPC)     1.006901
Bio::Map::Position A single position of a Marker, or the range over which that marker lies, in a Map     1.006901
Bio::Map::PositionHandler A Position Handler Implementation     1.006901
Bio::Map::PositionHandlerI A Position Handler Interface     1.006901
Bio::Map::PositionI Abstracts the notion of a position having a value in the context of a marker and a Map     1.006901
Bio::Map::PositionWithSequence A position with a sequence.     1.006901
Bio::Map::Prediction An object representing the predictions of something that can have multiple locations in several maps.     1.006901
Bio::Map::Relative Represents what a Position's coordiantes are relative to.     1.006901
Bio::Map::RelativeI Interface for describing what a Position's coordiantes are relative to.     1.006901
Bio::Map::SimpleMap A MapI implementation handling the basics of a Map     1.006901
Bio::Map::TranscriptionFactor A transcription factor modelled as a mappable element     1.006901
Bio::MapIO A Map Factory object     1.006901
Bio::MapIO::fpc A FPC Map reader     1.006901
Bio::MapIO::mapmaker A Mapmaker Map reader     1.006901
Bio::Matrix::Generic A generic matrix implementation     1.006901
Bio::Matrix::IO A factory for Matrix parsing     1.006901
Bio::Matrix::IO::mlagan A parser for the mlagan substitution matrix     1.006901
Bio::Matrix::IO::phylip A parser for PHYLIP distance matricies     1.006901
Bio::Matrix::IO::scoring A parser for PAM/BLOSUM matricies     1.006901
Bio::Matrix::MatrixI An interface for describing a Matrix     1.006901
Bio::Matrix::Mlagan A generic matrix with mlagan fields     1.006901
Bio::Matrix::PSM::IO PSM parser     1.006901
Bio::Matrix::PSM::IO::mast PSM mast parser implementation     1.006901
Bio::Matrix::PSM::IO::masta motif fasta format parser     1.006901
Bio::Matrix::PSM::IO::meme PSM meme parser implementation     1.006901
Bio::Matrix::PSM::IO::psiblast PSM psiblast parser     1.006901
Bio::Matrix::PSM::IO::transfac PSM transfac parser     1.006901
Bio::Matrix::PSM::InstanceSite A PSM site occurance     1.006901
Bio::Matrix::PSM::InstanceSiteI InstanceSite interface, holds an instance of a PSM     1.006901
Bio::Matrix::PSM::ProtMatrix SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) with log-odds scoring information.     1.006901
Bio::Matrix::PSM::ProtPsm handle combination of site matricies     1.006901
Bio::Matrix::PSM::Psm handle combination of site matricies     1.006901
Bio::Matrix::PSM::PsmHeader PSM mast parser implementation     1.006901
Bio::Matrix::PSM::PsmHeaderI handles the header data from a PSM file     1.006901
Bio::Matrix::PSM::PsmI abstract interface to handler of site matricies     1.006901
Bio::Matrix::PSM::SiteMatrix SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds     1.006901
Bio::Matrix::PSM::SiteMatrixI SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds     1.006901
Bio::Matrix::PhylipDist A Phylip Distance Matrix object     1.006901
Bio::Matrix::Scoring Object which can hold scoring matrix information     1.006901
Bio::MolEvol::CodonModel Codon Evolution Models     1.006901
Bio::Nexml::Factory A factory module for creating BioPerl and Bio::Phylo objects from/to nexml documents     1.006901
Bio::NexmlIO stream handler for NeXML documents     1.006901
Bio::Ontology::DocumentRegistry Keep track of where to find ontologies. Allows lookups by name.     1.006901
Bio::Ontology::GOterm representation of GO terms     1.006901
Bio::Ontology::InterProTerm Implementation of InterProI term interface     1.006901
Bio::Ontology::OBOEngine An Ontology Engine for OBO style flat file format from the Gene Ontology Consortium     1.006901
Bio::Ontology::OBOterm representation of OBO terms     1.006901
Bio::Ontology::Ontology standard implementation of an Ontology     1.006901
Bio::Ontology::OntologyEngineI Interface a minimal Ontology implementation should satisfy     1.006901
Bio::Ontology::OntologyI Interface for an ontology implementation     1.006901
Bio::Ontology::OntologyStore A repository of ontologies     1.006901
Bio::Ontology::Path a path for an ontology term graph     1.006901
Bio::Ontology::PathI Interface for a path between ontology terms     1.006901
Bio::Ontology::Relationship a relationship for an ontology     1.006901
Bio::Ontology::RelationshipFactory Instantiates a new Bio::Ontology::RelationshipI (or derived class) through a factory     1.006901
Bio::Ontology::RelationshipI Interface for a relationship between ontology terms     1.006901
Bio::Ontology::RelationshipType a relationship type for an ontology     1.006901
Bio::Ontology::SimpleGOEngine::GraphAdaptor Graph adaptor for Bio::Ontology::SimpleGOEngine     1.006901
Bio::Ontology::SimpleGOEngine::GraphAdaptor02 Graph adaptor (v02.x) for Bio::Ontology::SimpleGOEngine     1.006901
Bio::Ontology::SimpleOntologyEngine Implementation of OntologyEngineI interface     1.006901
Bio::Ontology::Term implementation of the interface for ontology terms     1.006901
Bio::Ontology::TermFactory Instantiates a new Bio::Ontology::TermI (or derived class) through a factory     1.006901
Bio::Ontology::TermI interface for ontology terms     1.006901
Bio::OntologyIO Parser factory for Ontology formats     1.006901
Bio::OntologyIO::Handlers::BaseSAXHandler base class for SAX Handlers     1.006901
Bio::OntologyIO::Handlers::InterProHandler XML handler class for InterProParser     1.006901
Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler parse an InterPro XML file and persist the resulting terms to a Biosql database     1.006901
Bio::OntologyIO::InterProParser Parser for InterPro xml files.     1.006901
Bio::OntologyIO::dagflat a base class parser for GO flat-file type formats     1.006901
Bio::OntologyIO::goflat a parser for the Gene Ontology flat-file format     1.006901
Bio::OntologyIO::obo a parser for OBO flat-file format from Gene Ontology Consortium     1.006901
Bio::OntologyIO::simplehierarchy a base class parser for simple hierarchy-by-indentation type formats     1.006901
Bio::OntologyIO::soflat a parser for the Sequence Ontology flat-file format     1.006901
Bio::ParameterBaseI Simple interface class for any parameter-related data such as IDs, database name, program arguments, and other odds and ends.     1.006901
Bio::Perl Functional access to BioPerl for people who don't know objects     1.006901
Bio::Phenotype::Correlate Representation of a correlating phenotype in a given species     1.006901
Bio::Phenotype::MeSH::Term A MeSH term     1.006901
Bio::Phenotype::MeSH::Twig Context for a MeSH term     1.006901
Bio::Phenotype::Measure Representation of context/value(-range)/unit triplets     1.006901
Bio::Phenotype::OMIM::MiniMIMentry Representation of a Mini MIM entry     1.006901
Bio::Phenotype::OMIM::OMIMentry represents OMIM (Online Mendelian Inheritance in Man) database entries     1.006901
Bio::Phenotype::OMIM::OMIMentryAllelicVariant Representation of a allelic variant of the OMIM database     1.006901
Bio::Phenotype::OMIM::OMIMparser parser for the OMIM database     1.006901
Bio::Phenotype::Phenotype A class for modeling phenotypes     1.006901
Bio::Phenotype::PhenotypeI An interface for classes modeling phenotypes     1.006901
Bio::PhyloNetwork Module to compute with Phylogenetic Networks     1.006901
Bio::PhyloNetwork::Factory Module to sequentially generate Phylogenetic Networks     1.006901
Bio::PhyloNetwork::FactoryX Module to sequentially generate Phylogenetic Networks     1.006901
Bio::PhyloNetwork::GraphViz Interface between PhyloNetwork and GraphViz     1.006901
Bio::PhyloNetwork::RandomFactory Module to generate random Phylogenetic Networks     1.006901
Bio::PhyloNetwork::TreeFactory Module to sequentially generate Phylogenetic Trees     1.006901
Bio::PhyloNetwork::TreeFactoryMulti Module to sequentially generate Phylogenetic Trees     1.006901
Bio::PhyloNetwork::TreeFactoryX Module to sequentially generate Phylogenetic Trees     1.006901
Bio::PhyloNetwork::muVector Module to compute with vectors of arbitrary dimension     1.006901
Bio::PopGen::Genotype An implementation of GenotypeI which is just an allele container     1.006901
Bio::PopGen::GenotypeI A marker and alleles for a specific individual     1.006901
Bio::PopGen::HtSNP Select htSNP from a haplotype set     1.006901
Bio::PopGen::IO Input individual,marker,allele information     1.006901
Bio::PopGen::IO::csv Extract individual allele data from a CSV parser     1.006901
Bio::PopGen::IO::hapmap A parser for HapMap output data     1.006901
Bio::PopGen::IO::phase A parser for Phase format data     1.006901
Bio::PopGen::IO::prettybase Extract individual allele data from PrettyBase format     1.006901
Bio::PopGen::Individual An implementation of an Individual who has Genotype or Sequence Results     1.006901
Bio::PopGen::IndividualI An individual who has Genotype or Sequence Results     1.006901
Bio::PopGen::Marker A genetic marker which one uses to generate genotypes     1.006901
Bio::PopGen::MarkerI A Population Genetic conceptual marker     1.006901
Bio::PopGen::PopStats A collection of methods for calculating statistics about a population or sets of populations     1.006901
Bio::PopGen::Population A population of individuals     1.006901
Bio::PopGen::PopulationI Interface for Populations     1.006901
Bio::PopGen::Simulation::Coalescent A Coalescent simulation factory     1.006901
Bio::PopGen::Simulation::GeneticDrift A simple genetic drift simulation     1.006901
Bio::PopGen::Statistics Population Genetics statistical tests     1.006901
Bio::PopGen::TagHaplotype Haplotype tag object.     1.006901
Bio::PopGen::Utilities Utilities for working with PopGen data and objects     1.006901
Bio::PrimarySeq Bioperl lightweight Sequence Object     1.006901
Bio::PrimarySeq::Fasta     1.006901
Bio::PrimarySeqI Interface definition for a Bio::PrimarySeq     1.006901
Bio::PullParserI A base module for fast 'pull' parsing     1.006901
Bio::Range Pure perl RangeI implementation     1.006901
Bio::RangeI Range interface     1.006901
Bio::Restriction::Analysis cutting sequences with restriction enzymes     1.006901
Bio::Restriction::Enzyme A single restriction endonuclease (cuts DNA at specific locations)     1.006901
Bio::Restriction::Enzyme::MultiCut A single restriction endonuclease     1.006901
Bio::Restriction::Enzyme::MultiSite A single restriction endonuclease     1.006901
Bio::Restriction::EnzymeCollection Set of restriction endonucleases     1.006901
Bio::Restriction::EnzymeI Interface class for restriction endonuclease     1.006901
Bio::Restriction::IO Handler for sequence variation IO Formats     1.006901
Bio::Restriction::IO::bairoch bairoch enzyme set     1.006901
Bio::Restriction::IO::base base enzyme set     1.006901
Bio::Restriction::IO::itype2 itype2 enzyme set     1.006901
Bio::Restriction::IO::prototype prototype enzyme set     1.006901
Bio::Restriction::IO::withrefm withrefm enzyme set     1.006901
Bio::Root::Build A common Module::Build subclass base for BioPerl distributions     1.006901
Bio::Root::Exception Generic exception objects for Bioperl     1.006901
Bio::Root::HTTPget module for fallback HTTP get operations when LWP:: is unavailable     1.006901
Bio::Root::IO module providing several methods often needed when dealing with file IO     1.006901
Bio::Root::Root Hash-based implementation of Bio::Root::RootI     1.006901
Bio::Root::RootI Abstract interface to root object code     1.006901
Bio::Root::Storable object serialisation methods     1.006901
Bio::Root::Test A common base for all Bioperl test scripts.     1.006901
Bio::Root::Test::Warn Perl extension to test Bioperl methods for warnings     1.006901
Bio::Root::Utilities General-purpose utility module     1.006901
Bio::Root::Version provide global, distribution-level versioning     1.006901
Bio::Search::BlastStatistics An object for Blast statistics     1.006901
Bio::Search::BlastUtils Utility functions for Bio::Search:: BLAST objects     1.006901
Bio::Search::DatabaseI Interface for a database used in a sequence search     1.006901
Bio::Search::GenericDatabase Generic implementation of Bio::Search::DatabaseI     1.006901
Bio::Search::GenericStatistics An object for statistics     1.006901
Bio::Search::HSP::BlastHSP Bioperl BLAST High-Scoring Pair object     1.006901
Bio::Search::HSP::BlastPullHSP A parser and HSP object for BlastN hsps     1.006901
Bio::Search::HSP::FastaHSP HSP object for FASTA specific data     1.006901
Bio::Search::HSP::GenericHSP A "Generic" implementation of a High Scoring Pair     1.006901
Bio::Search::HSP::HMMERHSP A HSP object for HMMER results     1.006901
Bio::Search::HSP::HSPFactory A factory to create Bio::Search::HSP::HSPI objects     1.006901
Bio::Search::HSP::HSPI Interface for a High Scoring Pair in a similarity search result     1.006901
Bio::Search::HSP::HmmpfamHSP A parser and HSP object for hmmpfam hsps     1.006901
Bio::Search::HSP::ModelHSP A HSP object for model-based searches     1.006901
Bio::Search::HSP::PSLHSP A HSP for PSL output     1.006901
Bio::Search::HSP::PsiBlastHSP Bioperl BLAST High-Scoring Pair object     1.006901
Bio::Search::HSP::PullHSPI Bio::Search::HSP::HSPI interface for pull parsers.     1.006901
Bio::Search::HSP::WABAHSP HSP object suitable for describing WABA alignments     1.006901
Bio::Search::HSP::hmmer3HSP DESCRIPTION of Object     1.006901
Bio::Search::Hit::BlastHit Blast-specific subclass of Bio::Search::Hit::GenericHit     1.006901
Bio::Search::Hit::BlastPullHit A parser and hit object for BLASTN hits     1.006901
Bio::Search::Hit::Fasta Hit object specific for Fasta-generated hits     1.006901
Bio::Search::Hit::GenericHit A generic implementation of the Bio::Search::Hit::HitI interface     1.006901
Bio::Search::Hit::HMMERHit A Hit module for HMMER hits     1.006901
Bio::Search::Hit::HitFactory A factory to create Bio::Search::Hit::HitI objects     1.006901
Bio::Search::Hit::HitI Interface for a hit in a similarity search result     1.006901
Bio::Search::Hit::HmmpfamHit A parser and hit object for hmmpfam hits     1.006901
Bio::Search::Hit::ModelHit A model-based implementation of the Bio::Search::Hit::HitI interface     1.006901
Bio::Search::Hit::PsiBlastHit Bioperl BLAST Hit object     1.006901
Bio::Search::Hit::PullHitI Bio::Search::Hit::HitI interface for pull parsers.     1.006901
Bio::Search::Hit::hmmer3Hit DESCRIPTION of Object     1.006901
Bio::Search::Iteration::GenericIteration A generic implementation of the Bio::Search::Iteration::IterationI interface.     1.006901
Bio::Search::Iteration::IterationI Abstract interface to an iteration from an iterated search result, such as PSI-BLAST.     1.006901
Bio::Search::Processor DESCRIPTION of Object     1.006901
Bio::Search::Result::BlastPullResult A parser and result object for BLASTN results     1.006901
Bio::Search::Result::BlastResult Blast-specific subclass of Bio::Search::Result::GenericResult     1.006901
Bio::Search::Result::CrossMatchResult CrossMatch-specific subclass of Bio::Search::Result::GenericResult     1.006901
Bio::Search::Result::GenericResult Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results.     1.006901
Bio::Search::Result::HMMERResult A Result object for HMMER results     1.006901
Bio::Search::Result::HmmpfamResult A parser and result object for hmmpfam results     1.006901
Bio::Search::Result::PullResultI Bio::Search::Result::ResultI interface for 'pull' parsers     1.006901
Bio::Search::Result::ResultFactory A factory to create Bio::Search::Result::ResultI objects     1.006901
Bio::Search::Result::ResultI Abstract interface to Search Result objects     1.006901
Bio::Search::Result::WABAResult Result object for WABA alignment output     1.006901
Bio::Search::Result::hmmer3Result DESCRIPTION of Object     1.006901
Bio::Search::SearchUtils Utility functions for Bio::Search:: objects     1.006901
Bio::Search::StatisticsI A Base object for statistics     1.006901
Bio::Search::Tiling::MapTileUtils utilities for manipulating closed intervals for an HSP tiling algorithm     1.006901
Bio::Search::Tiling::MapTiling An implementation of an HSP tiling algorithm, with methods to obtain frequently-requested statistics     1.006901
Bio::Search::Tiling::TilingI Abstract interface for an HSP tiling module     1.006901
Bio::SearchDist A perl wrapper around Sean Eddy's histogram object     1.006901
Bio::SearchIO Driver for parsing Sequence Database Searches (BLAST, FASTA, ...)     1.006901
Bio::SearchIO::EventHandlerI An abstract Event Handler for Search Result parsing     1.006901
Bio::SearchIO::FastHitEventBuilder Event Handler for SearchIO events.     1.006901
Bio::SearchIO::IteratedSearchResultEventBuilder Event Handler for SearchIO events.     1.006901
Bio::SearchIO::SearchResultEventBuilder Event Handler for SearchIO events.     1.006901
Bio::SearchIO::SearchWriterI Interface for outputting parsed Search results     1.006901
Bio::SearchIO::Writer::BSMLResultWriter BSML output writer     1.006901
Bio::SearchIO::Writer::GbrowseGFF Interface for outputting parsed search results in Gbrowse GFF format     1.006901
Bio::SearchIO::Writer::HSPTableWriter Tab-delimited data for Bio::Search::HSP::HSPI objects     1.006901
Bio::SearchIO::Writer::HTMLResultWriter write a Bio::Search::ResultI in HTML     1.006901
Bio::SearchIO::Writer::HitTableWriter Tab-delimited data for Bio::Search::Hit::HitI objects     1.006901
Bio::SearchIO::Writer::ResultTableWriter Outputs tab-delimited data for each Bio::Search::Result::ResultI object.     1.006901
Bio::SearchIO::Writer::TextResultWriter Object to implement writing a Bio::Search::ResultI in Text.     1.006901
Bio::SearchIO::XML::BlastHandler XML Handler for NCBI Blast XML parsing.     1.006901
Bio::SearchIO::XML::PsiBlastHandler XML Handler for NCBI Blast PSIBLAST XML parsing.     1.006901
Bio::SearchIO::axt a parser for axt format reports     1.006901
Bio::SearchIO::blast Event generator for event based parsing of blast reports     1.006901
Bio::SearchIO::blast_pull A parser for BLAST output     1.006901
Bio::SearchIO::blasttable Driver module for SearchIO for parsing NCBI -m 8/9 format     1.006901
Bio::SearchIO::blastxml A SearchIO implementation of NCBI Blast XML parsing.     1.006901
Bio::SearchIO::cross_match CrossMatch-specific subclass of Bio::SearchIO     1.006901
Bio::SearchIO::erpin SearchIO-based ERPIN parser     1.006901
Bio::SearchIO::exonerate parser for Exonerate     1.006901
Bio::SearchIO::fasta A SearchIO parser for FASTA results     1.006901
Bio::SearchIO::gmap_f9 Event generator for parsing gmap reports (Z format)     1.006901
Bio::SearchIO::hmmer A parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam)     1.006901
Bio::SearchIO::hmmer2 A parser for HMMER output (hmmpfam, hmmsearch)     1.006901
Bio::SearchIO::hmmer3 DESCRIPTION of Object     1.006901
Bio::SearchIO::hmmer_pull A parser for HMMER output     1.006901
Bio::SearchIO::infernal SearchIO-based Infernal parser     1.006901
Bio::SearchIO::megablast a driver module for Bio::SearchIO to parse megablast reports (format 0)     1.006901
Bio::SearchIO::psl A parser for PSL output (UCSC)     1.006901
Bio::SearchIO::rnamotif SearchIO-based RNAMotif parser     1.006901
Bio::SearchIO::sim4 parser for Sim4 alignments     1.006901
Bio::SearchIO::waba SearchIO parser for Jim Kent WABA program alignment output     1.006901
Bio::SearchIO::wise Parsing of wise output as alignments     1.006901
Bio::Seq Sequence object, with features     1.006901
Bio::Seq::BaseSeqProcessor Base implementation for a SequenceProcessor     1.006901
Bio::Seq::EncodedSeq subtype of Bio::LocatableSeq to store DNA that encodes a protein     1.006901
Bio::Seq::LargeLocatableSeq LocatableSeq object that stores sequence as files in the tempdir     1.006901
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     1.006901
Bio::Seq::LargeSeq SeqI compliant object that stores sequence as files in /tmp     1.006901
Bio::Seq::LargeSeqI Interface class for sequences that cache their residues in a temporary file     1.006901
Bio::Seq::Meta Generic superclass for sequence objects with residue-based meta information     1.006901
Bio::Seq::Meta::Array array-based generic implementation of a sequence class with residue-based meta information     1.006901
Bio::Seq::MetaI Interface for sequence objects with residue-based meta information     1.006901
Bio::Seq::PrimaryQual Bioperl lightweight Quality Object     1.006901
Bio::Seq::PrimaryQual::Qual     1.006901
Bio::Seq::PrimedSeq A representation of a sequence and two primers flanking a target region     1.006901
Bio::Seq::QualI Interface definition for a Bio::Seq::Qual     1.006901
Bio::Seq::Quality Implementation of sequence with residue quality and trace values     1.006901
Bio::Seq::RichSeq Module implementing a sequence created from a rich sequence database entry     1.006901
Bio::Seq::RichSeqI interface for sequences from rich data sources, mostly databases     1.006901
Bio::Seq::SeqBuilder Configurable object builder for sequence stream parsers     1.006901
Bio::Seq::SeqFactory Instantiates a new Bio::PrimarySeqI (or derived class) through a factory     1.006901
Bio::Seq::SeqFastaSpeedFactory Instantiates a new Bio::PrimarySeqI (or derived class) through a factory     1.006901
Bio::Seq::SeqWithQuality Bioperl object packaging a sequence with its quality. Deprecated class, use Bio::Seq::Quality instead!     1.006901
Bio::Seq::SequenceTrace Bioperl object packaging a sequence with its trace     1.006901
Bio::Seq::TraceI Interface definition for a Bio::Seq::Trace     1.006901
Bio::SeqAnalysisParserI Sequence analysis output parser interface     1.006901
Bio::SeqEvolution::DNAPoint evolve a sequence by point mutations     1.006901
Bio::SeqEvolution::EvolutionI the interface for evolving sequences     1.006901
Bio::SeqEvolution::Factory Factory object to instantiate sequence evolving classes     1.006901
Bio::SeqFeature::Annotated PLEASE PUT SOMETHING HERE     1.006901
Bio::SeqFeature::AnnotationAdaptor integrates SeqFeatureIs annotation     1.006901
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.     1.006901
Bio::SeqFeature::CollectionI An interface for a collection of SeqFeatureI objects.     1.006901
Bio::SeqFeature::Computation Computation SeqFeature     1.006901
Bio::SeqFeature::FeaturePair hold pair feature information e.g. blast hits     1.006901
Bio::SeqFeature::Gene::Exon a feature representing an exon     1.006901
Bio::SeqFeature::Gene::ExonI Interface for a feature representing an exon     1.006901
Bio::SeqFeature::Gene::GeneStructure A feature representing an arbitrarily complex structure of a gene     1.006901
Bio::SeqFeature::Gene::GeneStructureI A feature representing an arbitrarily complex structure of a gene     1.006901
Bio::SeqFeature::Gene::Intron An intron feature     1.006901
Bio::SeqFeature::Gene::NC_Feature superclass for non-coding features     1.006901
Bio::SeqFeature::Gene::Poly_A_site poly A feature     1.006901
Bio::SeqFeature::Gene::Promoter Describes a promoter     1.006901
Bio::SeqFeature::Gene::Transcript A feature representing a transcript     1.006901
Bio::SeqFeature::Gene::TranscriptI Interface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site.     1.006901
Bio::SeqFeature::Gene::UTR A feature representing an untranslated region that is part of a transcriptional unit     1.006901
Bio::SeqFeature::Generic Generic SeqFeature     1.006901
Bio::SeqFeature::Lite Lightweight Bio::SeqFeatureI class     1.006901
Bio::SeqFeature::PositionProxy handle features when truncation/revcom sequences span a feature     1.006901
Bio::SeqFeature::Primer Primer Generic SeqFeature     1.006901
Bio::SeqFeature::SiRNA::Oligo Perl object for small inhibitory RNAs.     1.006901
Bio::SeqFeature::SiRNA::Pair Perl object for small inhibitory RNA (SiRNA) oligo pairs     1.006901
Bio::SeqFeature::Similarity A sequence feature based on similarity     1.006901
Bio::SeqFeature::SimilarityPair Sequence feature based on the similarity of two sequences.     1.006901
Bio::SeqFeature::Tools::FeatureNamer generates unique persistent names for features     1.006901
Bio::SeqFeature::Tools::IDHandler maps $seq_feature->primary_tag     1.006901
Bio::SeqFeature::Tools::TypeMapper maps $seq_feature->primary_tag     1.006901
Bio::SeqFeature::Tools::Unflattener turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy     1.006901
Bio::SeqFeature::TypedSeqFeatureI a strongly typed SeqFeature     1.006901
Bio::SeqFeatureI Abstract interface of a Sequence Feature     1.006901
Bio::SeqI [Developers] Abstract Interface of Sequence (with features)     1.006901
Bio::SeqIO Handler for SeqIO Formats     1.006901
Bio::SeqIO::FTHelper Helper class for Embl/Genbank feature tables     1.006901
Bio::SeqIO::Handler::GenericRichSeqHandler Bio::HandlerI-based data handler for GenBank/EMBL/UniProt (and other) sequence data     1.006901
Bio::SeqIO::MultiFile Treating a set of files as a single input stream     1.006901
Bio::SeqIO::abi abi trace sequence input/output stream     1.006901
Bio::SeqIO::ace ace sequence input/output stream     1.006901
Bio::SeqIO::agave AGAVE sequence output stream.     1.006901
Bio::SeqIO::alf alf trace sequence input/output stream     1.006901
Bio::SeqIO::asciitree asciitree sequence input/output stream     1.006901
Bio::SeqIO::bsml BSML sequence input/output stream     1.006901
Bio::SeqIO::bsml_sax BSML sequence input/output stream using SAX     1.006901
Bio::SeqIO::chadoxml chadoxml sequence output stream     1.006901
Bio::SeqIO::chaos chaos sequence input/output stream     1.006901
Bio::SeqIO::chaosxml chaosxml sequence input/output stream     1.006901
Bio::SeqIO::ctf ctf trace sequence input/output stream     1.006901
Bio::SeqIO::embl EMBL sequence input/output stream     1.006901
Bio::SeqIO::embldriver EMBL sequence input/output stream     1.006901
Bio::SeqIO::entrezgene Entrez Gene ASN1 parser     1.006901
Bio::SeqIO::excel sequence input/output stream from a MSExcel-formatted table     1.006901
Bio::SeqIO::exp exp trace sequence input/output stream     1.006901
Bio::SeqIO::fasta fasta sequence input/output stream     1.006901
Bio::SeqIO::fastq fastq sequence input/output stream     1.006901
Bio::SeqIO::flybase_chadoxml FlyBase variant of chadoxml with sequence output stream     1.006901
Bio::SeqIO::game a class for parsing and writing game-XML     1.006901
Bio::SeqIO::game::featHandler a class for handling feature elements     1.006901
Bio::SeqIO::game::gameHandler PerlSAX handler for game-XML     1.006901
Bio::SeqIO::game::gameSubs a base class for game-XML parsing     1.006901
Bio::SeqIO::game::gameWriter a class for writing game-XML     1.006901
Bio::SeqIO::game::seqHandler a class for handling game-XML sequences     1.006901
Bio::SeqIO::gbdriver GenBank handler-based push parser     1.006901
Bio::SeqIO::gbxml GenBank sequence input/output stream using SAX     1.006901
Bio::SeqIO::gcg GCG sequence input/output stream     1.006901
Bio::SeqIO::genbank GenBank sequence input/output stream     1.006901
Bio::SeqIO::interpro InterProScan XML input/output stream     1.006901
Bio::SeqIO::kegg KEGG sequence input/output stream     1.006901
Bio::SeqIO::largefasta method i/o on very large fasta sequence files     1.006901
Bio::SeqIO::lasergene Lasergene sequence file input/output stream     1.006901
Bio::SeqIO::locuslink LocusLink input/output stream     1.006901
Bio::SeqIO::mbsout input stream for output by Teshima et al.'s mbs.     1.006901
Bio::SeqIO::metafasta metafasta sequence input/output stream     1.006901
Bio::SeqIO::msout input stream for output by Hudson's ms     1.006901
Bio::SeqIO::nexml NeXML sequence input/output stream     1.006901
Bio::SeqIO::phd phd file input/output stream     1.006901
Bio::SeqIO::pir PIR sequence input/output stream     1.006901
Bio::SeqIO::pln pln trace sequence input/output stream     1.006901
Bio::SeqIO::qual .qual file input/output stream     1.006901
Bio::SeqIO::raw raw sequence file input/output stream     1.006901
Bio::SeqIO::scf .scf file input/output stream     1.006901
Bio::SeqIO::seqxml SeqXML sequence input/output stream     1.006901
Bio::SeqIO::strider DNA strider sequence input/output stream     1.006901
Bio::SeqIO::swiss Swissprot sequence input/output stream     1.006901
Bio::SeqIO::swissdriver SwissProt/UniProt handler-based push parser     1.006901
Bio::SeqIO::tab nearly raw sequence file input/output stream. Reads/writes id"\t"sequence"\n"     1.006901
Bio::SeqIO::table sequence input/output stream from a delimited table     1.006901
Bio::SeqIO::tigr TIGR XML sequence input/output stream     1.006901
Bio::SeqIO::tigrxml Parse TIGR (new) XML     1.006901
Bio::SeqIO::tinyseq reading/writing sequences in NCBI TinySeq format     1.006901
Bio::SeqIO::tinyseq::tinyseqHandler XML event handlers to support NCBI TinySeq XML parsing     1.006901
Bio::SeqIO::ztr ztr trace sequence input/output stream     1.006901
Bio::SeqUtils Additional methods for PrimarySeq objects     1.006901
Bio::SimpleAlign Multiple alignments held as a set of sequences     1.006901
Bio::SimpleAnalysisI A simple interface to any (local or remote) analysis tool     1.006901
Bio::Species Generic species object.     1.006901
Bio::Structure::Atom Bioperl structure Object, describes an Atom     1.006901
Bio::Structure::Chain Bioperl structure Object, describes a chain     1.006901
Bio::Structure::Entry Bioperl structure Object, describes the whole entry     1.006901
Bio::Structure::IO Handler for Structure Formats     1.006901
Bio::Structure::IO::pdb PDB input/output stream     1.006901
Bio::Structure::Model Bioperl structure Object, describes a Model     1.006901
Bio::Structure::Residue Bioperl structure Object, describes a Residue     1.006901
Bio::Structure::SecStr::DSSP::Res Module for parsing/accessing dssp output     1.006901
Bio::Structure::SecStr::STRIDE::Res Module for parsing/accessing stride output     1.006901
Bio::Structure::StructureI Abstract Interface for a Structure objects     1.006901
Bio::Symbol::Alphabet BSANE/BioCORBA compliant symbol list alphabet     1.006901
Bio::Symbol::AlphabetI A Symbol Alphabet     1.006901
Bio::Symbol::DNAAlphabet A ready made DNA alphabet     1.006901
Bio::Symbol::ProteinAlphabet A ready made Protein alphabet     1.006901
Bio::Symbol::Symbol A biological symbol     1.006901
Bio::Symbol::SymbolI Interface for a Symbol     1.006901
Bio::Taxon A node in a represented taxonomy     1.006901
Bio::Taxonomy representing Taxonomy.     1.006901
Bio::Taxonomy::FactoryI interface to define how to access NCBI Taxonoy     1.006901
Bio::Taxonomy::Node A node in a represented taxonomy     1.006901
Bio::Taxonomy::Taxon Generic Taxonomic Entity object     1.006901
Bio::Taxonomy::Tree An Organism Level Implementation of TreeI interface.     1.006901
Bio::Tools::AlignFactory Base object for alignment factories     1.006901
Bio::Tools::Alignment::Consed A module to work with objects from consed .ace files     1.006901
Bio::Tools::Alignment::Trim A kludge to do specialized trimming of sequence based on quality.     1.006901
Bio::Tools::Analysis::DNA::ESEfinder a wrapper around ESEfinder server     1.006901
Bio::Tools::Analysis::Protein::Domcut a wrapper around Domcut server     1.006901
Bio::Tools::Analysis::Protein::ELM a wrapper around the ELM server which predicts short functional motifs on amino acid sequences     1.006901
Bio::Tools::Analysis::Protein::GOR4 a wrapper around GOR4 protein secondary structure prediction server     1.006901
Bio::Tools::Analysis::Protein::HNN a wrapper around the HNN protein secondary structure prediction server     1.006901
Bio::Tools::Analysis::Protein::Mitoprot a wrapper around Mitoprot server     1.006901
Bio::Tools::Analysis::Protein::NetPhos a wrapper around NetPhos server     1.006901
Bio::Tools::Analysis::Protein::Scansite a wrapper around the Scansite server     1.006901
Bio::Tools::Analysis::Protein::Sopma a wrapper around the Sopma protein secondary structure prediction server     1.006901
Bio::Tools::Analysis::SimpleAnalysisBase abstract superclass for SimpleAnalysis implementations     1.006901
Bio::Tools::AnalysisResult Base class for analysis result objects and parsers     1.006901
Bio::Tools::Blat parser for Blat program     1.006901
Bio::Tools::CodonTable Codon table object     1.006901
Bio::Tools::Coil parser for Coil output     1.006901
Bio::Tools::ECnumber representation of EC numbers (Enzyme Classification)     1.006901
Bio::Tools::EMBOSS::Palindrome parse EMBOSS palindrome output     1.006901
Bio::Tools::EPCR Parse ePCR output and make features     1.006901
Bio::Tools::ERPIN a parser for ERPIN output     1.006901
Bio::Tools::ESTScan Results of one ESTScan run     1.006901
Bio::Tools::EUtilities NCBI eutil XML parsers     1.006901
Bio::Tools::EUtilities::EUtilDataI eutil data object interface     1.006901
Bio::Tools::EUtilities::EUtilParameters Manipulation of NCBI eutil-based parameters for remote database requests.     1.006901
Bio::Tools::EUtilities::History lightweight implementation of HistoryI interface (not bound to filehandles, extraneous methods, etc).     1.006901
Bio::Tools::EUtilities::HistoryI simple extension of EUtilDataI interface class for classes which hold NCBI server history data     1.006901
Bio::Tools::EUtilities::Info interface class for storing einfo data     1.006901
Bio::Tools::EUtilities::Info::FieldInfo class for storing einfo field data     1.006901
Bio::Tools::EUtilities::Info::LinkInfo class for storing einfo link data     1.006901
Bio::Tools::EUtilities::Link general API for accessing data retrieved from elink queries     1.006901
Bio::Tools::EUtilities::Link::LinkSet class for EUtils LinkSets     1.006901
Bio::Tools::EUtilities::Link::UrlLink class for EUtils UrlLinks     1.006901
Bio::Tools::EUtilities::Query parse and collect esearch, epost, espell, egquery information     1.006901
Bio::Tools::EUtilities::Query::GlobalQuery container class for egquery data     1.006901
Bio::Tools::EUtilities::Summary class for handling data output (XML) from esummary.     1.006901
Bio::Tools::EUtilities::Summary::DocSum data object for document summary data from esummary     1.006901
Bio::Tools::EUtilities::Summary::Item simple layered object for DocSum item data     1.006901
Bio::Tools::EUtilities::Summary::ItemContainerI abtract interface methods for accessing Item information from any Item-containing class. This pertains to either DocSums or to Items themselves (which can be layered)     1.006901
Bio::Tools::Eponine Results of one Eponine run     1.006901
Bio::Tools::Est2Genome Parse est2genome output, makes simple Bio::SeqFeature::Generic objects     1.006901
Bio::Tools::Fgenesh parse results of one Fgenesh run     1.006901
Bio::Tools::FootPrinter write sequence features in FootPrinter format     1.006901
Bio::Tools::GFF A Bio::SeqAnalysisParserI compliant GFF format parser     1.006901
Bio::Tools::Gel Calculates relative electrophoretic migration distances     1.006901
Bio::Tools::Geneid Results of one geneid run     1.006901
Bio::Tools::Genemark Results of one Genemark run     1.006901
Bio::Tools::Genewise Results of one Genewise run     1.006901
Bio::Tools::Genomewise Results of one Genomewise run     1.006901
Bio::Tools::Genscan Results of one Genscan run     1.006901
Bio::Tools::Glimmer parser for Glimmer 2.X/3.X prokaryotic and GlimmerM/GlimmerHMM eukaryotic gene predictions     1.006901
Bio::Tools::Grail Results of one Grail run     1.006901
Bio::Tools::GuessSeqFormat Module for determining the sequence format of the contents of a file, a string, or through a filehandle.     1.006901
Bio::Tools::HMMER::Domain One particular domain hit from HMMER     1.006901
Bio::Tools::HMMER::Results Object representing HMMER output results     1.006901
Bio::Tools::HMMER::Set Set of identical domains from HMMER matches     1.006901
Bio::Tools::Hmmpfam Parser for Hmmpfam program     1.006901
Bio::Tools::IUPAC Generates unique Seq objects from an ambiguous Seq object     1.006901
Bio::Tools::Infernal A parser for Infernal output     1.006901
Bio::Tools::Lucy Object for analyzing the output from Lucy, a vector and quality trimming program from TIGR     1.006901
Bio::Tools::MZEF Results of one MZEF run     1.006901
Bio::Tools::Match Parses output from Transfac's match(TM)     1.006901
Bio::Tools::OddCodes Object holding alternative alphabet coding for one protein sequence     1.006901
Bio::Tools::Phylo::Gerp Parses output from GERP     1.006901
Bio::Tools::Phylo::Gumby Parses output from gumby     1.006901
Bio::Tools::Phylo::Molphy parser for Molphy output     1.006901
Bio::Tools::Phylo::Molphy::Result container for data parsed from a ProtML run     1.006901
Bio::Tools::Phylo::PAML Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00     1.006901
Bio::Tools::Phylo::PAML::Codeml Parses output from the PAML program codeml.     1.006901
Bio::Tools::Phylo::PAML::ModelResult A container for NSSite Model Result from PAML     1.006901
Bio::Tools::Phylo::PAML::Result A PAML result set object     1.006901
Bio::Tools::Phylo::Phylip::ProtDist parser for ProtDist output     1.006901
Bio::Tools::Prediction::Exon A predicted exon feature     1.006901
Bio::Tools::Prediction::Gene a predicted gene structure feature     1.006901
Bio::Tools::Primer3 Create input for and work with the output from the program primer3     1.006901
Bio::Tools::Primer::Assessor::Base base class for common assessor things     1.006901
Bio::Tools::Primer::AssessorI interface for assessing primer pairs     1.006901
Bio::Tools::Primer::Feature position of a single primer     1.006901
Bio::Tools::Primer::Pair two primers on left and right side     1.006901
Bio::Tools::Prints Parser for FingerPRINTScanII program     1.006901
Bio::Tools::Profile parse Profile output     1.006901
Bio::Tools::Promoterwise parser for Promoterwise tab format output     1.006901
Bio::Tools::PrositeScan Parser for ps_scan result     1.006901
Bio::Tools::Protparam submit to and parse output from protparam ;     1.006901
Bio::Tools::Pseudowise Results of one Pseudowise run     1.006901
Bio::Tools::QRNA A Parser for qrna output     1.006901
Bio::Tools::RNAMotif A parser for RNAMotif output     1.006901
Bio::Tools::RandomDistFunctions A set of routines useful for generating random data in different distributions     1.006901
Bio::Tools::RepeatMasker a parser for RepeatMasker output     1.006901
Bio::Tools::Run::GenericParameters An object for the parameters used to run programs     1.006901
Bio::Tools::Run::ParametersI A Base object for the parameters used to run programs     1.006901
Bio::Tools::Run::RemoteBlast Object for remote execution of the NCBI Blast via HTTP     1.006901
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.     1.006901
Bio::Tools::Run::StandAloneNCBIBlast Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). With experimental support for NCBI rpsblast.     1.006901
Bio::Tools::Run::StandAloneWUBlast Object for the local execution of WU-Blast.     1.006901
Bio::Tools::Run::WrapperBase A Base object for wrappers around executables     1.006901
Bio::Tools::Seg parse seg output     1.006901
Bio::Tools::SeqPattern represent a sequence pattern or motif     1.006901
Bio::Tools::SeqPattern::Backtranslate     1.006901
Bio::Tools::SeqStats Object holding statistics for one particular sequence     1.006901
Bio::Tools::SeqWords Object holding n-mer statistics for a sequence     1.006901
Bio::Tools::SiRNA Perl object for designing small inhibitory RNAs.     1.006901
Bio::Tools::SiRNA::Ruleset::saigo Perl object implementing the Saigo group's rules for designing small inhibitory RNAs     1.006901
Bio::Tools::SiRNA::Ruleset::tuschl Perl object implementing the tuschl group's rules for designing small inhibitory RNAs     1.006901
Bio::Tools::Sigcleave Bioperl object for sigcleave analysis     1.006901
Bio::Tools::Signalp parser for Signalp output     1.006901
Bio::Tools::Signalp::ExtendedSignalp enhanced parser for Signalp output     1.006901
Bio::Tools::Sim4::Exon A single exon determined by an alignment     1.006901
Bio::Tools::Sim4::Results Results of one Sim4 run     1.006901
Bio::Tools::Spidey::Exon A single exon determined by an alignment     1.006901
Bio::Tools::Spidey::Results Results of a Spidey run     1.006901
Bio::Tools::TandemRepeatsFinder a parser for Tandem Repeats Finder output     1.006901
Bio::Tools::TargetP Results of one TargetP run     1.006901
Bio::Tools::Tmhmm parse TMHMM output (TransMembrane HMM)     1.006901
Bio::Tools::dpAlign Perl extension to do pairwise dynamic programming sequence alignment     1.006901
Bio::Tools::ipcress Parse ipcress output and make features     1.006901
Bio::Tools::isPcr Parse isPcr output and make features     1.006901
Bio::Tools::pICalculator calculate the isoelectric point of a protein     1.006901
Bio::Tools::pSW pairwise Smith Waterman object     1.006901
Bio::Tools::tRNAscanSE A parser for tRNAscan-SE output     1.006901
Bio::Tree::AlleleNode A Node with Alleles attached     1.006901
Bio::Tree::AnnotatableNode A Tree Node with support for annotation     1.006901
Bio::Tree::Compatible Testing compatibility of phylogenetic trees with nested taxa.     1.006901
Bio::Tree::DistanceFactory Construct a tree using distance based methods     1.006901
Bio::Tree::Draw::Cladogram Drawing phylogenetic trees in Encapsulated PostScript (EPS) format.     1.006901
Bio::Tree::Node A Simple Tree Node     1.006901
Bio::Tree::NodeI Interface describing a Tree Node     1.006901
Bio::Tree::NodeNHX A Simple Tree Node with support for NHX tags     1.006901
Bio::Tree::RandomFactory TreeFactory for generating Random Trees     1.006901
Bio::Tree::Statistics Calculate certain statistics for a Tree     1.006901
Bio::Tree::Tree An Implementation of TreeI interface.     1.006901
Bio::Tree::TreeFunctionsI Decorated Interface implementing basic Tree exploration methods     1.006901
Bio::Tree::TreeI A Tree object suitable for lots of things, designed originally for Phylogenetic Trees.     1.006901
Bio::TreeIO Parser for Tree files     1.006901
Bio::TreeIO::NewickParser which implements a newick string parser as a finite state machine which enables it to parse the full Newick specification.     1.006901
Bio::TreeIO::TreeEventBuilder Build Bio::Tree::Tree's and Bio::Tree::Node's from Events     1.006901
Bio::TreeIO::cluster A TreeIO driver module for parsing Algorithm::Cluster::treecluster() output     1.006901
Bio::TreeIO::lintree Parser for lintree output trees     1.006901
Bio::TreeIO::newick TreeIO implementation for parsing Newick/New Hampshire/PHYLIP format.     1.006901
Bio::TreeIO::nexml A TreeIO driver module for parsing NeXML tree files     1.006901
Bio::TreeIO::nexus A TreeIO driver module for parsing Nexus tree output from PAUP     1.006901
Bio::TreeIO::nhx TreeIO implementation for parsing Newick/New Hampshire eXtendend (NHX) format.     1.006901
Bio::TreeIO::pag Bio::TreeIO driver for Pagel format     1.006901
Bio::TreeIO::phyloxml TreeIO implementation for parsing PhyloXML format.     1.006901
Bio::TreeIO::svggraph A simple output format that converts a Tree object to an SVG output     1.006901
Bio::TreeIO::tabtree A simple output format which displays a tree as an ASCII drawing     1.006901
Bio::UpdateableSeqI Descendant of Bio::SeqI that allows updates     1.006901
Bio::Variation::AAChange Sequence change class for polypeptides     1.006901
Bio::Variation::AAReverseMutate point mutation and codon information from single amino acid changes     1.006901
Bio::Variation::Allele Sequence object with allele-specific attributes     1.006901
Bio::Variation::DNAMutation DNA level mutation class     1.006901
Bio::Variation::IO Handler for sequence variation IO Formats     1.006901
Bio::Variation::IO::flat flat file sequence variation input/output stream     1.006901
Bio::Variation::IO::xml XML sequence variation input/output stream     1.006901
Bio::Variation::RNAChange Sequence change class for RNA level     1.006901
Bio::Variation::SNP submitted SNP     1.006901
Bio::Variation::SeqDiff Container class for mutation/variant descriptions     1.006901
Bio::Variation::VariantI Sequence Change SeqFeature abstract class     1.006901
Bio::WebAgent A base class for Web (any protocol) access     1.006901
BioPerl Perl Modules for Biology      
Deobfuscator get BioPerl method and package information from a Berkeley DB     0.0.3
FeatureStore     1.006901

Documentation

Bio::Tools::Run::WrapperBase::CommandExts Extensions to WrapperBase for handling programs with commands *ALPHA*  
[[%ask1]] DESCRIPTION of Object  
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_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_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_netinstall.pl  
bp_nrdb.PLS a script to emulate Warren Gish's nrdb, make a unique sequence database from a set of input databases  
bp_seqfeature_load.pl Load GFF into a SeqFeature database  
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  
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)  
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  
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.  
download_query_genbank script to query Genbank and retrieve records  
einfo.pl query einfo to find all available databases or information about a specific database (field information or links to other NCBI databases)  
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  
filter_search filters searchio results, outputting a tab delimited summary  
find_mod_deps.pl inspect only hard-coded dependencies of sets of perl files  
flanks finding flanking sequences for a variant in a sequence position  
gccalc GC content of nucleotide sequences  
genbank2gff3.pl Genbank->gbrowse-friendly GFF3  
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.  
hivq.PL an interactive command-line interface to Bio::DB::HIV and Bio::DB::Query::HIVQuery  
hmmer_to_table turn HMMER output into tabular format  
local_taxonomydb_query query a local TaxonomyDB for species or taxonid  
longorf.pl 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)  
reverse-translate.pl  
revtrans-motif Reverse translate a Profam-like protein motif  
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  
seq_length.pl lists the number of bases and number of sequences in specified sequence database files  
seqconvert generic BioPerl sequence format converter  
seqretsplit split a sequence (or stream) into a single file per sequence  
split_seq splits a sequence into equal sized chunks with an optional overlapping range  
symlink_script.pl install script to create symbolic links  
taxid4species simple script which returns the NCBI Taxonomic 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  

Other Files

Bio/LiveSeq/IO/README
Bio/Symbol/README.Symbol
Bio/Tools/Run/README
Bio/Variation/README
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