Christopher Fields > BioPerl

BioPerl

This Release BioPerl-1.6.924  [Download] [Browse 10 Jul 2014
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License The Perl 5 License (Artistic 1 & GPL 1)
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INSTALL
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MANIFEST
META.json
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Modules

Bio::Align::AlignI An interface for describing sequence alignments.     1.006924
Bio::Align::DNAStatistics Calculate some statistics for a DNA alignment     1.006924
Bio::Align::Graphics Graphic Rendering of Bio::Align::AlignI Objects     1.006924
Bio::Align::PairwiseStatistics Base statistic object for Pairwise Alignments     1.006924
Bio::Align::ProteinStatistics Calculate Protein Alignment statistics (mostly distances)     1.006924
Bio::Align::StatisticsI Calculate some statistics for an alignment     1.006924
Bio::Align::Utilities A collection of utilities regarding converting and manipulating alignment objects     1.006924
Bio::AlignIO Handler for AlignIO Formats     1.006924
Bio::AlignIO::Handler::GenericAlignHandler Bio::HandlerI-based generic data handler class for alignment-based data     1.006924
Bio::AlignIO::arp ARP MSA Sequence input/output stream     1.006924
Bio::AlignIO::bl2seq bl2seq sequence input/output stream     1.006924
Bio::AlignIO::clustalw clustalw sequence input/output stream     1.006924
Bio::AlignIO::emboss Parse EMBOSS alignment output (from applications water and needle)     1.006924
Bio::AlignIO::fasta fasta MSA Sequence input/output stream     1.006924
Bio::AlignIO::largemultifasta Largemultifasta MSA Sequence input/output stream     1.006924
Bio::AlignIO::maf Multiple Alignment Format sequence input stream     1.006924
Bio::AlignIO::mase mase sequence input/output stream     1.006924
Bio::AlignIO::mega Parse and Create MEGA format data files     1.006924
Bio::AlignIO::meme meme sequence input/output stream     1.006924
Bio::AlignIO::metafasta Metafasta MSA Sequence input/output stream     1.006924
Bio::AlignIO::msf msf sequence input/output stream     1.006924
Bio::AlignIO::nexml NeXML format sequence alignment input/output stream driver     1.006924
Bio::AlignIO::nexus NEXUS format sequence input/output stream     1.006924
Bio::AlignIO::pfam pfam sequence input/output stream     1.006924
Bio::AlignIO::phylip PHYLIP format sequence input/output stream     1.006924
Bio::AlignIO::po po MSA Sequence input/output stream     1.006924
Bio::AlignIO::proda proda sequence input/output stream     1.006924
Bio::AlignIO::prodom prodom sequence input/output stream     1.006924
Bio::AlignIO::psi Read/Write PSI-BLAST profile alignment files     1.006924
Bio::AlignIO::selex selex sequence input/output stream     1.006924
Bio::AlignIO::stockholm stockholm sequence input/output stream     1.006924
Bio::AlignIO::xmfa XMFA MSA Sequence input/output stream     1.006924
Bio::AnalysisI An interface to any (local or remote) analysis tool     1.006924
Bio::AnalysisI::JobI     1.006924
Bio::AnalysisParserI Generic analysis output parser interface     1.006924
Bio::AnalysisResultI Interface for analysis result objects     1.006924
Bio::AnnotatableI the base interface an annotatable object must implement     1.006924
Bio::Annotation::AnnotationFactory Instantiates a new Bio::AnnotationI (or derived class) through a factory     1.006924
Bio::Annotation::Collection Default Perl implementation of AnnotationCollectionI     1.006924
Bio::Annotation::Comment A comment object, holding text     1.006924
Bio::Annotation::DBLink untyped links between databases     1.006924
Bio::Annotation::OntologyTerm An ontology term adapted to AnnotationI     1.006924
Bio::Annotation::Reference Specialised DBLink object for Literature References     1.006924
Bio::Annotation::Relation Relationship (pairwise) with other objects SeqI and NodeI;     1.006924
Bio::Annotation::SimpleValue A simple scalar     1.006924
Bio::Annotation::StructuredValue A scalar with embedded structured information     1.006924
Bio::Annotation::TagTree AnnotationI with tree-like hierarchal key-value relationships ('structured tags') that can be represented as simple text.     1.006924
Bio::Annotation::Target Provides an object which represents a target (ie, a similarity hit) from one object to something in another database     1.006924
Bio::Annotation::Tree Provide a tree as an annotation to a Bio::AnnotatableI object     1.006924
Bio::Annotation::TypeManager Manages types for annotation collections     1.006924
Bio::AnnotationCollectionI Interface for annotation collections     1.006924
Bio::AnnotationI Annotation interface     1.006924
Bio::Assembly::Contig Perl module to hold and manipulate sequence assembly contigs.     1.006924
Bio::Assembly::ContigAnalysis Perform analysis on sequence assembly contigs.     1.006924
Bio::Assembly::IO Handler for Assembly::IO Formats     1.006924
Bio::Assembly::IO::ace module to load ACE files from various assembly programs     1.006924
Bio::Assembly::IO::bowtie An IO module for assemblies in Bowtie format *BETA*     1.006924
Bio::Assembly::IO::maq Driver to read assembly files in maq format *BETA*     1.006924
Bio::Assembly::IO::phrap driver to load phrap.out files.     1.006924
Bio::Assembly::IO::sam An IO module for assemblies in Sam format *BETA*     1.006924
Bio::Assembly::IO::tigr Driver to read and write assembly files in the TIGR Assembler v2 default format.     1.006924
Bio::Assembly::Scaffold Perl module to hold and manipulate sequence assembly data.     1.006924
Bio::Assembly::ScaffoldI Abstract Inteface of Sequence Assemblies     1.006924
Bio::Assembly::Singlet Perl module to hold and manipulate singlets from sequence assembly contigs.     1.006924
Bio::Assembly::Tools::ContigSpectrum create and manipulate contig spectra     1.006924
Bio::Cluster::ClusterFactory Instantiates a new Bio::ClusterI (or derived class) through a factory     1.006924
Bio::Cluster::FamilyI Family Interface     1.006924
Bio::Cluster::SequenceFamily Sequence Family object     1.006924
Bio::Cluster::UniGene UniGene object     1.006924
Bio::Cluster::UniGeneI abstract interface of UniGene object     1.006924
Bio::ClusterI Cluster Interface     1.006924
Bio::ClusterIO Handler for Cluster Formats     1.006924
Bio::ClusterIO::dbsnp dbSNP input stream     1.006924
Bio::ClusterIO::unigene UniGene input stream     1.006924
Bio::CodonUsage::IO for reading and writing codon usage tables to file     1.006924
Bio::CodonUsage::Table for access to the Codon usage Database at http://www.kazusa.or.jp/codon.     1.006924
Bio::Coordinate::Chain     1.006924
Bio::Coordinate::Collection     1.006924
Bio::Coordinate::ExtrapolatingPair     1.006924
Bio::Coordinate::GeneMapper     1.006924
Bio::Coordinate::Graph     1.006924
Bio::Coordinate::MapperI     1.006924
Bio::Coordinate::Pair     1.006924
Bio::Coordinate::Result     1.006924
Bio::Coordinate::Result::Gap     1.006924
Bio::Coordinate::Result::Match     1.006924
Bio::Coordinate::ResultI     1.006924
Bio::Coordinate::Utils     1.006924
Bio::DB::Ace Database object interface to ACeDB servers     1.006924
Bio::DB::BioFetch Database object interface to BioFetch retrieval     1.006924
Bio::DB::CUTG for access to the Codon usage Database at http://www.kazusa.or.jp/codon.     1.006924
Bio::DB::DBFetch Database object for retrieving using the dbfetch script     1.006924
Bio::DB::EMBL Database object interface for EMBL entry retrieval     1.006924
Bio::DB::EntrezGene Database object interface to Entrez Gene     1.006924
Bio::DB::Expression DESCRIPTION of Object     1.006924
Bio::DB::Expression::geo *** DESCRIPTION of Class     1.006924
Bio::DB::Failover A Bio::DB::RandomAccessI compliant class which wraps a prioritized list of DBs     1.006924
Bio::DB::Fasta Fast indexed access to fasta files     1.006924
Bio::DB::Fasta::Subdir     1.006924
Bio::DB::FileCache In file cache for BioSeq objects     1.006924
Bio::DB::Flat Interface for indexed flat files     1.006924
Bio::DB::Flat::BDB Interface for BioHackathon standard BDB-indexed flat file     1.006924
Bio::DB::Flat::BDB::embl embl adaptor for Open-bio standard BDB-indexed flat file     1.006924
Bio::DB::Flat::BDB::fasta fasta adaptor for Open-bio standard BDB-indexed flat file     1.006924
Bio::DB::Flat::BDB::genbank genbank adaptor for Open-bio standard BDB-indexed flat file     1.006924
Bio::DB::Flat::BDB::swiss swissprot adaptor for Open-bio standard BDB-indexed flat file     1.006924
Bio::DB::Flat::BinarySearch BinarySearch search indexing system for sequence files     1.006924
Bio::DB::GFF Storage and retrieval of sequence annotation data     1.006924
Bio::DB::GFF::Adaptor::ace ace interface (for multiple inheritance)     1.006924
Bio::DB::GFF::Adaptor::berkeleydb Bio::DB::GFF database adaptor for in-memory databases     1.006924
Bio::DB::GFF::Adaptor::berkeleydb::iterator iterator for Bio::DB::GFF::Adaptor::berkeleydb     1.006924
Bio::DB::GFF::Adaptor::biofetch Cache BioFetch objects in a Bio::DB::GFF database     1.006924
Bio::DB::GFF::Adaptor::biofetch_oracle Cache BioFetch objects in a Bio::DB::GFF database     1.006924
Bio::DB::GFF::Adaptor::dbi Database adaptor for DBI (SQL) databases     1.006924
Bio::DB::GFF::Adaptor::dbi::caching_handle Cache for database handles     1.006924
Bio::DB::GFF::Adaptor::dbi::faux_dbh     1.006924
Bio::DB::GFF::Adaptor::dbi::iterator iterator for Bio::DB::GFF::Adaptor::dbi     1.006924
Bio::DB::GFF::Adaptor::dbi::mysql Database adaptor for a specific mysql schema     1.006924
Bio::DB::GFF::Adaptor::dbi::mysqlace Unholy union between mysql GFF database and acedb database     1.006924
Bio::DB::GFF::Adaptor::dbi::mysqlcmap Database adaptor for an integraded CMap/GBrowse mysql schema     1.006924
Bio::DB::GFF::Adaptor::dbi::mysqlopt Deprecated database adaptor     1.006924
Bio::DB::GFF::Adaptor::dbi::oracle Database adaptor for a specific oracle schema     1.006924
Bio::DB::GFF::Adaptor::dbi::oracleace Unholy union between oracle GFF database and acedb database     1.006924
Bio::DB::GFF::Adaptor::dbi::pg Database adaptor for a specific postgres schema     1.006924
Bio::DB::GFF::Adaptor::dbi::pg_fts Database adaptor for a specific postgres schema with a TSearch2 implementation     1.006924
Bio::DB::GFF::Adaptor::memory Bio::DB::GFF database adaptor for in-memory databases     1.006924
Bio::DB::GFF::Adaptor::memory::feature_serializer utility methods for serializing and deserializing GFF features     1.006924
Bio::DB::GFF::Adaptor::memory::iterator iterator for Bio::DB::GFF::Adaptor::memory     1.006924
Bio::DB::GFF::Aggregator Aggregate GFF groups into composite features     1.006924
Bio::DB::GFF::Aggregator::alignment Alignment aggregator     1.006924
Bio::DB::GFF::Aggregator::clone Clone aggregator     1.006924
Bio::DB::GFF::Aggregator::coding The Coding Region Aggregator     1.006924
Bio::DB::GFF::Aggregator::gene Sequence Ontology Geene     1.006924
Bio::DB::GFF::Aggregator::match Match aggregator     1.006924
Bio::DB::GFF::Aggregator::none No aggregation     1.006924
Bio::DB::GFF::Aggregator::orf An aggregator for orf regions     1.006924
Bio::DB::GFF::Aggregator::processed_transcript Sequence Ontology Transcript     1.006924
Bio::DB::GFF::Aggregator::so_transcript Sequence Ontology Transcript     1.006924
Bio::DB::GFF::Aggregator::transcript Transcript aggregator     1.006924
Bio::DB::GFF::Aggregator::ucsc_acembly UCSC acembly aggregator     1.006924
Bio::DB::GFF::Aggregator::ucsc_ensgene UCSC ensGene aggregator     1.006924
Bio::DB::GFF::Aggregator::ucsc_genscan UCSC genscan aggregator     1.006924
Bio::DB::GFF::Aggregator::ucsc_refgene UCSC refGene aggregator     1.006924
Bio::DB::GFF::Aggregator::ucsc_sanger22 UCSC sanger22 aggregator     1.006924
Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo UCSC sanger22pseudo aggregator     1.006924
Bio::DB::GFF::Aggregator::ucsc_softberry UCSC softberry aggregator     1.006924
Bio::DB::GFF::Aggregator::ucsc_twinscan UCSC twinscan aggregator     1.006924
Bio::DB::GFF::Aggregator::ucsc_unigene UCSC UniGene aggregator     1.006924
Bio::DB::GFF::Featname The name of a feature     1.006924
Bio::DB::GFF::Feature A relative segment identified by a feature type     1.006924
Bio::DB::GFF::FeatureIterator     1.006924
Bio::DB::GFF::Homol A segment of DNA that is homologous to another     1.006924
Bio::DB::GFF::ID_Iterator     1.006924
Bio::DB::GFF::RelSegment Sequence segment with relative coordinate support     1.006924
Bio::DB::GFF::Segment Simple DNA segment object     1.006924
Bio::DB::GFF::Typename The name of a feature type     1.006924
Bio::DB::GFF::Util::Binning binning utility for Bio::DB::GFF index     1.006924
Bio::DB::GFF::Util::Rearrange rearrange utility     1.006924
Bio::DB::GenBank Database object interface to GenBank     1.006924
Bio::DB::GenPept Database object interface to GenPept     1.006924
Bio::DB::GenericWebAgent helper base class for parameter-based remote server access and response retrieval.     1.006924
Bio::DB::HIV Database object interface to the Los Alamos HIV Sequence Database     1.006924
Bio::DB::HIV::HIVAnnotProcessor Adds HIV-specific annotations to Bio::SeqIO streams     1.006924
Bio::DB::HIV::HIVQueryHelper Routines and packages used by Bio::DB::HIV and Bio::DB::Query::HIVQuery     1.006924
Bio::DB::InMemoryCache Abstract interface for a sequence database     1.006924
Bio::DB::Indexed::Stream     1.006924
Bio::DB::IndexedBase Base class for modules using indexed sequence files     1.006924
Bio::DB::LocationI A RandomAccessI-like abstract interface for retrieving location data from a sequence database and returning Bio::LocationI objects     1.006924
Bio::DB::MeSH Term retrieval from a Web MeSH database     1.006924
Bio::DB::NCBIHelper A collection of routines useful for queries to NCBI databases.     1.006924
Bio::DB::Qual Fast indexed access to quality files     1.006924
Bio::DB::Query::GenBank Build a GenBank Entrez Query     1.006924
Bio::DB::Query::HIVQuery Query interface to the Los Alamos HIV Sequence Database     1.006924
Bio::DB::Query::WebQuery Helper class for web-based sequence queryies     1.006924
Bio::DB::QueryI Object Interface to queryable sequence databases     1.006924
Bio::DB::RandomAccessI Abstract interface for a sequence database     1.006924
Bio::DB::RefSeq Database object interface for RefSeq retrieval     1.006924
Bio::DB::ReferenceI A RandomAccessI-like abstract interface for retrieving Reference data from a sequence database and returning Bio::Annotation::Reference objects     1.006924
Bio::DB::Registry Access to the Open Bio Database Access registry scheme     1.006924
Bio::DB::SeqFeature Normalized feature for use with Bio::DB::SeqFeature::Store     1.006924
Bio::DB::SeqFeature::NormalizedFeature Normalized feature for use with Bio::DB::SeqFeature::Store     1.006924
Bio::DB::SeqFeature::NormalizedFeatureI Interface for normalized features     1.006924
Bio::DB::SeqFeature::NormalizedTableFeatureI Interface for normalized features whose hierarchy is stored in a table     1.006924
Bio::DB::SeqFeature::Segment Location-based access to genome annotation data     1.006924
Bio::DB::SeqFeature::Store Storage and retrieval of sequence annotation data     1.006924
Bio::DB::SeqFeature::Store::DBI::Iterator utility methods for creating and iterating over SeqFeature records     1.006924
Bio::DB::SeqFeature::Store::DBI::Pg PostgreSQL implementation of Bio::DB::SeqFeature::Store     1.006924
Bio::DB::SeqFeature::Store::DBI::SQLite SQLite implementation of Bio::DB::SeqFeature::Store     1.006924
Bio::DB::SeqFeature::Store::DBI::mysql Mysql implementation of Bio::DB::SeqFeature::Store     1.006924
Bio::DB::SeqFeature::Store::FeatureFileLoader feature file loader for Bio::DB::SeqFeature::Store     1.006924
Bio::DB::SeqFeature::Store::FeatureIterator     1.006924
Bio::DB::SeqFeature::Store::GFF2Loader GFF2 file loader for Bio::DB::SeqFeature::Store     1.006924
Bio::DB::SeqFeature::Store::GFF3Loader GFF3 file loader for Bio::DB::SeqFeature::Store     1.006924
Bio::DB::SeqFeature::Store::LoadHelper Internal utility for Bio::DB::SeqFeature::Store     1.006924
Bio::DB::SeqFeature::Store::Loader Loader     1.006924
Bio::DB::SeqFeature::Store::bdb fetch and store objects from a BerkeleyDB     1.006924
Bio::DB::SeqFeature::Store::berkeleydb Storage and retrieval of sequence annotation data in Berkeleydb files     1.006924
Bio::DB::SeqFeature::Store::berkeleydb3 Storage and retrieval of sequence annotation data in Berkeleydb files     1.006924
Bio::DB::SeqFeature::Store::berkeleydb::Iterator     1.006924
Bio::DB::SeqFeature::Store::memory In-memory implementation of Bio::DB::SeqFeature::Store     1.006924
Bio::DB::SeqFeature::Store::memory::Iterator     1.006924
Bio::DB::SeqHound Database object interface to SeqHound     1.006924
Bio::DB::SeqI Abstract Interface for Sequence databases     1.006924
Bio::DB::SeqVersion front end to querying databases for identifier versions     1.006924
Bio::DB::SeqVersion::gi interface to NCBI Sequence Revision History page     1.006924
Bio::DB::SwissProt Database object interface to SwissProt retrieval     1.006924
Bio::DB::TFBS Access to a Transcription Factor Binding Site database     1.006924
Bio::DB::TFBS::transfac_pro An implementation of Bio::DB::TFBS which uses local flat files for transfac pro     1.006924
Bio::DB::Taxonomy Access to a taxonomy database     1.006924
Bio::DB::Taxonomy::entrez Taxonomy Entrez driver     1.006924
Bio::DB::Taxonomy::flatfile Use the NCBI taxonomy from local indexed flat files     1.006924
Bio::DB::Taxonomy::greengenes Use the Greengenes taxonomy     1.006924
Bio::DB::Taxonomy::list An implementation of Bio::DB::Taxonomy that accepts lists of words to build a database     1.006924
Bio::DB::Taxonomy::silva Use the Silva taxonomy     1.006924
Bio::DB::Universal Artificial database that delegates to specific databases     1.006924
Bio::DB::UpdateableSeqI An interface for writing to a database of sequences.     1.006924
Bio::DB::WebDBSeqI Object Interface to generalize Web Databases for retrieving sequences     1.006924
Bio::DBLinkContainerI Abstract interface for any object wanting to use database cross references     1.006924
Bio::Das::FeatureTypeI Simple interface to Sequence Ontology feature types     1.006924
Bio::Das::SegmentI DAS-style access to a feature database     1.006924
Bio::DasI DAS-style access to a feature database     1.006924
Bio::DescribableI interface for objects with human readable names and descriptions     1.006924
Bio::Draw::Pictogram generate SVG output of Pictogram display for consensus motifs     1.006924
Bio::Event::EventGeneratorI This interface describes the basic event generator class.     1.006924
Bio::Event::EventHandlerI An Event Handler Interface     1.006924
Bio::Factory::AnalysisI An interface to analysis tool factory     1.006924
Bio::Factory::ApplicationFactoryI Interface class for Application Factories     1.006924
Bio::Factory::DriverFactory Base class for factory classes loading drivers     1.006924
Bio::Factory::FTLocationFactory A FeatureTable Location Parser     1.006924
Bio::Factory::LocationFactoryI A factory interface for generating locations from a string     1.006924
Bio::Factory::MapFactoryI A Factory for getting markers     1.006924
Bio::Factory::ObjectBuilderI Interface for an object builder     1.006924
Bio::Factory::ObjectFactory Instantiates a new Bio::Root::RootI (or derived class) through a factory     1.006924
Bio::Factory::ObjectFactoryI A General object creator factory     1.006924
Bio::Factory::SeqAnalysisParserFactory class capable of creating SeqAnalysisParserI compliant parsers     1.006924
Bio::Factory::SeqAnalysisParserFactoryI interface describing objects capable of creating SeqAnalysisParserI compliant parsers     1.006924
Bio::Factory::SequenceFactoryI This interface allows for generic building of sequences in factories which create sequences (like SeqIO)     1.006924
Bio::Factory::SequenceProcessorI Interface for chained sequence processing algorithms     1.006924
Bio::Factory::SequenceStreamI Interface describing the basics of a Sequence Stream.     1.006924
Bio::Factory::TreeFactoryI Factory Interface for getting and writing trees from/to a data stream     1.006924
Bio::FeatureHolderI the base interface an object with features must implement     1.006924
Bio::HandlerBaseI Interface class for handler methods which interact with any event-driven parsers (drivers).     1.006924
Bio::IdCollectionI interface for objects with multiple identifiers     1.006924
Bio::IdentifiableI interface for objects with identifiers     1.006924
Bio::Index::Abstract Abstract interface for indexing a flat file     1.006924
Bio::Index::AbstractSeq base class for AbstractSeq     1.006924
Bio::Index::Blast Indexes Blast reports and supports retrieval based on query accession(s)     1.006924
Bio::Index::BlastTable Indexes tabular Blast reports (-m 8 or -m 9 format) and supports retrieval based on query accession(s)     1.006924
Bio::Index::EMBL Interface for indexing (multiple) EMBL/Swissprot .dat files (i.e. flat file EMBL/Swissprot format).     1.006924
Bio::Index::Fasta Interface for indexing (multiple) fasta files     1.006924
Bio::Index::Fastq Interface for indexing (multiple) fastq files     1.006924
Bio::Index::GenBank Interface for indexing one or more GenBank files (i.e. flat file GenBank format).     1.006924
Bio::Index::Hmmer indexes HMMER reports and supports retreival based on query     1.006924
Bio::Index::Qual Interface for indexing (multiple) fasta qual files     1.006924
Bio::Index::Stockholm     1.006924
Bio::Index::SwissPfam Interface for indexing swisspfam files     1.006924
Bio::Index::Swissprot Interface for indexing one or more Swissprot files.     1.006924
Bio::LiveSeq::AARange AARange abstract class for LiveSeq     1.006924
Bio::LiveSeq::Chain DoubleChain DataStructure for Perl     1.006924
Bio::LiveSeq::ChainI Double linked chain data structure     1.006924
Bio::LiveSeq::DNA DNA object for LiveSeq     1.006924
Bio::LiveSeq::Exon Range abstract class for LiveSeq     1.006924
Bio::LiveSeq::Gene Range abstract class for LiveSeq     1.006924
Bio::LiveSeq::IO::BioPerl Loader for LiveSeq from EMBL entries with BioPerl     1.006924
Bio::LiveSeq::IO::Loader Parent Loader for LiveSeq     1.006924
Bio::LiveSeq::Intron Range abstract class for LiveSeq     1.006924
Bio::LiveSeq::Mutation Mutation event descriptor class     1.006924
Bio::LiveSeq::Mutator Package mutating LiveSequences     1.006924
Bio::LiveSeq::Prim_Transcript Prim_Transcript class for LiveSeq     1.006924
Bio::LiveSeq::Range Range abstract class for LiveSeq     1.006924
Bio::LiveSeq::Repeat_Region Repeat_Region class for LiveSeq     1.006924
Bio::LiveSeq::Repeat_Unit Repeat_Unit class for LiveSeq     1.006924
Bio::LiveSeq::SeqI Abstract sequence interface class for LiveSeq     1.006924
Bio::LiveSeq::Transcript Transcript class for LiveSeq     1.006924
Bio::LiveSeq::Translation Translation class for LiveSeq     1.006924
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.     1.006924
Bio::Location::Atomic Implementation of a Atomic Location on a Sequence     1.006924
Bio::Location::AvWithinCoordPolicy class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise     1.006924
Bio::Location::CoordinatePolicyI Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location     1.006924
Bio::Location::Fuzzy Implementation of a Location on a Sequence which has unclear start and/or end locations     1.006924
Bio::Location::FuzzyLocationI Abstract interface of a Location on a Sequence which has unclear start/end location     1.006924
Bio::Location::NarrowestCoordPolicy class implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range     1.006924
Bio::Location::Simple Implementation of a Simple Location on a Sequence     1.006924
Bio::Location::Split Implementation of a Location on a Sequence which has multiple locations (start/end points)     1.006924
Bio::Location::SplitLocationI Abstract interface of a Location on a Sequence which has multiple locations (start/end points)     1.006924
Bio::Location::WidestCoordPolicy class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable range     1.006924
Bio::LocationI Abstract interface of a Location on a Sequence     1.006924
Bio::Map::Clone An central map object representing a clone     1.006924
Bio::Map::Contig A MapI implementation handling the contigs of a Physical Map (such as FPC)     1.006924
Bio::Map::CytoMap A Bio::MapI compliant map implementation handling cytogenic bands     1.006924
Bio::Map::CytoMarker An object representing a marker.     1.006924
Bio::Map::CytoPosition Marker class with cytogenetic band storing attributes     1.006924
Bio::Map::EntityI An Entity Interface     1.006924
Bio::Map::FPCMarker An central map object representing a marker     1.006924
Bio::Map::Gene An gene modelled as a mappable element.     1.006924
Bio::Map::GeneMap A MapI implementation to represent the area around a gene     1.006924
Bio::Map::GenePosition A typed position, suitable for modelling the various regions of a gene.     1.006924
Bio::Map::GeneRelative Represents being relative to named sub-regions of a gene.     1.006924
Bio::Map::LinkageMap A representation of a genetic linkage map.     1.006924
Bio::Map::LinkagePosition Create a Position for a Marker that will be placed on a Bio::Map::LinkageMap     1.006924
Bio::Map::MapI Interface for describing Map objects in bioperl     1.006924
Bio::Map::Mappable An object representing a generic map element that can have multiple locations in several maps.     1.006924
Bio::Map::MappableI An object that can be placed in a map     1.006924
Bio::Map::Marker An central map object representing a generic marker that can have multiple location in several maps.     1.006924
Bio::Map::MarkerI Interface for basic marker functionality     1.006924
Bio::Map::Microsatellite An object representing a Microsatellite marker.     1.006924
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.     1.006924
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.     1.006924
Bio::Map::Physical A class for handling a Physical Map (such as FPC)     1.006924
Bio::Map::Position A single position of a Marker, or the range over which that marker lies, in a Map     1.006924
Bio::Map::PositionHandler A Position Handler Implementation     1.006924
Bio::Map::PositionHandlerI A Position Handler Interface     1.006924
Bio::Map::PositionI Abstracts the notion of a position having a value in the context of a marker and a Map     1.006924
Bio::Map::PositionWithSequence A position with a sequence.     1.006924
Bio::Map::Prediction An object representing the predictions of something that can have multiple locations in several maps.     1.006924
Bio::Map::Relative Represents what a Position's coordiantes are relative to.     1.006924
Bio::Map::RelativeI Interface for describing what a Position's coordiantes are relative to.     1.006924
Bio::Map::SimpleMap A MapI implementation handling the basics of a Map     1.006924
Bio::Map::TranscriptionFactor A transcription factor modelled as a mappable element     1.006924
Bio::MapIO A Map Factory object     1.006924
Bio::MapIO::fpc A FPC Map reader     1.006924
Bio::MapIO::mapmaker A Mapmaker Map reader     1.006924
Bio::Matrix::Generic A generic matrix implementation     1.006924
Bio::Matrix::IO A factory for Matrix parsing     1.006924
Bio::Matrix::IO::mlagan A parser for the mlagan substitution matrix     1.006924
Bio::Matrix::IO::phylip A parser for PHYLIP distance matricies     1.006924
Bio::Matrix::IO::scoring A parser for PAM/BLOSUM matricies     1.006924
Bio::Matrix::MatrixI An interface for describing a Matrix     1.006924
Bio::Matrix::Mlagan A generic matrix with mlagan fields     1.006924
Bio::Matrix::PSM::IO PSM parser     1.006924
Bio::Matrix::PSM::IO::mast PSM mast parser implementation     1.006924
Bio::Matrix::PSM::IO::masta motif fasta format parser     1.006924
Bio::Matrix::PSM::IO::meme PSM meme parser implementation     1.006924
Bio::Matrix::PSM::IO::psiblast PSM psiblast parser     1.006924
Bio::Matrix::PSM::IO::transfac PSM transfac parser     1.006924
Bio::Matrix::PSM::InstanceSite A PSM site occurance     1.006924
Bio::Matrix::PSM::InstanceSiteI InstanceSite interface, holds an instance of a PSM     1.006924
Bio::Matrix::PSM::ProtMatrix SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) with log-odds scoring information.     1.006924
Bio::Matrix::PSM::ProtPsm handle combination of site matricies     1.006924
Bio::Matrix::PSM::Psm handle combination of site matricies     1.006924
Bio::Matrix::PSM::PsmHeader PSM mast parser implementation     1.006924
Bio::Matrix::PSM::PsmHeaderI handles the header data from a PSM file     1.006924
Bio::Matrix::PSM::PsmI abstract interface to handler of site matricies     1.006924
Bio::Matrix::PSM::SiteMatrix SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds     1.006924
Bio::Matrix::PSM::SiteMatrixI SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds     1.006924
Bio::Matrix::PhylipDist A Phylip Distance Matrix object     1.006924
Bio::Matrix::Scoring Object which can hold scoring matrix information     1.006924
Bio::MolEvol::CodonModel Codon Evolution Models     1.006924
Bio::Nexml::Factory A factory module for creating BioPerl and Bio::Phylo objects from/to nexml documents     1.006924
Bio::NexmlIO stream handler for NeXML documents     1.006924
Bio::Ontology::DocumentRegistry Keep track of where to find ontologies. Allows lookups by name.     1.006924
Bio::Ontology::GOterm representation of GO terms     1.006924
Bio::Ontology::InterProTerm Implementation of InterProI term interface     1.006924
Bio::Ontology::OBOEngine An Ontology Engine for OBO style flat file format from the Gene Ontology Consortium     1.006924
Bio::Ontology::OBOterm representation of OBO terms     1.006924
Bio::Ontology::Ontology standard implementation of an Ontology     1.006924
Bio::Ontology::OntologyEngineI Interface a minimal Ontology implementation should satisfy     1.006924
Bio::Ontology::OntologyI Interface for an ontology implementation     1.006924
Bio::Ontology::OntologyStore A repository of ontologies     1.006924
Bio::Ontology::Path a path for an ontology term graph     1.006924
Bio::Ontology::PathI Interface for a path between ontology terms     1.006924
Bio::Ontology::Relationship a relationship for an ontology     1.006924
Bio::Ontology::RelationshipFactory Instantiates a new Bio::Ontology::RelationshipI (or derived class) through a factory     1.006924
Bio::Ontology::RelationshipI Interface for a relationship between ontology terms     1.006924
Bio::Ontology::RelationshipType a relationship type for an ontology     1.006924
Bio::Ontology::SimpleGOEngine::GraphAdaptor Graph adaptor for Bio::Ontology::SimpleGOEngine     1.006924
Bio::Ontology::SimpleOntologyEngine Implementation of OntologyEngineI interface     1.006924
Bio::Ontology::Term implementation of the interface for ontology terms     1.006924
Bio::Ontology::TermFactory Instantiates a new Bio::Ontology::TermI (or derived class) through a factory     1.006924
Bio::Ontology::TermI interface for ontology terms     1.006924
Bio::OntologyIO Parser factory for Ontology formats     1.006924
Bio::OntologyIO::Handlers::BaseSAXHandler base class for SAX Handlers     1.006924
Bio::OntologyIO::Handlers::InterProHandler XML handler class for InterProParser     1.006924
Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler parse an InterPro XML file and persist the resulting terms to a Biosql database     1.006924
Bio::OntologyIO::InterProParser Parser for InterPro xml files.     1.006924
Bio::OntologyIO::dagflat a base class parser for GO flat-file type formats     1.006924
Bio::OntologyIO::goflat a parser for the Gene Ontology flat-file format     1.006924
Bio::OntologyIO::obo a parser for OBO flat-file format from Gene Ontology Consortium     1.006924
Bio::OntologyIO::simplehierarchy a base class parser for simple hierarchy-by-indentation type formats     1.006924
Bio::OntologyIO::soflat a parser for the Sequence Ontology flat-file format     1.006924
Bio::ParameterBaseI Simple interface class for any parameter-related data such as IDs, database name, program arguments, and other odds and ends.     1.006924
Bio::Perl Functional access to BioPerl for people who don't know objects     1.006924
Bio::Phenotype::Correlate Representation of a correlating phenotype in a given species     1.006924
Bio::Phenotype::MeSH::Term A MeSH term     1.006924
Bio::Phenotype::MeSH::Twig Context for a MeSH term     1.006924
Bio::Phenotype::Measure Representation of context/value(-range)/unit triplets     1.006924
Bio::Phenotype::OMIM::MiniMIMentry Representation of a Mini MIM entry     1.006924
Bio::Phenotype::OMIM::OMIMentry represents OMIM (Online Mendelian Inheritance in Man) database entries     1.006924
Bio::Phenotype::OMIM::OMIMentryAllelicVariant Representation of a allelic variant of the OMIM database     1.006924
Bio::Phenotype::OMIM::OMIMparser parser for the OMIM database     1.006924
Bio::Phenotype::Phenotype A class for modeling phenotypes     1.006924
Bio::Phenotype::PhenotypeI An interface for classes modeling phenotypes     1.006924
Bio::PhyloNetwork Module to compute with Phylogenetic Networks     1.006924
Bio::PhyloNetwork::Factory Module to sequentially generate Phylogenetic Networks     1.006924
Bio::PhyloNetwork::FactoryX Module to sequentially generate Phylogenetic Networks     1.006924
Bio::PhyloNetwork::GraphViz Interface between PhyloNetwork and GraphViz     1.006924
Bio::PhyloNetwork::RandomFactory Module to generate random Phylogenetic Networks     1.006924
Bio::PhyloNetwork::TreeFactory Module to sequentially generate Phylogenetic Trees     1.006924
Bio::PhyloNetwork::TreeFactoryMulti Module to sequentially generate Phylogenetic Trees     1.006924
Bio::PhyloNetwork::TreeFactoryX Module to sequentially generate Phylogenetic Trees     1.006924
Bio::PhyloNetwork::muVector Module to compute with vectors of arbitrary dimension     1.006924
Bio::PopGen::Genotype An implementation of GenotypeI which is just an allele container     1.006924
Bio::PopGen::GenotypeI A marker and alleles for a specific individual     1.006924
Bio::PopGen::HtSNP Select htSNP from a haplotype set     1.006924
Bio::PopGen::IO Input individual,marker,allele information     1.006924
Bio::PopGen::IO::csv Extract individual allele data from a CSV parser     1.006924
Bio::PopGen::IO::hapmap A parser for HapMap output data     1.006924
Bio::PopGen::IO::phase A parser for Phase format data     1.006924
Bio::PopGen::IO::prettybase Extract individual allele data from PrettyBase format     1.006924
Bio::PopGen::Individual An implementation of an Individual who has Genotype or Sequence Results     1.006924
Bio::PopGen::IndividualI An individual who has Genotype or Sequence Results     1.006924
Bio::PopGen::Marker A genetic marker which one uses to generate genotypes     1.006924
Bio::PopGen::MarkerI A Population Genetic conceptual marker     1.006924
Bio::PopGen::PopStats A collection of methods for calculating statistics about a population or sets of populations     1.006924
Bio::PopGen::Population A population of individuals     1.006924
Bio::PopGen::PopulationI Interface for Populations     1.006924
Bio::PopGen::Simulation::Coalescent A Coalescent simulation factory     1.006924
Bio::PopGen::Simulation::GeneticDrift A simple genetic drift simulation     1.006924
Bio::PopGen::Statistics Population Genetics statistical tests     1.006924
Bio::PopGen::TagHaplotype Haplotype tag object.     1.006924
Bio::PopGen::Utilities Utilities for working with PopGen data and objects     1.006924
Bio::PrimarySeq Bioperl lightweight sequence object     1.006924
Bio::PrimarySeq::Fasta     1.006924
Bio::PrimarySeqI Interface definition for a Bio::PrimarySeq     1.006924
Bio::PullParserI A base module for fast 'pull' parsing     1.006924
Bio::Range Pure perl RangeI implementation     1.006924
Bio::RangeI Range interface     1.006924
Bio::Restriction::Analysis cutting sequences with restriction enzymes     1.006924
Bio::Restriction::Enzyme A single restriction endonuclease (cuts DNA at specific locations)     1.006924
Bio::Restriction::Enzyme::MultiCut A single restriction endonuclease     1.006924
Bio::Restriction::Enzyme::MultiSite A single restriction endonuclease     1.006924
Bio::Restriction::EnzymeCollection Set of restriction endonucleases     1.006924
Bio::Restriction::EnzymeI Interface class for restriction endonuclease     1.006924
Bio::Restriction::IO Handler for sequence variation IO Formats     1.006924
Bio::Restriction::IO::bairoch bairoch enzyme set     1.006924
Bio::Restriction::IO::base base enzyme set     1.006924
Bio::Restriction::IO::itype2 itype2 enzyme set     1.006924
Bio::Restriction::IO::prototype prototype enzyme set     1.006924
Bio::Restriction::IO::withrefm withrefm enzyme set     1.006924
Bio::Root::Build     1.006924
Bio::Root::Exception     1.006924
Bio::Root::HTTPget module for fallback HTTP get operations when LWP:: is unavailable     1.006924
Bio::Root::IO     1.006924
Bio::Root::Root     1.006924
Bio::Root::RootI     1.006924
Bio::Root::Storable     1.006924
Bio::Root::Test     1.006924
Bio::Root::Utilities     1.006924
Bio::Root::Version     1.006924
Bio::Search::BlastStatistics An object for Blast statistics     1.006924
Bio::Search::BlastUtils Utility functions for Bio::Search:: BLAST objects     1.006924
Bio::Search::DatabaseI Interface for a database used in a sequence search     1.006924
Bio::Search::GenericDatabase Generic implementation of Bio::Search::DatabaseI     1.006924
Bio::Search::GenericStatistics An object for statistics     1.006924
Bio::Search::HSP::BlastHSP Bioperl BLAST High-Scoring Pair object     1.006924
Bio::Search::HSP::BlastPullHSP A parser and HSP object for BlastN hsps     1.006924
Bio::Search::HSP::FastaHSP HSP object for FASTA specific data     1.006924
Bio::Search::HSP::GenericHSP A "Generic" implementation of a High Scoring Pair     1.006924
Bio::Search::HSP::HMMERHSP A HSP object for HMMER results     1.006924
Bio::Search::HSP::HSPFactory A factory to create Bio::Search::HSP::HSPI objects     1.006924
Bio::Search::HSP::HSPI Interface for a High Scoring Pair in a similarity search result     1.006924
Bio::Search::HSP::HmmpfamHSP A parser and HSP object for hmmpfam hsps     1.006924
Bio::Search::HSP::ModelHSP A HSP object for model-based searches     1.006924
Bio::Search::HSP::PSLHSP A HSP for PSL output     1.006924
Bio::Search::HSP::PsiBlastHSP Bioperl BLAST High-Scoring Pair object     1.006924
Bio::Search::HSP::PullHSPI Bio::Search::HSP::HSPI interface for pull parsers.     1.006924
Bio::Search::HSP::WABAHSP HSP object suitable for describing WABA alignments     1.006924
Bio::Search::Hit::BlastHit Blast-specific subclass of Bio::Search::Hit::GenericHit     1.006924
Bio::Search::Hit::BlastPullHit A parser and hit object for BLASTN hits     1.006924
Bio::Search::Hit::Fasta Hit object specific for Fasta-generated hits     1.006924
Bio::Search::Hit::GenericHit A generic implementation of the Bio::Search::Hit::HitI interface     1.006924
Bio::Search::Hit::HMMERHit A Hit module for HMMER hits     1.006924
Bio::Search::Hit::HitFactory A factory to create Bio::Search::Hit::HitI objects     1.006924
Bio::Search::Hit::HitI Interface for a hit in a similarity search result     1.006924
Bio::Search::Hit::HmmpfamHit A parser and hit object for hmmpfam hits     1.006924
Bio::Search::Hit::ModelHit A model-based implementation of the Bio::Search::Hit::HitI interface     1.006924
Bio::Search::Hit::PsiBlastHit Bioperl BLAST Hit object     1.006924
Bio::Search::Hit::PullHitI Bio::Search::Hit::HitI interface for pull parsers.     1.006924
Bio::Search::Hit::hmmer3Hit DESCRIPTION of Object     1.006924
Bio::Search::Iteration::GenericIteration A generic implementation of the Bio::Search::Iteration::IterationI interface.     1.006924
Bio::Search::Iteration::IterationI Abstract interface to an iteration from an iterated search result, such as PSI-BLAST.     1.006924
Bio::Search::Processor DESCRIPTION of Object     1.006924
Bio::Search::Result::BlastPullResult A parser and result object for BLASTN results     1.006924
Bio::Search::Result::BlastResult Blast-specific subclass of Bio::Search::Result::GenericResult     1.006924
Bio::Search::Result::CrossMatchResult CrossMatch-specific subclass of Bio::Search::Result::GenericResult     1.006924
Bio::Search::Result::GenericResult Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results.     1.006924
Bio::Search::Result::HMMERResult A Result object for HMMER results     1.006924
Bio::Search::Result::HmmpfamResult A parser and result object for hmmpfam results     1.006924
Bio::Search::Result::PullResultI Bio::Search::Result::ResultI interface for 'pull' parsers     1.006924
Bio::Search::Result::ResultFactory A factory to create Bio::Search::Result::ResultI objects     1.006924
Bio::Search::Result::ResultI Abstract interface to Search Result objects     1.006924
Bio::Search::Result::WABAResult Result object for WABA alignment output     1.006924
Bio::Search::Result::hmmer3Result DESCRIPTION of Object     1.006924
Bio::Search::SearchUtils Utility functions for Bio::Search:: objects     1.006924
Bio::Search::StatisticsI A Base object for statistics     1.006924
Bio::Search::Tiling::MapTileUtils utilities for manipulating closed intervals for an HSP tiling algorithm     1.006924
Bio::Search::Tiling::MapTiling An implementation of an HSP tiling algorithm, with methods to obtain frequently-requested statistics     1.006924
Bio::Search::Tiling::TilingI Abstract interface for an HSP tiling module     1.006924
Bio::SearchDist A perl wrapper around Sean Eddy's histogram object     1.006924
Bio::SearchIO Driver for parsing Sequence Database Searches (BLAST, FASTA, ...)     1.006924
Bio::SearchIO::EventHandlerI An abstract Event Handler for Search Result parsing     1.006924
Bio::SearchIO::FastHitEventBuilder Event Handler for SearchIO events.     1.006924
Bio::SearchIO::IteratedSearchResultEventBuilder Event Handler for SearchIO events.     1.006924
Bio::SearchIO::SearchResultEventBuilder Event Handler for SearchIO events.     1.006924
Bio::SearchIO::SearchWriterI Interface for outputting parsed Search results     1.006924
Bio::SearchIO::Writer::BSMLResultWriter BSML output writer     1.006924
Bio::SearchIO::Writer::GbrowseGFF Interface for outputting parsed search results in Gbrowse GFF format     1.006924
Bio::SearchIO::Writer::HSPTableWriter Tab-delimited data for Bio::Search::HSP::HSPI objects     1.006924
Bio::SearchIO::Writer::HTMLResultWriter write a Bio::Search::ResultI in HTML     1.006924
Bio::SearchIO::Writer::HitTableWriter Tab-delimited data for Bio::Search::Hit::HitI objects     1.006924
Bio::SearchIO::Writer::ResultTableWriter Outputs tab-delimited data for each Bio::Search::Result::ResultI object.     1.006924
Bio::SearchIO::Writer::TextResultWriter Object to implement writing a Bio::Search::ResultI in Text.     1.006924
Bio::SearchIO::XML::BlastHandler XML Handler for NCBI Blast XML parsing.     1.006924
Bio::SearchIO::XML::PsiBlastHandler XML Handler for NCBI Blast PSIBLAST XML parsing.     1.006924
Bio::SearchIO::axt a parser for axt format reports     1.006924
Bio::SearchIO::blast Event generator for event based parsing of blast reports     1.006924
Bio::SearchIO::blast_pull A parser for BLAST output     1.006924
Bio::SearchIO::blasttable Driver module for SearchIO for parsing NCBI -m 8/9 format     1.006924
Bio::SearchIO::blastxml A SearchIO implementation of NCBI Blast XML parsing.     1.006924
Bio::SearchIO::cross_match CrossMatch-specific subclass of Bio::SearchIO     1.006924
Bio::SearchIO::erpin SearchIO-based ERPIN parser     1.006924
Bio::SearchIO::exonerate parser for Exonerate     1.006924
Bio::SearchIO::fasta A SearchIO parser for FASTA results     1.006924
Bio::SearchIO::gmap_f9 Event generator for parsing gmap reports (Z format)     1.006924
Bio::SearchIO::hmmer A parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam)     1.006924
Bio::SearchIO::hmmer2 A parser for HMMER output (hmmpfam, hmmsearch)     1.006924
Bio::SearchIO::hmmer3     1.006924
Bio::SearchIO::hmmer_pull A parser for HMMER output     1.006924
Bio::SearchIO::infernal SearchIO-based Infernal parser     1.006924
Bio::SearchIO::megablast a driver module for Bio::SearchIO to parse megablast reports (format 0)     1.006924
Bio::SearchIO::psl A parser for PSL output (UCSC)     1.006924
Bio::SearchIO::rnamotif SearchIO-based RNAMotif parser     1.006924
Bio::SearchIO::sim4 parser for Sim4 alignments     1.006924
Bio::SearchIO::waba SearchIO parser for Jim Kent WABA program alignment output     1.006924
Bio::SearchIO::wise Parsing of wise output as alignments     1.006924
Bio::Seq Sequence object, with features     1.006924
Bio::Seq::BaseSeqProcessor Base implementation for a SequenceProcessor     1.006924
Bio::Seq::EncodedSeq subtype of Bio::LocatableSeq to store DNA that encodes a protein     1.006924
Bio::Seq::LargeLocatableSeq LocatableSeq object that stores sequence as files in the tempdir     1.006924
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     1.006924
Bio::Seq::LargeSeq SeqI compliant object that stores sequence as files in /tmp     1.006924
Bio::Seq::LargeSeqI Interface class for sequences that cache their residues in a temporary file     1.006924
Bio::Seq::Meta Generic superclass for sequence objects with residue-based meta information     1.006924
Bio::Seq::Meta::Array array-based generic implementation of a sequence class with residue-based meta information     1.006924
Bio::Seq::MetaI Interface for sequence objects with residue-based meta information     1.006924
Bio::Seq::PrimaryQual Bioperl lightweight Quality Object     1.006924
Bio::Seq::PrimaryQual::Qual     1.006924
Bio::Seq::PrimedSeq A sequence and a pair of primers matching on it     1.006924
Bio::Seq::QualI Interface definition for a Bio::Seq::Qual     1.006924
Bio::Seq::Quality Implementation of sequence with residue quality and trace values     1.006924
Bio::Seq::RichSeq Module implementing a sequence created from a rich sequence database entry     1.006924
Bio::Seq::RichSeqI interface for sequences from rich data sources, mostly databases     1.006924
Bio::Seq::SeqBuilder Configurable object builder for sequence stream parsers     1.006924
Bio::Seq::SeqFactory Instantiation of generic Bio::PrimarySeqI (or derived) objects through a factory     1.006924
Bio::Seq::SeqFastaSpeedFactory Rapid creation of Bio::Seq objects through a factory     1.006924
Bio::Seq::SeqWithQuality Bioperl object packaging a sequence with its quality. Deprecated class, use Bio::Seq::Quality instead!     1.006924
Bio::Seq::SequenceTrace Bioperl object packaging a sequence with its trace     1.006924
Bio::Seq::SimulatedRead Read with sequencing errors taken from a reference sequence     1.006924
Bio::Seq::TraceI Interface definition for a Bio::Seq::Trace     1.006924
Bio::SeqAnalysisParserI Sequence analysis output parser interface     1.006924
Bio::SeqEvolution::DNAPoint evolve a sequence by point mutations     1.006924
Bio::SeqEvolution::EvolutionI the interface for evolving sequences     1.006924
Bio::SeqEvolution::Factory Factory object to instantiate sequence evolving classes     1.006924
Bio::SeqFeature::Amplicon Amplicon feature     1.006924
Bio::SeqFeature::AnnotationAdaptor integrates SeqFeatureIs annotation     1.006924
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.     1.006924
Bio::SeqFeature::CollectionI An interface for a collection of SeqFeatureI objects.     1.006924
Bio::SeqFeature::Computation Computation SeqFeature     1.006924
Bio::SeqFeature::FeaturePair hold pair feature information e.g. blast hits     1.006924
Bio::SeqFeature::Gene::Exon a feature representing an exon     1.006924
Bio::SeqFeature::Gene::ExonI Interface for a feature representing an exon     1.006924
Bio::SeqFeature::Gene::GeneStructure A feature representing an arbitrarily complex structure of a gene     1.006924
Bio::SeqFeature::Gene::GeneStructureI A feature representing an arbitrarily complex structure of a gene     1.006924
Bio::SeqFeature::Gene::Intron An intron feature     1.006924
Bio::SeqFeature::Gene::NC_Feature superclass for non-coding features     1.006924
Bio::SeqFeature::Gene::Poly_A_site poly A feature     1.006924
Bio::SeqFeature::Gene::Promoter Describes a promoter     1.006924
Bio::SeqFeature::Gene::Transcript A feature representing a transcript     1.006924
Bio::SeqFeature::Gene::TranscriptI Interface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site.     1.006924
Bio::SeqFeature::Gene::UTR A feature representing an untranslated region that is part of a transcriptional unit     1.006924
Bio::SeqFeature::Generic Generic SeqFeature     1.006924
Bio::SeqFeature::Lite Lightweight Bio::SeqFeatureI class     1.006924
Bio::SeqFeature::PositionProxy handle features when truncation/revcom sequences span a feature     1.006924
Bio::SeqFeature::Primer Primer Generic SeqFeature     1.006924
Bio::SeqFeature::SiRNA::Oligo Perl object for small inhibitory RNAs.     1.006924
Bio::SeqFeature::SiRNA::Pair Perl object for small inhibitory RNA (SiRNA) oligo pairs     1.006924
Bio::SeqFeature::Similarity A sequence feature based on similarity     1.006924
Bio::SeqFeature::SimilarityPair Sequence feature based on the similarity of two sequences.     1.006924
Bio::SeqFeature::SubSeq Feature representing a subsequence     1.006924
Bio::SeqFeature::Tools::FeatureNamer generates unique persistent names for features     1.006924
Bio::SeqFeature::Tools::IDHandler maps $seq_feature->primary_tag     1.006924
Bio::SeqFeature::Tools::TypeMapper maps $seq_feature->primary_tag     1.006924
Bio::SeqFeature::Tools::Unflattener turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy     1.006924
Bio::SeqFeature::TypedSeqFeatureI a strongly typed SeqFeature     1.006924
Bio::SeqFeatureI Abstract interface of a Sequence Feature     1.006924
Bio::SeqI [Developers] Abstract Interface of Sequence (with features)     1.006924
Bio::SeqIO Handler for SeqIO Formats     1.006924
Bio::SeqIO::FTHelper Helper class for EMBL/Genbank feature tables     1.006924
Bio::SeqIO::Handler::GenericRichSeqHandler Bio::HandlerI-based data handler for GenBank/EMBL/UniProt (and other) sequence data     1.006924
Bio::SeqIO::MultiFile Treating a set of files as a single input stream     1.006924
Bio::SeqIO::abi abi trace sequence input/output stream     1.006924
Bio::SeqIO::ace ace sequence input/output stream     1.006924
Bio::SeqIO::agave AGAVE sequence output stream.     1.006924
Bio::SeqIO::alf alf trace sequence input/output stream     1.006924
Bio::SeqIO::asciitree asciitree sequence input/output stream     1.006924
Bio::SeqIO::bsml BSML sequence input/output stream     1.006924
Bio::SeqIO::bsml_sax BSML sequence input/output stream using SAX     1.006924
Bio::SeqIO::chadoxml chadoxml sequence output stream     1.006924
Bio::SeqIO::chaos chaos sequence input/output stream     1.006924
Bio::SeqIO::chaosxml chaosxml sequence input/output stream     1.006924
Bio::SeqIO::ctf ctf trace sequence input/output stream     1.006924
Bio::SeqIO::embl EMBL sequence input/output stream     1.006924
Bio::SeqIO::embldriver EMBL sequence input/output stream     1.006924
Bio::SeqIO::entrezgene Entrez Gene ASN1 parser     1.006924
Bio::SeqIO::excel sequence input/output stream from a MSExcel-formatted table     1.006924
Bio::SeqIO::exp exp trace sequence input/output stream     1.006924
Bio::SeqIO::fasta fasta sequence input/output stream     1.006924
Bio::SeqIO::fastq fastq sequence input/output stream     1.006924
Bio::SeqIO::flybase_chadoxml FlyBase variant of chadoxml with sequence output stream     1.006924
Bio::SeqIO::game a class for parsing and writing game-XML     1.006924
Bio::SeqIO::game::featHandler a class for handling feature elements     1.006924
Bio::SeqIO::game::gameHandler PerlSAX handler for game-XML     1.006924
Bio::SeqIO::game::gameSubs a base class for game-XML parsing     1.006924
Bio::SeqIO::game::gameWriter a class for writing game-XML     1.006924
Bio::SeqIO::game::seqHandler a class for handling game-XML sequences     1.006924
Bio::SeqIO::gbdriver GenBank handler-based push parser     1.006924
Bio::SeqIO::gbxml GenBank sequence input/output stream using SAX     1.006924
Bio::SeqIO::gcg GCG sequence input/output stream     1.006924
Bio::SeqIO::genbank GenBank sequence input/output stream     1.006924
Bio::SeqIO::interpro InterProScan XML input/output stream     1.006924
Bio::SeqIO::kegg KEGG sequence input/output stream     1.006924
Bio::SeqIO::largefasta method i/o on very large fasta sequence files     1.006924
Bio::SeqIO::lasergene Lasergene sequence file input/output stream     1.006924
Bio::SeqIO::locuslink LocusLink input/output stream     1.006924
Bio::SeqIO::mbsout input stream for output by Teshima et al.'s mbs.     1.006924
Bio::SeqIO::metafasta metafasta sequence input/output stream     1.006924
Bio::SeqIO::msout input stream for output by Hudson's ms     1.006924
Bio::SeqIO::nexml NeXML sequence input/output stream     1.006924
Bio::SeqIO::phd phd file input/output stream     1.006924
Bio::SeqIO::pir PIR sequence input/output stream     1.006924
Bio::SeqIO::pln pln trace sequence input/output stream     1.006924
Bio::SeqIO::qual .qual file input/output stream     1.006924
Bio::SeqIO::raw raw sequence file input/output stream     1.006924
Bio::SeqIO::scf .scf file input/output stream     1.006924
Bio::SeqIO::seqxml SeqXML sequence input/output stream     1.006924
Bio::SeqIO::strider DNA strider sequence input/output stream     1.006924
Bio::SeqIO::swiss Swissprot sequence input/output stream     1.006924
Bio::SeqIO::swissdriver SwissProt/UniProt handler-based push parser     1.006924
Bio::SeqIO::tab nearly raw sequence file input/output stream. Reads/writes id"\t"sequence"\n"     1.006924
Bio::SeqIO::table sequence input/output stream from a delimited table     1.006924
Bio::SeqIO::tigr TIGR XML sequence input/output stream     1.006924
Bio::SeqIO::tigrxml Parse TIGR (new) XML     1.006924
Bio::SeqIO::tinyseq reading/writing sequences in NCBI TinySeq format     1.006924
Bio::SeqIO::tinyseq::tinyseqHandler XML event handlers to support NCBI TinySeq XML parsing     1.006924
Bio::SeqIO::ztr ztr trace sequence input/output stream     1.006924
Bio::SeqUtils Additional methods for PrimarySeq objects     1.006924
Bio::SimpleAlign Multiple alignments held as a set of sequences     1.006924
Bio::SimpleAnalysisI A simple interface to any (local or remote) analysis tool     1.006924
Bio::Species Generic species object.     1.006924
Bio::Structure::Atom Bioperl structure Object, describes an Atom     1.006924
Bio::Structure::Chain Bioperl structure Object, describes a chain     1.006924
Bio::Structure::Entry Bioperl structure Object, describes the whole entry     1.006924
Bio::Structure::IO Handler for Structure Formats     1.006924
Bio::Structure::IO::pdb PDB input/output stream     1.006924
Bio::Structure::Model Bioperl structure Object, describes a Model     1.006924
Bio::Structure::Residue Bioperl structure Object, describes a Residue     1.006924
Bio::Structure::SecStr::DSSP::Res Module for parsing/accessing dssp output     1.006924
Bio::Structure::SecStr::STRIDE::Res Module for parsing/accessing stride output     1.006924
Bio::Structure::StructureI Abstract Interface for a Structure objects     1.006924
Bio::Symbol::Alphabet BSANE/BioCORBA compliant symbol list alphabet     1.006924
Bio::Symbol::AlphabetI A Symbol Alphabet     1.006924
Bio::Symbol::DNAAlphabet A ready made DNA alphabet     1.006924
Bio::Symbol::ProteinAlphabet A ready made Protein alphabet     1.006924
Bio::Symbol::Symbol A biological symbol     1.006924
Bio::Symbol::SymbolI Interface for a Symbol     1.006924
Bio::Taxon A node in a represented taxonomy     1.006924
Bio::Taxonomy representing Taxonomy.     1.006924
Bio::Taxonomy::FactoryI interface to define how to access NCBI Taxonoy     1.006924
Bio::Taxonomy::Node A node in a represented taxonomy     1.006924
Bio::Taxonomy::Taxon Generic Taxonomic Entity object     1.006924
Bio::Taxonomy::Tree An Organism Level Implementation of TreeI interface.     1.006924
Bio::Tools::AlignFactory Base object for alignment factories     1.006924
Bio::Tools::Alignment::Consed A module to work with objects from consed .ace files     1.006924
Bio::Tools::Alignment::Trim A kludge to do specialized trimming of sequence based on quality.     1.006924
Bio::Tools::AmpliconSearch Find amplicons in a template using degenerate PCR primers     1.006924
Bio::Tools::Analysis::DNA::ESEfinder a wrapper around ESEfinder server     1.006924
Bio::Tools::Analysis::Protein::Domcut a wrapper around Domcut server     1.006924
Bio::Tools::Analysis::Protein::ELM a wrapper around the ELM server which predicts short functional motifs on amino acid sequences     1.006924
Bio::Tools::Analysis::Protein::GOR4 a wrapper around GOR4 protein secondary structure prediction server     1.006924
Bio::Tools::Analysis::Protein::HNN a wrapper around the HNN protein secondary structure prediction server     1.006924
Bio::Tools::Analysis::Protein::Mitoprot a wrapper around Mitoprot server     1.006924
Bio::Tools::Analysis::Protein::NetPhos a wrapper around NetPhos server     1.006924
Bio::Tools::Analysis::Protein::Scansite a wrapper around the Scansite server     1.006924
Bio::Tools::Analysis::Protein::Sopma a wrapper around the Sopma protein secondary structure prediction server     1.006924
Bio::Tools::Analysis::SimpleAnalysisBase abstract superclass for SimpleAnalysis implementations     1.006924
Bio::Tools::AnalysisResult Base class for analysis result objects and parsers     1.006924
Bio::Tools::Blat parser for Blat program     1.006924
Bio::Tools::CodonTable Codon table object     1.006924
Bio::Tools::Coil parser for Coil output     1.006924
Bio::Tools::ECnumber representation of EC numbers (Enzyme Classification)     1.006924
Bio::Tools::EMBOSS::Palindrome parse EMBOSS palindrome output     1.006924
Bio::Tools::EPCR Parse ePCR output and make features     1.006924
Bio::Tools::ERPIN a parser for ERPIN output     1.006924
Bio::Tools::ESTScan Results of one ESTScan run     1.006924
Bio::Tools::Eponine Results of one Eponine run     1.006924
Bio::Tools::Est2Genome Parse est2genome output, makes simple Bio::SeqFeature::Generic objects     1.006924
Bio::Tools::Fgenesh parse results of one Fgenesh run     1.006924
Bio::Tools::FootPrinter write sequence features in FootPrinter format     1.006924
Bio::Tools::GFF A Bio::SeqAnalysisParserI compliant GFF format parser     1.006924
Bio::Tools::Gel Calculates relative electrophoretic migration distances     1.006924
Bio::Tools::Geneid Results of one geneid run     1.006924
Bio::Tools::Genemark Results of one Genemark run     1.006924
Bio::Tools::Genewise Results of one Genewise run     1.006924
Bio::Tools::Genomewise Results of one Genomewise run     1.006924
Bio::Tools::Genscan Results of one Genscan run     1.006924
Bio::Tools::Glimmer parser for Glimmer 2.X/3.X prokaryotic and GlimmerM/GlimmerHMM eukaryotic gene predictions     1.006924
Bio::Tools::Grail Results of one Grail run     1.006924
Bio::Tools::GuessSeqFormat Module for determining the sequence format of the contents of a file, a string, or through a filehandle.     1.006924
Bio::Tools::HMMER::Domain One particular domain hit from HMMER     1.006924
Bio::Tools::HMMER::Results Object representing HMMER output results     1.006924
Bio::Tools::HMMER::Set Set of identical domains from HMMER matches     1.006924
Bio::Tools::Hmmpfam Parser for Hmmpfam program     1.006924
Bio::Tools::IUPAC Generates unique sequence objects or regular expressions from an ambiguous IUPAC sequence     1.006924
Bio::Tools::Infernal A parser for Infernal output     1.006924
Bio::Tools::Lucy Object for analyzing the output from Lucy, a vector and quality trimming program from TIGR     1.006924
Bio::Tools::MZEF Results of one MZEF run     1.006924
Bio::Tools::Match Parses output from Transfac's match(TM)     1.006924
Bio::Tools::OddCodes Object holding alternative alphabet coding for one protein sequence     1.006924
Bio::Tools::Phylo::Gerp Parses output from GERP     1.006924
Bio::Tools::Phylo::Gumby Parses output from gumby     1.006924
Bio::Tools::Phylo::Molphy parser for Molphy output     1.006924
Bio::Tools::Phylo::Molphy::Result container for data parsed from a ProtML run     1.006924
Bio::Tools::Phylo::PAML Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00     1.006924
Bio::Tools::Phylo::PAML::Codeml Parses output from the PAML program codeml.     1.006924
Bio::Tools::Phylo::PAML::ModelResult A container for NSSite Model Result from PAML     1.006924
Bio::Tools::Phylo::PAML::Result A PAML result set object     1.006924
Bio::Tools::Phylo::Phylip::ProtDist parser for ProtDist output     1.006924
Bio::Tools::Prediction::Exon A predicted exon feature     1.006924
Bio::Tools::Prediction::Gene a predicted gene structure feature     1.006924
Bio::Tools::Primer3 Create input for and work with the output from the program primer3     1.006924
Bio::Tools::Primer::Assessor::Base base class for common assessor things     1.006924
Bio::Tools::Primer::AssessorI interface for assessing primer pairs     1.006924
Bio::Tools::Primer::Feature position of a single primer     1.006924
Bio::Tools::Primer::Pair two primers on left and right side     1.006924
Bio::Tools::Prints Parser for FingerPRINTScanII program     1.006924
Bio::Tools::Profile parse Profile output     1.006924
Bio::Tools::Promoterwise parser for Promoterwise tab format output     1.006924
Bio::Tools::PrositeScan Parser for ps_scan result     1.006924
Bio::Tools::Protparam submit to and parse output from protparam ;     1.006924
Bio::Tools::Pseudowise Results of one Pseudowise run     1.006924
Bio::Tools::QRNA A Parser for qrna output     1.006924
Bio::Tools::RNAMotif A parser for RNAMotif output     1.006924
Bio::Tools::RandomDistFunctions A set of routines useful for generating random data in different distributions     1.006924
Bio::Tools::RepeatMasker a parser for RepeatMasker output     1.006924
Bio::Tools::Run::GenericParameters An object for the parameters used to run programs     1.006924
Bio::Tools::Run::ParametersI A Base object for the parameters used to run programs     1.006924
Bio::Tools::Run::RemoteBlast Object for remote execution of the NCBI Blast via HTTP     1.006924
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.     1.006924
Bio::Tools::Run::StandAloneNCBIBlast Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). With experimental support for NCBI rpsblast.     1.006924
Bio::Tools::Run::StandAloneWUBlast Object for the local execution of WU-Blast.     1.006924
Bio::Tools::Run::WrapperBase A Base object for wrappers around executables     1.006924
Bio::Tools::Seg parse seg output     1.006924
Bio::Tools::SeqPattern represent a sequence pattern or motif     1.006924
Bio::Tools::SeqPattern::Backtranslate     1.006924
Bio::Tools::SeqStats Object holding statistics for one particular sequence     1.006924
Bio::Tools::SeqWords Object holding n-mer statistics for a sequence     1.006924
Bio::Tools::SiRNA Perl object for designing small inhibitory RNAs.     1.006924
Bio::Tools::SiRNA::Ruleset::saigo Perl object implementing the Saigo group's rules for designing small inhibitory RNAs     1.006924
Bio::Tools::SiRNA::Ruleset::tuschl Perl object implementing the tuschl group's rules for designing small inhibitory RNAs     1.006924
Bio::Tools::Sigcleave Bioperl object for sigcleave analysis     1.006924
Bio::Tools::Signalp parser for Signalp output     1.006924
Bio::Tools::Signalp::ExtendedSignalp enhanced parser for Signalp output     1.006924
Bio::Tools::Sim4::Exon A single exon determined by an alignment     1.006924
Bio::Tools::Sim4::Results Results of one Sim4 run     1.006924
Bio::Tools::Spidey::Exon A single exon determined by an alignment     1.006924
Bio::Tools::Spidey::Results Results of a Spidey run     1.006924
Bio::Tools::TandemRepeatsFinder a parser for Tandem Repeats Finder output     1.006924
Bio::Tools::TargetP Results of one TargetP run     1.006924
Bio::Tools::Tmhmm parse TMHMM output (TransMembrane HMM)     1.006924
Bio::Tools::dpAlign Perl extension to do pairwise dynamic programming sequence alignment     1.006924
Bio::Tools::ipcress Parse ipcress output and make features     1.006924
Bio::Tools::isPcr Parse isPcr output and make features     1.006924
Bio::Tools::pICalculator calculate the isoelectric point of a protein     1.006924
Bio::Tools::pSW pairwise Smith Waterman object     1.006924
Bio::Tools::tRNAscanSE A parser for tRNAscan-SE output     1.006924
Bio::Tree::AlleleNode A Node with Alleles attached     1.006924
Bio::Tree::AnnotatableNode A Tree Node with support for annotation     1.006924
Bio::Tree::Compatible Testing compatibility of phylogenetic trees with nested taxa.     1.006924
Bio::Tree::DistanceFactory Construct a tree using distance based methods     1.006924
Bio::Tree::Draw::Cladogram Drawing phylogenetic trees in Encapsulated PostScript (EPS) format.     1.006924
Bio::Tree::Node A Simple Tree Node     1.006924
Bio::Tree::NodeI Interface describing a Tree Node     1.006924
Bio::Tree::NodeNHX A Simple Tree Node with support for NHX tags     1.006924
Bio::Tree::RandomFactory TreeFactory for generating Random Trees     1.006924
Bio::Tree::Statistics Calculate certain statistics for a Tree     1.006924
Bio::Tree::Tree An implementation of the TreeI interface.     1.006924
Bio::Tree::TreeFunctionsI Decorated Interface implementing basic Tree exploration methods     1.006924
Bio::Tree::TreeI A Tree object suitable for lots of things, designed originally for Phylogenetic Trees.     1.006924
Bio::TreeIO Parser for Tree files     1.006924
Bio::TreeIO::NewickParser which implements a newick string parser as a finite state machine which enables it to parse the full Newick specification.     1.006924
Bio::TreeIO::TreeEventBuilder Build Bio::Tree::Tree's and Bio::Tree::Node's from Events     1.006924
Bio::TreeIO::cluster A TreeIO driver module for parsing Algorithm::Cluster::treecluster() output     1.006924
Bio::TreeIO::lintree Parser for lintree output trees     1.006924
Bio::TreeIO::newick     1.006924
Bio::TreeIO::nexml A TreeIO driver module for parsing NeXML tree files     1.006924
Bio::TreeIO::nexus A TreeIO driver module for parsing Nexus tree output from PAUP     1.006924
Bio::TreeIO::nhx TreeIO implementation for parsing Newick/New Hampshire eXtendend (NHX) format.     1.006924
Bio::TreeIO::pag Bio::TreeIO driver for Pagel format     1.006924
Bio::TreeIO::phyloxml TreeIO implementation for parsing PhyloXML format.     1.006924
Bio::TreeIO::svggraph A simple output format that converts a Tree object to an SVG output     1.006924
Bio::TreeIO::tabtree A simple output format which displays a tree as an ASCII drawing     1.006924
Bio::UpdateableSeqI Descendant of Bio::SeqI that allows updates     1.006924
Bio::Variation::AAChange Sequence change class for polypeptides     1.006924
Bio::Variation::AAReverseMutate point mutation and codon information from single amino acid changes     1.006924
Bio::Variation::Allele Sequence object with allele-specific attributes     1.006924
Bio::Variation::DNAMutation DNA level mutation class     1.006924
Bio::Variation::IO Handler for sequence variation IO Formats     1.006924
Bio::Variation::IO::flat flat file sequence variation input/output stream     1.006924
Bio::Variation::IO::xml XML sequence variation input/output stream     1.006924
Bio::Variation::RNAChange Sequence change class for RNA level     1.006924
Bio::Variation::SNP submitted SNP     1.006924
Bio::Variation::SeqDiff Container class for mutation/variant descriptions     1.006924
Bio::Variation::VariantI Sequence Change SeqFeature abstract class     1.006924
Bio::WebAgent A base class for Web (any protocol) access     1.006924
BioPerl Perl Modules for Biology      
Deobfuscator get BioPerl method and package information from a Berkeley DB     0.0.3
FeatureStore     1.006924
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*  
[[%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