Christopher Fields > BioPerl

BioPerl

This Release BioPerl-1.007001  [Download] [Browse 05 Nov 2016
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License The Perl 5 License (Artistic 1 & GPL 1)
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MANIFEST
META.json

Modules

Bio::Align::AlignI An interface for describing sequence alignments.     1.007001
Bio::Align::DNAStatistics Calculate some statistics for a DNA alignment     1.007001
Bio::Align::Graphics Graphic Rendering of Bio::Align::AlignI Objects     1.007001
Bio::Align::PairwiseStatistics Base statistic object for Pairwise Alignments     1.007001
Bio::Align::ProteinStatistics Calculate Protein Alignment statistics (mostly distances)     1.007001
Bio::Align::StatisticsI Calculate some statistics for an alignment     1.007001
Bio::Align::Utilities A collection of utilities regarding converting and manipulating alignment objects     1.007001
Bio::AlignIO Handler for AlignIO Formats     1.007001
Bio::AlignIO::Handler::GenericAlignHandler Bio::HandlerI-based generic data handler class for alignment-based data     1.007001
Bio::AlignIO::arp ARP MSA Sequence input/output stream     1.007001
Bio::AlignIO::bl2seq bl2seq sequence input/output stream     1.007001
Bio::AlignIO::clustalw clustalw sequence input/output stream     1.007001
Bio::AlignIO::emboss Parse EMBOSS alignment output (from applications water and needle)     1.007001
Bio::AlignIO::fasta fasta MSA Sequence input/output stream     1.007001
Bio::AlignIO::largemultifasta Largemultifasta MSA Sequence input/output stream     1.007001
Bio::AlignIO::maf Multiple Alignment Format sequence input stream     1.007001
Bio::AlignIO::mase mase sequence input/output stream     1.007001
Bio::AlignIO::mega Parse and Create MEGA format data files     1.007001
Bio::AlignIO::meme meme sequence input/output stream     1.007001
Bio::AlignIO::metafasta Metafasta MSA Sequence input/output stream     1.007001
Bio::AlignIO::msf msf sequence input/output stream     1.007001
Bio::AlignIO::nexml NeXML format sequence alignment input/output stream driver     1.007001
Bio::AlignIO::nexus NEXUS format sequence input/output stream     1.007001
Bio::AlignIO::pfam pfam sequence input/output stream     1.007001
Bio::AlignIO::phylip PHYLIP format sequence input/output stream     1.007001
Bio::AlignIO::po po MSA Sequence input/output stream     1.007001
Bio::AlignIO::proda proda sequence input/output stream     1.007001
Bio::AlignIO::prodom prodom sequence input/output stream     1.007001
Bio::AlignIO::psi Read/Write PSI-BLAST profile alignment files     1.007001
Bio::AlignIO::selex selex sequence input/output stream     1.007001
Bio::AlignIO::stockholm stockholm sequence input/output stream     1.007001
Bio::AlignIO::xmfa XMFA MSA Sequence input/output stream     1.007001
Bio::AnalysisI An interface to any (local or remote) analysis tool     1.007001
Bio::AnalysisI::JobI     1.007001
Bio::AnalysisParserI Generic analysis output parser interface     1.007001
Bio::AnalysisResultI Interface for analysis result objects     1.007001
Bio::AnnotatableI the base interface an annotatable object must implement     1.007001
Bio::Annotation::AnnotationFactory Instantiates a new Bio::AnnotationI (or derived class) through a factory     1.007001
Bio::Annotation::Collection Default Perl implementation of AnnotationCollectionI     1.007001
Bio::Annotation::Comment A comment object, holding text     1.007001
Bio::Annotation::DBLink untyped links between databases     1.007001
Bio::Annotation::OntologyTerm An ontology term adapted to AnnotationI     1.007001
Bio::Annotation::Reference Specialised DBLink object for Literature References     1.007001
Bio::Annotation::Relation Relationship (pairwise) with other objects SeqI and NodeI;     1.007001
Bio::Annotation::SimpleValue A simple scalar     1.007001
Bio::Annotation::StructuredValue A scalar with embedded structured information     1.007001
Bio::Annotation::TagTree AnnotationI with tree-like hierarchal key-value relationships ('structured tags') that can be represented as simple text.     1.007001
Bio::Annotation::Target Provides an object which represents a target (ie, a similarity hit) from one object to something in another database     1.007001
Bio::Annotation::Tree Provide a tree as an annotation to a Bio::AnnotatableI object     1.007001
Bio::Annotation::TypeManager Manages types for annotation collections     1.007001
Bio::AnnotationCollectionI Interface for annotation collections     1.007001
Bio::AnnotationI Annotation interface     1.007001
Bio::Assembly::Contig Perl module to hold and manipulate sequence assembly contigs.     1.007001
Bio::Assembly::ContigAnalysis Perform analysis on sequence assembly contigs.     1.007001
Bio::Assembly::IO Handler for Assembly::IO Formats     1.007001
Bio::Assembly::IO::ace module to load ACE files from various assembly programs     1.007001
Bio::Assembly::IO::bowtie An IO module for assemblies in Bowtie format *BETA*     1.007001
Bio::Assembly::IO::maq Driver to read assembly files in maq format *BETA*     1.007001
Bio::Assembly::IO::phrap driver to load phrap.out files.     1.007001
Bio::Assembly::IO::sam An IO module for assemblies in Sam format *BETA*     1.007001
Bio::Assembly::IO::tigr Driver to read and write assembly files in the TIGR Assembler v2 default format.     1.007001
Bio::Assembly::Scaffold Perl module to hold and manipulate sequence assembly data.     1.007001
Bio::Assembly::ScaffoldI Abstract Inteface of Sequence Assemblies     1.007001
Bio::Assembly::Singlet Perl module to hold and manipulate singlets from sequence assembly contigs.     1.007001
Bio::Assembly::Tools::ContigSpectrum create and manipulate contig spectra     1.007001
Bio::Cluster::ClusterFactory Instantiates a new Bio::ClusterI (or derived class) through a factory     1.007001
Bio::Cluster::FamilyI Family Interface     1.007001
Bio::Cluster::SequenceFamily Sequence Family object     1.007001
Bio::Cluster::UniGene UniGene object     1.007001
Bio::Cluster::UniGeneI abstract interface of UniGene object     1.007001
Bio::ClusterI Cluster Interface     1.007001
Bio::ClusterIO Handler for Cluster Formats     1.007001
Bio::ClusterIO::dbsnp dbSNP input stream     1.007001
Bio::ClusterIO::unigene UniGene input stream     1.007001
Bio::CodonUsage::IO for reading and writing codon usage tables to file     1.007001
Bio::CodonUsage::Table for access to the Codon usage Database at http://www.kazusa.or.jp/codon.     1.007001
Bio::DB::Ace Database object interface to ACeDB servers     1.007001
Bio::DB::BioFetch Database object interface to BioFetch retrieval     1.007001
Bio::DB::CUTG for access to the Codon usage Database at http://www.kazusa.or.jp/codon.     1.007001
Bio::DB::DBFetch Database object for retrieving using the dbfetch script     1.007001
Bio::DB::EMBL Database object interface for EMBL entry retrieval     1.007001
Bio::DB::EntrezGene Database object interface to Entrez Gene     1.007001
Bio::DB::Expression DESCRIPTION of Object     1.007001
Bio::DB::Expression::geo *** DESCRIPTION of Class     1.007001
Bio::DB::Failover A Bio::DB::RandomAccessI compliant class which wraps a prioritized list of DBs     1.007001
Bio::DB::Fasta Fast indexed access to fasta files     1.007001
Bio::DB::Fasta::Subdir     1.007001
Bio::DB::FileCache In file cache for BioSeq objects     1.007001
Bio::DB::Flat Interface for indexed flat files     1.007001
Bio::DB::Flat::BDB Interface for BioHackathon standard BDB-indexed flat file     1.007001
Bio::DB::Flat::BDB::embl embl adaptor for Open-bio standard BDB-indexed flat file     1.007001
Bio::DB::Flat::BDB::fasta fasta adaptor for Open-bio standard BDB-indexed flat file     1.007001
Bio::DB::Flat::BDB::genbank genbank adaptor for Open-bio standard BDB-indexed flat file     1.007001
Bio::DB::Flat::BDB::swiss swissprot adaptor for Open-bio standard BDB-indexed flat file     1.007001
Bio::DB::Flat::BinarySearch BinarySearch search indexing system for sequence files     1.007001
Bio::DB::GFF Storage and retrieval of sequence annotation data     1.007001
Bio::DB::GFF::Adaptor::ace ace interface (for multiple inheritance)     1.007001
Bio::DB::GFF::Adaptor::berkeleydb Bio::DB::GFF database adaptor for in-memory databases     1.007001
Bio::DB::GFF::Adaptor::berkeleydb::iterator iterator for Bio::DB::GFF::Adaptor::berkeleydb     1.007001
Bio::DB::GFF::Adaptor::biofetch Cache BioFetch objects in a Bio::DB::GFF database     1.007001
Bio::DB::GFF::Adaptor::biofetch_oracle Cache BioFetch objects in a Bio::DB::GFF database     1.007001
Bio::DB::GFF::Adaptor::dbi Database adaptor for DBI (SQL) databases     1.007001
Bio::DB::GFF::Adaptor::dbi::caching_handle Cache for database handles     1.007001
Bio::DB::GFF::Adaptor::dbi::faux_dbh     1.007001
Bio::DB::GFF::Adaptor::dbi::iterator iterator for Bio::DB::GFF::Adaptor::dbi     1.007001
Bio::DB::GFF::Adaptor::dbi::mysql Database adaptor for a specific mysql schema     1.007001
Bio::DB::GFF::Adaptor::dbi::mysqlace Unholy union between mysql GFF database and acedb database     1.007001
Bio::DB::GFF::Adaptor::dbi::mysqlcmap Database adaptor for an integraded CMap/GBrowse mysql schema     1.007001
Bio::DB::GFF::Adaptor::dbi::mysqlopt Deprecated database adaptor     1.007001
Bio::DB::GFF::Adaptor::dbi::oracle Database adaptor for a specific oracle schema     1.007001
Bio::DB::GFF::Adaptor::dbi::oracleace Unholy union between oracle GFF database and acedb database     1.007001
Bio::DB::GFF::Adaptor::dbi::pg Database adaptor for a specific postgres schema     1.007001
Bio::DB::GFF::Adaptor::dbi::pg_fts Database adaptor for a specific postgres schema with a TSearch2 implementation     1.007001
Bio::DB::GFF::Adaptor::memory Bio::DB::GFF database adaptor for in-memory databases     1.007001
Bio::DB::GFF::Adaptor::memory::feature_serializer utility methods for serializing and deserializing GFF features     1.007001
Bio::DB::GFF::Adaptor::memory::iterator iterator for Bio::DB::GFF::Adaptor::memory     1.007001
Bio::DB::GFF::Aggregator Aggregate GFF groups into composite features     1.007001
Bio::DB::GFF::Aggregator::alignment Alignment aggregator     1.007001
Bio::DB::GFF::Aggregator::clone Clone aggregator     1.007001
Bio::DB::GFF::Aggregator::coding The Coding Region Aggregator     1.007001
Bio::DB::GFF::Aggregator::gene Sequence Ontology Geene     1.007001
Bio::DB::GFF::Aggregator::match Match aggregator     1.007001
Bio::DB::GFF::Aggregator::none No aggregation     1.007001
Bio::DB::GFF::Aggregator::orf An aggregator for orf regions     1.007001
Bio::DB::GFF::Aggregator::processed_transcript Sequence Ontology Transcript     1.007001
Bio::DB::GFF::Aggregator::so_transcript Sequence Ontology Transcript     1.007001
Bio::DB::GFF::Aggregator::transcript Transcript aggregator     1.007001
Bio::DB::GFF::Aggregator::ucsc_acembly UCSC acembly aggregator     1.007001
Bio::DB::GFF::Aggregator::ucsc_ensgene UCSC ensGene aggregator     1.007001
Bio::DB::GFF::Aggregator::ucsc_genscan UCSC genscan aggregator     1.007001
Bio::DB::GFF::Aggregator::ucsc_refgene UCSC refGene aggregator     1.007001
Bio::DB::GFF::Aggregator::ucsc_sanger22 UCSC sanger22 aggregator     1.007001
Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo UCSC sanger22pseudo aggregator     1.007001
Bio::DB::GFF::Aggregator::ucsc_softberry UCSC softberry aggregator     1.007001
Bio::DB::GFF::Aggregator::ucsc_twinscan UCSC twinscan aggregator     1.007001
Bio::DB::GFF::Aggregator::ucsc_unigene UCSC UniGene aggregator     1.007001
Bio::DB::GFF::Featname The name of a feature     1.007001
Bio::DB::GFF::Feature A relative segment identified by a feature type     1.007001
Bio::DB::GFF::FeatureIterator     1.007001
Bio::DB::GFF::Homol A segment of DNA that is homologous to another     1.007001
Bio::DB::GFF::ID_Iterator     1.007001
Bio::DB::GFF::RelSegment Sequence segment with relative coordinate support     1.007001
Bio::DB::GFF::Segment Simple DNA segment object     1.007001
Bio::DB::GFF::Typename The name of a feature type     1.007001
Bio::DB::GFF::Util::Binning binning utility for Bio::DB::GFF index     1.007001
Bio::DB::GFF::Util::Rearrange rearrange utility     1.007001
Bio::DB::GenBank Database object interface to GenBank     1.007001
Bio::DB::GenPept Database object interface to GenPept     1.007001
Bio::DB::GenericWebAgent helper base class for parameter-based remote server access and response retrieval.     1.007001
Bio::DB::HIV Database object interface to the Los Alamos HIV Sequence Database     1.007001
Bio::DB::HIV::HIVAnnotProcessor Adds HIV-specific annotations to Bio::SeqIO streams     1.007001
Bio::DB::HIV::HIVQueryHelper Routines and packages used by Bio::DB::HIV and Bio::DB::Query::HIVQuery     1.007001
Bio::DB::InMemoryCache Abstract interface for a sequence database     1.007001
Bio::DB::Indexed::Stream     1.007001
Bio::DB::IndexedBase Base class for modules using indexed sequence files     1.007001
Bio::DB::LocationI A RandomAccessI-like abstract interface for retrieving location data from a sequence database and returning Bio::LocationI objects     1.007001
Bio::DB::MeSH Term retrieval from a Web MeSH database     1.007001
Bio::DB::NCBIHelper A collection of routines useful for queries to NCBI databases.     1.007001
Bio::DB::Qual Fast indexed access to quality files     1.007001
Bio::DB::Query::GenBank Build a GenBank Entrez Query     1.007001
Bio::DB::Query::HIVQuery Query interface to the Los Alamos HIV Sequence Database     1.007001
Bio::DB::Query::WebQuery Helper class for web-based sequence queryies     1.007001
Bio::DB::QueryI Object Interface to queryable sequence databases     1.007001
Bio::DB::RandomAccessI Abstract interface for a sequence database     1.007001
Bio::DB::RefSeq Database object interface for RefSeq retrieval     1.007001
Bio::DB::ReferenceI A RandomAccessI-like abstract interface for retrieving Reference data from a sequence database and returning Bio::Annotation::Reference objects     1.007001
Bio::DB::Registry Access to the Open Bio Database Access registry scheme     1.007001
Bio::DB::SeqFeature Normalized feature for use with Bio::DB::SeqFeature::Store     1.007001
Bio::DB::SeqFeature::NormalizedFeature Normalized feature for use with Bio::DB::SeqFeature::Store     1.007001
Bio::DB::SeqFeature::NormalizedFeatureI Interface for normalized features     1.007001
Bio::DB::SeqFeature::NormalizedTableFeatureI Interface for normalized features whose hierarchy is stored in a table     1.007001
Bio::DB::SeqFeature::Segment Location-based access to genome annotation data     1.007001
Bio::DB::SeqFeature::Store Storage and retrieval of sequence annotation data     1.007001
Bio::DB::SeqFeature::Store::DBI::Iterator utility methods for creating and iterating over SeqFeature records     1.007001
Bio::DB::SeqFeature::Store::DBI::Pg PostgreSQL implementation of Bio::DB::SeqFeature::Store     1.007001
Bio::DB::SeqFeature::Store::DBI::SQLite SQLite implementation of Bio::DB::SeqFeature::Store     1.007001
Bio::DB::SeqFeature::Store::DBI::mysql Mysql implementation of Bio::DB::SeqFeature::Store     1.007001
Bio::DB::SeqFeature::Store::FeatureFileLoader feature file loader for Bio::DB::SeqFeature::Store     1.007001
Bio::DB::SeqFeature::Store::FeatureIterator     1.007001
Bio::DB::SeqFeature::Store::GFF2Loader GFF2 file loader for Bio::DB::SeqFeature::Store     1.007001
Bio::DB::SeqFeature::Store::GFF3Loader GFF3 file loader for Bio::DB::SeqFeature::Store     1.007001
Bio::DB::SeqFeature::Store::LoadHelper Internal utility for Bio::DB::SeqFeature::Store     1.12
Bio::DB::SeqFeature::Store::Loader Loader     1.007001
Bio::DB::SeqFeature::Store::bdb fetch and store objects from a BerkeleyDB     1.007001
Bio::DB::SeqFeature::Store::berkeleydb Storage and retrieval of sequence annotation data in Berkeleydb files     1.007001
Bio::DB::SeqFeature::Store::berkeleydb3 Storage and retrieval of sequence annotation data in Berkeleydb files     1.007001
Bio::DB::SeqFeature::Store::berkeleydb::Iterator     1.007001
Bio::DB::SeqFeature::Store::memory In-memory implementation of Bio::DB::SeqFeature::Store     1.007001
Bio::DB::SeqFeature::Store::memory::Iterator     1.007001
Bio::DB::SeqI Abstract Interface for Sequence databases     1.007001
Bio::DB::SeqVersion front end to querying databases for identifier versions     1.007001
Bio::DB::SeqVersion::gi interface to NCBI Sequence Revision History page     1.007001
Bio::DB::SwissProt Database object interface to SwissProt retrieval     1.007001
Bio::DB::TFBS Access to a Transcription Factor Binding Site database     1.007001
Bio::DB::TFBS::transfac_pro An implementation of Bio::DB::TFBS which uses local flat files for transfac pro     1.007001
Bio::DB::Taxonomy Access to a taxonomy database     1.007001
Bio::DB::Taxonomy::entrez Taxonomy Entrez driver     1.007001
Bio::DB::Taxonomy::flatfile Use the NCBI taxonomy from local indexed flat files     1.007001
Bio::DB::Taxonomy::greengenes Use the Greengenes taxonomy     1.007001
Bio::DB::Taxonomy::list An implementation of Bio::DB::Taxonomy that accepts lists of words to build a database     1.007001
Bio::DB::Taxonomy::silva Use the Silva taxonomy     1.007001
Bio::DB::Taxonomy::sqlite SQLite-based implementation of Bio::DB::Taxonomy::flatfile     1.007001
Bio::DB::Universal Artificial database that delegates to specific databases     1.007001
Bio::DB::UpdateableSeqI An interface for writing to a database of sequences.     1.007001
Bio::DB::WebDBSeqI Object Interface to generalize Web Databases for retrieving sequences     1.007001
Bio::DBLinkContainerI Abstract interface for any object wanting to use database cross references     1.007001
Bio::Das::FeatureTypeI Simple interface to Sequence Ontology feature types     1.007001
Bio::Das::SegmentI DAS-style access to a feature database     1.007001
Bio::DasI DAS-style access to a feature database     1.007001
Bio::DescribableI interface for objects with human readable names and descriptions     1.007001
Bio::Draw::Pictogram generate SVG output of Pictogram display for consensus motifs     1.007001
Bio::Event::EventGeneratorI This interface describes the basic event generator class.     1.007001
Bio::Event::EventHandlerI An Event Handler Interface     1.007001
Bio::Factory::AnalysisI An interface to analysis tool factory     1.007001
Bio::Factory::ApplicationFactoryI Interface class for Application Factories     1.007001
Bio::Factory::DriverFactory Base class for factory classes loading drivers     1.007001
Bio::Factory::FTLocationFactory A FeatureTable Location Parser     1.007001
Bio::Factory::LocationFactoryI A factory interface for generating locations from a string     1.007001
Bio::Factory::MapFactoryI A Factory for getting markers     1.007001
Bio::Factory::ObjectBuilderI Interface for an object builder     1.007001
Bio::Factory::ObjectFactory Instantiates a new Bio::Root::RootI (or derived class) through a factory     1.007001
Bio::Factory::ObjectFactoryI A General object creator factory     1.007001
Bio::Factory::SeqAnalysisParserFactory class capable of creating SeqAnalysisParserI compliant parsers     1.007001
Bio::Factory::SeqAnalysisParserFactoryI interface describing objects capable of creating SeqAnalysisParserI compliant parsers     1.007001
Bio::Factory::SequenceFactoryI This interface allows for generic building of sequences in factories which create sequences (like SeqIO)     1.007001
Bio::Factory::SequenceProcessorI Interface for chained sequence processing algorithms     1.007001
Bio::Factory::SequenceStreamI Interface describing the basics of a Sequence Stream.     1.007001
Bio::Factory::TreeFactoryI Factory Interface for getting and writing trees from/to a data stream     1.007001
Bio::FeatureHolderI the base interface an object with features must implement     1.007001
Bio::HandlerBaseI Interface class for handler methods which interact with any event-driven parsers (drivers).     1.007001
Bio::IdCollectionI interface for objects with multiple identifiers     1.007001
Bio::IdentifiableI interface for objects with identifiers     1.007001
Bio::Index::Abstract Abstract interface for indexing a flat file     1.007001
Bio::Index::AbstractSeq base class for AbstractSeq     1.007001
Bio::Index::Blast Indexes Blast reports and supports retrieval based on query accession(s)     1.007001
Bio::Index::BlastTable Indexes tabular Blast reports (-m 8 or -m 9 format) and supports retrieval based on query accession(s)     1.007001
Bio::Index::EMBL Interface for indexing (multiple) EMBL/Swissprot .dat files (i.e. flat file EMBL/Swissprot format).     1.007001
Bio::Index::Fasta Interface for indexing (multiple) fasta files     1.007001
Bio::Index::Fastq Interface for indexing (multiple) fastq files     1.007001
Bio::Index::GenBank Interface for indexing one or more GenBank files (i.e. flat file GenBank format).     1.007001
Bio::Index::Hmmer indexes HMMER reports and supports retreival based on query     1.007001
Bio::Index::Qual Interface for indexing (multiple) fasta qual files     1.007001
Bio::Index::Stockholm     1.007001
Bio::Index::SwissPfam Interface for indexing swisspfam files     1.007001
Bio::Index::Swissprot Interface for indexing one or more Swissprot files.     1.007001
Bio::LiveSeq::AARange AARange abstract class for LiveSeq     1.007001
Bio::LiveSeq::Chain DoubleChain DataStructure for Perl     1.007001
Bio::LiveSeq::ChainI Double linked chain data structure     1.007001
Bio::LiveSeq::DNA DNA object for LiveSeq     1.007001
Bio::LiveSeq::Exon Range abstract class for LiveSeq     1.007001
Bio::LiveSeq::Gene Range abstract class for LiveSeq     1.007001
Bio::LiveSeq::IO::BioPerl Loader for LiveSeq from EMBL entries with BioPerl     1.007001
Bio::LiveSeq::IO::Loader Parent Loader for LiveSeq     1.007001
Bio::LiveSeq::Intron Range abstract class for LiveSeq     1.007001
Bio::LiveSeq::Mutation Mutation event descriptor class     1.007001
Bio::LiveSeq::Mutator Package mutating LiveSequences     1.007001
Bio::LiveSeq::Prim_Transcript Prim_Transcript class for LiveSeq     1.007001
Bio::LiveSeq::Range Range abstract class for LiveSeq     1.007001
Bio::LiveSeq::Repeat_Region Repeat_Region class for LiveSeq     1.007001
Bio::LiveSeq::Repeat_Unit Repeat_Unit class for LiveSeq     1.007001
Bio::LiveSeq::SeqI Abstract sequence interface class for LiveSeq     1.007001
Bio::LiveSeq::Transcript Transcript class for LiveSeq     1.007001
Bio::LiveSeq::Translation Translation class for LiveSeq     1.007001
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.     1.007001
Bio::Location::Atomic Implementation of a Atomic Location on a Sequence     1.007001
Bio::Location::AvWithinCoordPolicy class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise     1.007001
Bio::Location::CoordinatePolicyI Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location     1.007001
Bio::Location::Fuzzy Implementation of a Location on a Sequence which has unclear start and/or end locations     1.007001
Bio::Location::FuzzyLocationI Abstract interface of a Location on a Sequence which has unclear start/end location     1.007001
Bio::Location::NarrowestCoordPolicy class implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range     1.007001
Bio::Location::Simple Implementation of a Simple Location on a Sequence     1.007001
Bio::Location::Split Implementation of a Location on a Sequence which has multiple locations (start/end points)     1.007001
Bio::Location::SplitLocationI Abstract interface of a Location on a Sequence which has multiple locations (start/end points)     1.007001
Bio::Location::WidestCoordPolicy class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable range     1.007001
Bio::LocationI Abstract interface of a Location on a Sequence     1.007001
Bio::Map::Clone An central map object representing a clone     1.007001
Bio::Map::Contig A MapI implementation handling the contigs of a Physical Map (such as FPC)     1.007001
Bio::Map::CytoMap A Bio::MapI compliant map implementation handling cytogenic bands     1.007001
Bio::Map::CytoMarker An object representing a marker.     1.007001
Bio::Map::CytoPosition Marker class with cytogenetic band storing attributes     1.007001
Bio::Map::EntityI An Entity Interface     1.007001
Bio::Map::FPCMarker An central map object representing a marker     1.007001
Bio::Map::Gene An gene modelled as a mappable element.     1.007001
Bio::Map::GeneMap A MapI implementation to represent the area around a gene     1.007001
Bio::Map::GenePosition A typed position, suitable for modelling the various regions of a gene.     1.007001
Bio::Map::GeneRelative Represents being relative to named sub-regions of a gene.     1.007001
Bio::Map::LinkageMap A representation of a genetic linkage map.     1.007001
Bio::Map::LinkagePosition Create a Position for a Marker that will be placed on a Bio::Map::LinkageMap     1.007001
Bio::Map::MapI Interface for describing Map objects in bioperl     1.007001
Bio::Map::Mappable An object representing a generic map element that can have multiple locations in several maps.     1.007001
Bio::Map::MappableI An object that can be placed in a map     1.007001
Bio::Map::Marker An central map object representing a generic marker that can have multiple location in several maps.     1.007001
Bio::Map::MarkerI Interface for basic marker functionality     1.007001
Bio::Map::Microsatellite An object representing a Microsatellite marker.     1.007001
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.     1.007001
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.     1.007001
Bio::Map::Physical A class for handling a Physical Map (such as FPC)     1.007001
Bio::Map::Position A single position of a Marker, or the range over which that marker lies, in a Map     1.007001
Bio::Map::PositionHandler A Position Handler Implementation     1.007001
Bio::Map::PositionHandlerI A Position Handler Interface     1.007001
Bio::Map::PositionI Abstracts the notion of a position having a value in the context of a marker and a Map     1.007001
Bio::Map::PositionWithSequence A position with a sequence.     1.007001
Bio::Map::Prediction An object representing the predictions of something that can have multiple locations in several maps.     1.007001
Bio::Map::Relative Represents what a Position's coordiantes are relative to.     1.007001
Bio::Map::RelativeI Interface for describing what a Position's coordiantes are relative to.     1.007001
Bio::Map::SimpleMap A MapI implementation handling the basics of a Map     1.007001
Bio::Map::TranscriptionFactor A transcription factor modelled as a mappable element     1.007001
Bio::MapIO A Map Factory object     1.007001
Bio::MapIO::fpc A FPC Map reader     1.007001
Bio::MapIO::mapmaker A Mapmaker Map reader     1.007001
Bio::Matrix::Generic A generic matrix implementation     1.007001
Bio::Matrix::IO A factory for Matrix parsing     1.007001
Bio::Matrix::IO::mlagan A parser for the mlagan substitution matrix     1.007001
Bio::Matrix::IO::phylip A parser for PHYLIP distance matricies     1.007001
Bio::Matrix::IO::scoring A parser for PAM/BLOSUM matricies     1.007001
Bio::Matrix::MatrixI An interface for describing a Matrix     1.007001
Bio::Matrix::Mlagan A generic matrix with mlagan fields     1.007001
Bio::Matrix::PSM::IO PSM parser     1.007001
Bio::Matrix::PSM::IO::mast PSM mast parser implementation     1.007001
Bio::Matrix::PSM::IO::masta motif fasta format parser     1.007001
Bio::Matrix::PSM::IO::meme PSM meme parser implementation     1.007001
Bio::Matrix::PSM::IO::psiblast PSM psiblast parser     1.007001
Bio::Matrix::PSM::IO::transfac PSM transfac parser     1.007001
Bio::Matrix::PSM::InstanceSite A PSM site occurance     1.007001
Bio::Matrix::PSM::InstanceSiteI InstanceSite interface, holds an instance of a PSM     1.007001
Bio::Matrix::PSM::ProtMatrix SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) with log-odds scoring information.     1.007001
Bio::Matrix::PSM::ProtPsm handle combination of site matricies     1.007001
Bio::Matrix::PSM::Psm handle combination of site matricies     1.007001
Bio::Matrix::PSM::PsmHeader PSM mast parser implementation     1.007001
Bio::Matrix::PSM::PsmHeaderI handles the header data from a PSM file     1.007001
Bio::Matrix::PSM::PsmI abstract interface to handler of site matricies     1.007001
Bio::Matrix::PSM::SiteMatrix SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds     1.007001
Bio::Matrix::PSM::SiteMatrixI SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds     1.007001
Bio::Matrix::PhylipDist A Phylip Distance Matrix object     1.007001
Bio::Matrix::Scoring Object which can hold scoring matrix information     1.007001
Bio::MolEvol::CodonModel Codon Evolution Models     1.007001
Bio::Nexml::Factory A factory module for creating BioPerl and Bio::Phylo objects from/to nexml documents     1.007001
Bio::NexmlIO stream handler for NeXML documents     1.007001
Bio::Ontology::DocumentRegistry Keep track of where to find ontologies. Allows lookups by name.     1.007001
Bio::Ontology::GOterm representation of GO terms     1.007001
Bio::Ontology::InterProTerm Implementation of InterProI term interface     1.007001
Bio::Ontology::OBOEngine An Ontology Engine for OBO style flat file format from the Gene Ontology Consortium     1.007001
Bio::Ontology::OBOterm representation of OBO terms     1.007001
Bio::Ontology::Ontology standard implementation of an Ontology     1.007001
Bio::Ontology::OntologyEngineI Interface a minimal Ontology implementation should satisfy     1.007001
Bio::Ontology::OntologyI Interface for an ontology implementation     1.007001
Bio::Ontology::OntologyStore A repository of ontologies     1.007001
Bio::Ontology::Path a path for an ontology term graph     1.007001
Bio::Ontology::PathI Interface for a path between ontology terms     1.007001
Bio::Ontology::Relationship a relationship for an ontology     1.007001
Bio::Ontology::RelationshipFactory Instantiates a new Bio::Ontology::RelationshipI (or derived class) through a factory     1.007001
Bio::Ontology::RelationshipI Interface for a relationship between ontology terms     1.007001
Bio::Ontology::RelationshipType a relationship type for an ontology     1.007001
Bio::Ontology::SimpleGOEngine::GraphAdaptor Graph adaptor for Bio::Ontology::SimpleGOEngine     1.007001
Bio::Ontology::SimpleOntologyEngine Implementation of OntologyEngineI interface     1.007001
Bio::Ontology::Term implementation of the interface for ontology terms     1.007001
Bio::Ontology::TermFactory Instantiates a new Bio::Ontology::TermI (or derived class) through a factory     1.007001
Bio::Ontology::TermI interface for ontology terms     1.007001
Bio::OntologyIO Parser factory for Ontology formats     1.007001
Bio::OntologyIO::Handlers::BaseSAXHandler base class for SAX Handlers     1.007001
Bio::OntologyIO::Handlers::InterProHandler XML handler class for InterProParser     1.007001
Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler parse an InterPro XML file and persist the resulting terms to a Biosql database     1.007001
Bio::OntologyIO::InterProParser Parser for InterPro xml files.     1.007001
Bio::OntologyIO::dagflat a base class parser for GO flat-file type formats     1.007001
Bio::OntologyIO::goflat a parser for the Gene Ontology flat-file format     1.007001
Bio::OntologyIO::obo     1.007001
Bio::OntologyIO::simplehierarchy a base class parser for simple hierarchy-by-indentation type formats     1.007001
Bio::OntologyIO::soflat a parser for the Sequence Ontology flat-file format     1.007001
Bio::ParameterBaseI Simple interface class for any parameter-related data such as IDs, database name, program arguments, and other odds and ends.     1.007001
Bio::Perl Functional access to BioPerl for people who don't know objects     1.007001
Bio::Phenotype::Correlate Representation of a correlating phenotype in a given species     1.007001
Bio::Phenotype::MeSH::Term A MeSH term     1.007001
Bio::Phenotype::MeSH::Twig Context for a MeSH term     1.007001
Bio::Phenotype::Measure Representation of context/value(-range)/unit triplets     1.007001
Bio::Phenotype::OMIM::MiniMIMentry Representation of a Mini MIM entry     1.007001
Bio::Phenotype::OMIM::OMIMentry represents OMIM (Online Mendelian Inheritance in Man) database entries     1.007001
Bio::Phenotype::OMIM::OMIMentryAllelicVariant Representation of a allelic variant of the OMIM database     1.007001
Bio::Phenotype::OMIM::OMIMparser parser for the OMIM database     1.007001
Bio::Phenotype::Phenotype A class for modeling phenotypes     1.007001
Bio::Phenotype::PhenotypeI An interface for classes modeling phenotypes     1.007001
Bio::PhyloNetwork Module to compute with Phylogenetic Networks     1.007001
Bio::PhyloNetwork::Factory Module to sequentially generate Phylogenetic Networks     1.007001
Bio::PhyloNetwork::FactoryX Module to sequentially generate Phylogenetic Networks     1.007001
Bio::PhyloNetwork::GraphViz Interface between PhyloNetwork and GraphViz     1.007001
Bio::PhyloNetwork::RandomFactory Module to generate random Phylogenetic Networks     1.007001
Bio::PhyloNetwork::TreeFactory Module to sequentially generate Phylogenetic Trees     1.007001
Bio::PhyloNetwork::TreeFactoryMulti Module to sequentially generate Phylogenetic Trees     1.007001
Bio::PhyloNetwork::TreeFactoryX Module to sequentially generate Phylogenetic Trees     1.007001
Bio::PhyloNetwork::muVector Module to compute with vectors of arbitrary dimension     1.007001
Bio::PopGen::Genotype An implementation of GenotypeI which is just an allele container     1.007001
Bio::PopGen::GenotypeI A marker and alleles for a specific individual     1.007001
Bio::PopGen::HtSNP Select htSNP from a haplotype set     1.007001
Bio::PopGen::IO Input individual,marker,allele information     1.007001
Bio::PopGen::IO::csv Extract individual allele data from a CSV parser     1.007001
Bio::PopGen::IO::hapmap A parser for HapMap output data     1.007001
Bio::PopGen::IO::phase A parser for Phase format data     1.007001
Bio::PopGen::IO::prettybase Extract individual allele data from PrettyBase format     1.007001
Bio::PopGen::Individual An implementation of an Individual who has Genotype or Sequence Results     1.007001
Bio::PopGen::IndividualI An individual who has Genotype or Sequence Results     1.007001
Bio::PopGen::Marker A genetic marker which one uses to generate genotypes     1.007001
Bio::PopGen::MarkerI A Population Genetic conceptual marker     1.007001
Bio::PopGen::PopStats A collection of methods for calculating statistics about a population or sets of populations     1.007001
Bio::PopGen::Population A population of individuals     1.007001
Bio::PopGen::PopulationI Interface for Populations     1.007001
Bio::PopGen::Simulation::Coalescent A Coalescent simulation factory     1.007001
Bio::PopGen::Simulation::GeneticDrift A simple genetic drift simulation     1.007001
Bio::PopGen::Statistics Population Genetics statistical tests     1.007001
Bio::PopGen::TagHaplotype Haplotype tag object.     1.007001
Bio::PopGen::Utilities Utilities for working with PopGen data and objects     1.007001
Bio::PrimarySeq Bioperl lightweight sequence object     1.007001
Bio::PrimarySeq::Fasta     1.007001
Bio::PrimarySeqI Interface definition for a Bio::PrimarySeq     1.007001
Bio::PullParserI A base module for fast 'pull' parsing     1.007001
Bio::Range Pure perl RangeI implementation     1.007001
Bio::RangeI Range interface     1.007001
Bio::Restriction::Analysis cutting sequences with restriction enzymes     1.007001
Bio::Restriction::Enzyme A single restriction endonuclease (cuts DNA at specific locations)     1.007001
Bio::Restriction::Enzyme::MultiCut A single restriction endonuclease     1.007001
Bio::Restriction::Enzyme::MultiSite A single restriction endonuclease     1.007001
Bio::Restriction::EnzymeCollection Set of restriction endonucleases     1.007001
Bio::Restriction::EnzymeI Interface class for restriction endonuclease     1.007001
Bio::Restriction::IO Handler for sequence variation IO Formats     1.007001
Bio::Restriction::IO::bairoch bairoch enzyme set     1.007001
Bio::Restriction::IO::base base enzyme set     1.007001
Bio::Restriction::IO::itype2 itype2 enzyme set     1.007001
Bio::Restriction::IO::prototype prototype enzyme set     1.007001
Bio::Restriction::IO::withrefm withrefm enzyme set     1.007001
Bio::Root::Build     1.007001
Bio::Root::Exception     1.007001
Bio::Root::HTTPget module for fallback HTTP get operations when LWP:: is unavailable     1.007001
Bio::Root::IO     1.007001
Bio::Root::Root     1.007001
Bio::Root::RootI     1.007001
Bio::Root::Storable     1.007001
Bio::Root::Test     1.007001
Bio::Root::TestObject An implementation of TestInterface     1.007001
Bio::Root::Utilities     1.007001
Bio::Root::Version     1.007001
Bio::Search::BlastStatistics An object for Blast statistics     1.007001
Bio::Search::BlastUtils Utility functions for Bio::Search:: BLAST objects     1.007001
Bio::Search::DatabaseI Interface for a database used in a sequence search     1.007001
Bio::Search::GenericDatabase Generic implementation of Bio::Search::DatabaseI     1.007001
Bio::Search::GenericStatistics An object for statistics     1.007001
Bio::Search::HSP::BlastHSP Bioperl BLAST High-Scoring Pair object     1.007001
Bio::Search::HSP::BlastPullHSP A parser and HSP object for BlastN hsps     1.007001
Bio::Search::HSP::FastaHSP HSP object for FASTA specific data     1.007001
Bio::Search::HSP::GenericHSP A "Generic" implementation of a High Scoring Pair     1.007001
Bio::Search::HSP::HMMERHSP A HSP object for HMMER results     1.007001
Bio::Search::HSP::HSPFactory A factory to create Bio::Search::HSP::HSPI objects     1.007001
Bio::Search::HSP::HSPI Interface for a High Scoring Pair in a similarity search result     1.007001
Bio::Search::HSP::HmmpfamHSP A parser and HSP object for hmmpfam hsps     1.007001
Bio::Search::HSP::ModelHSP A HSP object for model-based searches     1.007001
Bio::Search::HSP::PSLHSP A HSP for PSL output     1.007001
Bio::Search::HSP::PsiBlastHSP Bioperl BLAST High-Scoring Pair object     1.007001
Bio::Search::HSP::PullHSPI Bio::Search::HSP::HSPI interface for pull parsers.     1.007001
Bio::Search::HSP::WABAHSP HSP object suitable for describing WABA alignments     1.007001
Bio::Search::Hit::BlastHit Blast-specific subclass of Bio::Search::Hit::GenericHit     1.007001
Bio::Search::Hit::BlastPullHit A parser and hit object for BLASTN hits     1.007001
Bio::Search::Hit::Fasta Hit object specific for Fasta-generated hits     1.007001
Bio::Search::Hit::GenericHit A generic implementation of the Bio::Search::Hit::HitI interface     1.007001
Bio::Search::Hit::HMMERHit A Hit module for HMMER hits     1.007001
Bio::Search::Hit::HitFactory A factory to create Bio::Search::Hit::HitI objects     1.007001
Bio::Search::Hit::HitI Interface for a hit in a similarity search result     1.007001
Bio::Search::Hit::HmmpfamHit A parser and hit object for hmmpfam hits     1.007001
Bio::Search::Hit::ModelHit A model-based implementation of the Bio::Search::Hit::HitI interface     1.007001
Bio::Search::Hit::PsiBlastHit Bioperl BLAST Hit object     1.007001
Bio::Search::Hit::PullHitI Bio::Search::Hit::HitI interface for pull parsers.     1.007001
Bio::Search::Hit::hmmer3Hit DESCRIPTION of Object     1.007001
Bio::Search::Iteration::GenericIteration A generic implementation of the Bio::Search::Iteration::IterationI interface.     1.007001
Bio::Search::Iteration::IterationI Abstract interface to an iteration from an iterated search result, such as PSI-BLAST.     1.007001
Bio::Search::Processor DESCRIPTION of Object     1.007001
Bio::Search::Result::BlastPullResult A parser and result object for BLASTN results     1.007001
Bio::Search::Result::BlastResult Blast-specific subclass of Bio::Search::Result::GenericResult     1.007001
Bio::Search::Result::CrossMatchResult CrossMatch-specific subclass of Bio::Search::Result::GenericResult     1.007001
Bio::Search::Result::GenericResult Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results.     1.007001
Bio::Search::Result::HMMERResult A Result object for HMMER results     1.007001
Bio::Search::Result::HmmpfamResult A parser and result object for hmmpfam results     1.007001
Bio::Search::Result::INFERNALResult A Result object for INFERNAL results     1.007001
Bio::Search::Result::PullResultI Bio::Search::Result::ResultI interface for 'pull' parsers     1.007001
Bio::Search::Result::ResultFactory A factory to create Bio::Search::Result::ResultI objects     1.007001
Bio::Search::Result::ResultI Abstract interface to Search Result objects     1.007001
Bio::Search::Result::WABAResult Result object for WABA alignment output     1.007001
Bio::Search::Result::hmmer3Result DESCRIPTION of Object     1.007001
Bio::Search::SearchUtils Utility functions for Bio::Search:: objects     1.007001
Bio::Search::StatisticsI A Base object for statistics     1.007001
Bio::Search::Tiling::MapTileUtils utilities for manipulating closed intervals for an HSP tiling algorithm     1.007001
Bio::Search::Tiling::MapTiling An implementation of an HSP tiling algorithm, with methods to obtain frequently-requested statistics     1.007001
Bio::Search::Tiling::TilingI Abstract interface for an HSP tiling module     1.007001
Bio::SearchDist A perl wrapper around Sean Eddy's histogram object     1.007001
Bio::SearchIO Driver for parsing Sequence Database Searches (BLAST, FASTA, ...)     1.007001
Bio::SearchIO::EventHandlerI An abstract Event Handler for Search Result parsing     1.007001
Bio::SearchIO::FastHitEventBuilder Event Handler for SearchIO events.     1.007001
Bio::SearchIO::IteratedSearchResultEventBuilder Event Handler for SearchIO events.     1.007001
Bio::SearchIO::SearchResultEventBuilder Event Handler for SearchIO events.     1.007001
Bio::SearchIO::SearchWriterI Interface for outputting parsed Search results     1.007001
Bio::SearchIO::Writer::GbrowseGFF Interface for outputting parsed search results in Gbrowse GFF format     1.007001
Bio::SearchIO::Writer::HSPTableWriter Tab-delimited data for Bio::Search::HSP::HSPI objects     1.007001
Bio::SearchIO::Writer::HTMLResultWriter write a Bio::Search::ResultI in HTML     1.007001
Bio::SearchIO::Writer::HitTableWriter Tab-delimited data for Bio::Search::Hit::HitI objects     1.007001
Bio::SearchIO::Writer::ResultTableWriter Outputs tab-delimited data for each Bio::Search::Result::ResultI object.     1.007001
Bio::SearchIO::Writer::TextResultWriter Object to implement writing a Bio::Search::ResultI in Text.     1.007001
Bio::SearchIO::axt a parser for axt format reports     1.007001
Bio::SearchIO::blast Event generator for event based parsing of blast reports     1.007001
Bio::SearchIO::blast_pull A parser for BLAST output     1.007001
Bio::SearchIO::blasttable Driver module for SearchIO for parsing NCBI -m 8/9 format     1.007001
Bio::SearchIO::cross_match CrossMatch-specific subclass of Bio::SearchIO     1.007001
Bio::SearchIO::erpin SearchIO-based ERPIN parser     1.007001
Bio::SearchIO::exonerate parser for Exonerate     1.007001
Bio::SearchIO::fasta A SearchIO parser for FASTA results     1.007001
Bio::SearchIO::gmap_f9 Event generator for parsing gmap reports (Z format)     1.007001
Bio::SearchIO::hmmer A parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam)     1.007001
Bio::SearchIO::hmmer2 A parser for HMMER output (hmmpfam, hmmsearch)     1.007001
Bio::SearchIO::hmmer3     1.007001
Bio::SearchIO::hmmer_pull A parser for HMMER output     1.007001
Bio::SearchIO::infernal SearchIO-based Infernal parser     1.007001
Bio::SearchIO::megablast a driver module for Bio::SearchIO to parse megablast reports (format 0)     1.007001
Bio::SearchIO::psl A parser for PSL output (UCSC)     1.007001
Bio::SearchIO::rnamotif SearchIO-based RNAMotif parser     1.007001
Bio::SearchIO::sim4 parser for Sim4 alignments     1.007001
Bio::SearchIO::waba SearchIO parser for Jim Kent WABA program alignment output     1.007001
Bio::SearchIO::wise Parsing of wise output as alignments     1.007001
Bio::Seq Sequence object, with features     1.007001
Bio::Seq::BaseSeqProcessor Base implementation for a SequenceProcessor     1.007001
Bio::Seq::EncodedSeq subtype of Bio::LocatableSeq to store DNA that encodes a protein     1.007001
Bio::Seq::LargeLocatableSeq LocatableSeq object that stores sequence as files in the tempdir     1.007001
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     1.007001
Bio::Seq::LargeSeq SeqI compliant object that stores sequence as files in /tmp     1.007001
Bio::Seq::LargeSeqI Interface class for sequences that cache their residues in a temporary file     1.007001
Bio::Seq::Meta Generic superclass for sequence objects with residue-based meta information     1.007001
Bio::Seq::Meta::Array array-based generic implementation of a sequence class with residue-based meta information     1.007001
Bio::Seq::MetaI Interface for sequence objects with residue-based meta information     1.007001
Bio::Seq::PrimaryQual Bioperl lightweight Quality Object     1.007001
Bio::Seq::PrimaryQual::Qual     1.007001
Bio::Seq::PrimedSeq A sequence and a pair of primers matching on it     1.007001
Bio::Seq::QualI Interface definition for a Bio::Seq::Qual     1.007001
Bio::Seq::Quality Implementation of sequence with residue quality and trace values     1.007001
Bio::Seq::RichSeq Module implementing a sequence created from a rich sequence database entry     1.007001
Bio::Seq::RichSeqI interface for sequences from rich data sources, mostly databases     1.007001
Bio::Seq::SeqBuilder Configurable object builder for sequence stream parsers     1.007001
Bio::Seq::SeqFactory Instantiation of generic Bio::PrimarySeqI (or derived) objects through a factory     1.007001
Bio::Seq::SeqFastaSpeedFactory Rapid creation of Bio::Seq objects through a factory     1.007001
Bio::Seq::SeqWithQuality Bioperl object packaging a sequence with its quality. Deprecated class, use Bio::Seq::Quality instead!     1.007001
Bio::Seq::SequenceTrace Bioperl object packaging a sequence with its trace     1.007001
Bio::Seq::SimulatedRead Read with sequencing errors taken from a reference sequence     1.007001
Bio::Seq::TraceI Interface definition for a Bio::Seq::Trace     1.007001
Bio::SeqAnalysisParserI Sequence analysis output parser interface     1.007001
Bio::SeqEvolution::DNAPoint evolve a sequence by point mutations     1.007001
Bio::SeqEvolution::EvolutionI the interface for evolving sequences     1.007001
Bio::SeqEvolution::Factory Factory object to instantiate sequence evolving classes     1.007001
Bio::SeqFeature::Amplicon Amplicon feature     1.007001
Bio::SeqFeature::AnnotationAdaptor integrates SeqFeatureIs annotation     1.007001
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.     1.007001
Bio::SeqFeature::CollectionI An interface for a collection of SeqFeatureI objects.     1.007001
Bio::SeqFeature::Computation Computation SeqFeature     1.007001
Bio::SeqFeature::FeaturePair hold pair feature information e.g. blast hits     1.007001
Bio::SeqFeature::Gene::Exon a feature representing an exon     1.007001
Bio::SeqFeature::Gene::ExonI Interface for a feature representing an exon     1.007001
Bio::SeqFeature::Gene::GeneStructure A feature representing an arbitrarily complex structure of a gene     1.007001
Bio::SeqFeature::Gene::GeneStructureI A feature representing an arbitrarily complex structure of a gene     1.007001
Bio::SeqFeature::Gene::Intron An intron feature     1.007001
Bio::SeqFeature::Gene::NC_Feature superclass for non-coding features     1.007001
Bio::SeqFeature::Gene::Poly_A_site poly A feature     1.007001
Bio::SeqFeature::Gene::Promoter Describes a promoter     1.007001
Bio::SeqFeature::Gene::Transcript A feature representing a transcript     1.007001
Bio::SeqFeature::Gene::TranscriptI Interface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site.     1.007001
Bio::SeqFeature::Gene::UTR A feature representing an untranslated region that is part of a transcriptional unit     1.007001
Bio::SeqFeature::Generic Generic SeqFeature     1.007001
Bio::SeqFeature::Lite Lightweight Bio::SeqFeatureI class     1.007001
Bio::SeqFeature::PositionProxy handle features when truncation/revcom sequences span a feature     1.007001
Bio::SeqFeature::Primer Primer Generic SeqFeature     1.007001
Bio::SeqFeature::SiRNA::Oligo Perl object for small inhibitory RNAs.     1.007001
Bio::SeqFeature::SiRNA::Pair Perl object for small inhibitory RNA (SiRNA) oligo pairs     1.007001
Bio::SeqFeature::Similarity A sequence feature based on similarity     1.007001
Bio::SeqFeature::SimilarityPair Sequence feature based on the similarity of two sequences.     1.007001
Bio::SeqFeature::SubSeq Feature representing a subsequence     1.007001
Bio::SeqFeature::Tools::FeatureNamer generates unique persistent names for features     1.007001
Bio::SeqFeature::Tools::IDHandler maps $seq_feature->primary_tag     1.007001
Bio::SeqFeature::Tools::TypeMapper maps $seq_feature->primary_tag     1.007001
Bio::SeqFeature::Tools::Unflattener turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy     1.007001
Bio::SeqFeature::TypedSeqFeatureI a strongly typed SeqFeature     1.007001
Bio::SeqFeatureI Abstract interface of a Sequence Feature     1.007001
Bio::SeqI [Developers] Abstract Interface of Sequence (with features)     1.007001
Bio::SeqIO Handler for SeqIO Formats     1.007001
Bio::SeqIO::FTHelper Helper class for EMBL/Genbank feature tables     1.007001
Bio::SeqIO::Handler::GenericRichSeqHandler Bio::HandlerI-based data handler for GenBank/EMBL/UniProt (and other) sequence data     1.007001
Bio::SeqIO::MultiFile Treating a set of files as a single input stream     1.007001
Bio::SeqIO::abi abi trace sequence input/output stream     1.007001
Bio::SeqIO::ace ace sequence input/output stream     1.007001
Bio::SeqIO::agave AGAVE sequence output stream.     1.007001
Bio::SeqIO::alf alf trace sequence input/output stream     1.007001
Bio::SeqIO::asciitree asciitree sequence input/output stream     1.007001
Bio::SeqIO::bsml BSML sequence input/output stream     1.007001
Bio::SeqIO::bsml_sax BSML sequence input/output stream using SAX     1.007001
Bio::SeqIO::chadoxml chadoxml sequence output stream     1.007001
Bio::SeqIO::chaos chaos sequence input/output stream     1.007001
Bio::SeqIO::chaosxml chaosxml sequence input/output stream     1.007001
Bio::SeqIO::ctf ctf trace sequence input/output stream     1.007001
Bio::SeqIO::embl EMBL sequence input/output stream     1.007001
Bio::SeqIO::embldriver EMBL sequence input/output stream     1.007001
Bio::SeqIO::entrezgene Entrez Gene ASN1 parser     1.007001
Bio::SeqIO::excel sequence input/output stream from a MSExcel-formatted table     1.007001
Bio::SeqIO::exp exp trace sequence input/output stream     1.007001
Bio::SeqIO::fasta fasta sequence input/output stream     1.007001
Bio::SeqIO::fastq fastq sequence input/output stream     1.007001
Bio::SeqIO::flybase_chadoxml FlyBase variant of chadoxml with sequence output stream     1.007001
Bio::SeqIO::game a class for parsing and writing game-XML     1.007001
Bio::SeqIO::game::featHandler a class for handling feature elements     1.007001
Bio::SeqIO::game::gameHandler PerlSAX handler for game-XML     1.007001
Bio::SeqIO::game::gameSubs a base class for game-XML parsing     1.007001
Bio::SeqIO::game::gameWriter a class for writing game-XML     1.007001
Bio::SeqIO::game::seqHandler a class for handling game-XML sequences     1.007001
Bio::SeqIO::gbdriver GenBank handler-based push parser     1.007001
Bio::SeqIO::gbxml GenBank sequence input/output stream using SAX     1.007001
Bio::SeqIO::gcg GCG sequence input/output stream     1.007001
Bio::SeqIO::genbank GenBank sequence input/output stream     1.007001
Bio::SeqIO::interpro InterProScan XML input/output stream     1.007001
Bio::SeqIO::kegg KEGG sequence input/output stream     1.007001
Bio::SeqIO::largefasta method i/o on very large fasta sequence files     1.007001
Bio::SeqIO::lasergene Lasergene sequence file input/output stream     1.007001
Bio::SeqIO::locuslink LocusLink input/output stream     1.007001
Bio::SeqIO::mbsout input stream for output by Teshima et al.'s mbs.     1.007001
Bio::SeqIO::metafasta metafasta sequence input/output stream     1.007001
Bio::SeqIO::msout input stream for output by Hudson's ms     1.007001
Bio::SeqIO::nexml NeXML sequence input/output stream     1.007001
Bio::SeqIO::phd phd file input/output stream     1.007001
Bio::SeqIO::pir PIR sequence input/output stream     1.007001
Bio::SeqIO::pln pln trace sequence input/output stream     1.007001
Bio::SeqIO::qual .qual file input/output stream     1.007001
Bio::SeqIO::raw raw sequence file input/output stream     1.007001
Bio::SeqIO::scf .scf file input/output stream     1.007001
Bio::SeqIO::seqxml SeqXML sequence input/output stream     1.007001
Bio::SeqIO::strider DNA strider sequence input/output stream     1.007001
Bio::SeqIO::swiss Swissprot sequence input/output stream     1.007001
Bio::SeqIO::swissdriver SwissProt/UniProt handler-based push parser     1.007001
Bio::SeqIO::tab nearly raw sequence file input/output stream. Reads/writes id"\t"sequence"\n"     1.007001
Bio::SeqIO::table sequence input/output stream from a delimited table     1.007001
Bio::SeqIO::tigr TIGR XML sequence input/output stream     1.007001
Bio::SeqIO::tigrxml Parse TIGR (new) XML     1.007001
Bio::SeqIO::tinyseq reading/writing sequences in NCBI TinySeq format     1.007001
Bio::SeqIO::tinyseq::tinyseqHandler XML event handlers to support NCBI TinySeq XML parsing     1.007001
Bio::SeqIO::ztr ztr trace sequence input/output stream     1.007001
Bio::SeqUtils Additional methods for PrimarySeq objects     1.007001
Bio::SimpleAlign Multiple alignments held as a set of sequences     1.007001
Bio::SimpleAnalysisI A simple interface to any (local or remote) analysis tool     1.007001
Bio::Species Generic species object.     1.007001
Bio::Structure::Atom Bioperl structure Object, describes an Atom     1.007001
Bio::Structure::Chain Bioperl structure Object, describes a chain     1.007001
Bio::Structure::Entry Bioperl structure Object, describes the whole entry     1.007001
Bio::Structure::IO Handler for Structure Formats     1.007001
Bio::Structure::IO::pdb PDB input/output stream     1.007001
Bio::Structure::Model Bioperl structure Object, describes a Model     1.007001
Bio::Structure::Residue Bioperl structure Object, describes a Residue     1.007001
Bio::Structure::SecStr::DSSP::Res Module for parsing/accessing dssp output     1.007001
Bio::Structure::SecStr::STRIDE::Res Module for parsing/accessing stride output     1.007001
Bio::Structure::StructureI Abstract Interface for a Structure objects     1.007001
Bio::Symbol::Alphabet BSANE/BioCORBA compliant symbol list alphabet     1.007001
Bio::Symbol::AlphabetI A Symbol Alphabet     1.007001
Bio::Symbol::DNAAlphabet A ready made DNA alphabet     1.007001
Bio::Symbol::ProteinAlphabet A ready made Protein alphabet     1.007001
Bio::Symbol::Symbol A biological symbol     1.007001
Bio::Symbol::SymbolI Interface for a Symbol     1.007001
Bio::Taxon A node in a represented taxonomy     1.007001
Bio::Taxonomy representing Taxonomy.     1.007001
Bio::Taxonomy::FactoryI interface to define how to access NCBI Taxonoy     1.007001
Bio::Taxonomy::Node A node in a represented taxonomy     1.007001
Bio::Taxonomy::Taxon Generic Taxonomic Entity object     1.007001
Bio::Taxonomy::Tree An Organism Level Implementation of TreeI interface.     1.007001
Bio::Tools::AlignFactory Base object for alignment factories     1.007001
Bio::Tools::Alignment::Consed A module to work with objects from consed .ace files     1.007001
Bio::Tools::Alignment::Trim A kludge to do specialized trimming of sequence based on quality.     1.007001
Bio::Tools::AmpliconSearch Find amplicons in a template using degenerate PCR primers     1.007001
Bio::Tools::Analysis::DNA::ESEfinder a wrapper around ESEfinder server     1.007001
Bio::Tools::Analysis::Protein::Domcut a wrapper around Domcut server     1.007001
Bio::Tools::Analysis::Protein::ELM a wrapper around the ELM server which predicts short functional motifs on amino acid sequences     1.007001
Bio::Tools::Analysis::Protein::GOR4 a wrapper around GOR4 protein secondary structure prediction server     1.007001
Bio::Tools::Analysis::Protein::HNN a wrapper around the HNN protein secondary structure prediction server     1.007001
Bio::Tools::Analysis::Protein::NetPhos a wrapper around NetPhos server     1.007001
Bio::Tools::Analysis::Protein::Scansite a wrapper around the Scansite server     1.007001
Bio::Tools::Analysis::Protein::Sopma a wrapper around the Sopma protein secondary structure prediction server     1.007001
Bio::Tools::Analysis::SimpleAnalysisBase abstract superclass for SimpleAnalysis implementations     1.007001
Bio::Tools::AnalysisResult Base class for analysis result objects and parsers     1.007001
Bio::Tools::Blat parser for Blat program     1.007001
Bio::Tools::CodonTable Codon table object     1.007001
Bio::Tools::Coil parser for Coil output     1.007001
Bio::Tools::ECnumber representation of EC numbers (Enzyme Classification)     1.007001
Bio::Tools::EMBOSS::Palindrome parse EMBOSS palindrome output     1.007001
Bio::Tools::EPCR Parse ePCR output and make features     1.007001
Bio::Tools::ESTScan Results of one ESTScan run     1.007001
Bio::Tools::Eponine Results of one Eponine run     1.007001
Bio::Tools::Est2Genome Parse est2genome output, makes simple Bio::SeqFeature::Generic objects     1.007001
Bio::Tools::Fgenesh parse results of one Fgenesh run     1.007001
Bio::Tools::FootPrinter write sequence features in FootPrinter format     1.007001
Bio::Tools::GFF A Bio::SeqAnalysisParserI compliant GFF format parser     1.007001
Bio::Tools::Gel Calculates relative electrophoretic migration distances     1.007001
Bio::Tools::Geneid Results of one geneid run     1.007001
Bio::Tools::Genemark Results of one Genemark run     1.007001
Bio::Tools::Genewise Results of one Genewise run     1.007001
Bio::Tools::Genomewise Results of one Genomewise run     1.007001
Bio::Tools::Genscan Results of one Genscan run     1.007001
Bio::Tools::Glimmer parser for Glimmer 2.X/3.X prokaryotic and GlimmerM/GlimmerHMM eukaryotic gene predictions     1.007001
Bio::Tools::Grail Results of one Grail run     1.007001
Bio::Tools::GuessSeqFormat Module for determining the sequence format of the contents of a file, a string, or through a filehandle.     1.007001
Bio::Tools::HMMER::Domain One particular domain hit from HMMER     1.007001
Bio::Tools::HMMER::Results Object representing HMMER output results     1.007001
Bio::Tools::HMMER::Set Set of identical domains from HMMER matches     1.007001
Bio::Tools::Hmmpfam Parser for Hmmpfam program     1.007001
Bio::Tools::IUPAC Generates unique sequence objects or regular expressions from an ambiguous IUPAC sequence     1.007001
Bio::Tools::Lucy Object for analyzing the output from Lucy, a vector and quality trimming program from TIGR     1.007001
Bio::Tools::MZEF Results of one MZEF run     1.007001
Bio::Tools::Match Parses output from Transfac's match(TM)     1.007001
Bio::Tools::OddCodes Object holding alternative alphabet coding for one protein sequence     1.007001
Bio::Tools::Phylo::Gerp Parses output from GERP     1.007001
Bio::Tools::Phylo::Gumby Parses output from gumby     1.007001
Bio::Tools::Phylo::Molphy parser for Molphy output     1.007001
Bio::Tools::Phylo::Molphy::Result container for data parsed from a ProtML run     1.007001
Bio::Tools::Phylo::PAML Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00     1.007001
Bio::Tools::Phylo::PAML::Codeml Parses output from the PAML program codeml.     1.007001
Bio::Tools::Phylo::PAML::ModelResult A container for NSSite Model Result from PAML     1.007001
Bio::Tools::Phylo::PAML::Result A PAML result set object     1.007001
Bio::Tools::Phylo::Phylip::ProtDist parser for ProtDist output     1.007001
Bio::Tools::Prediction::Exon A predicted exon feature     1.007001
Bio::Tools::Prediction::Gene a predicted gene structure feature     1.007001
Bio::Tools::Primer3 Create input for and work with the output from the program primer3     1.007001
Bio::Tools::Primer::Assessor::Base base class for common assessor things     1.007001
Bio::Tools::Primer::AssessorI interface for assessing primer pairs     1.007001
Bio::Tools::Primer::Feature position of a single primer     1.007001
Bio::Tools::Primer::Pair two primers on left and right side     1.007001
Bio::Tools::Prints Parser for FingerPRINTScanII program     1.007001
Bio::Tools::Profile parse Profile output     1.007001
Bio::Tools::Promoterwise parser for Promoterwise tab format output     1.007001
Bio::Tools::PrositeScan Parser for ps_scan result     1.007001
Bio::Tools::Protparam submit to and parse output from protparam ;     1.007001
Bio::Tools::Pseudowise Results of one Pseudowise run     1.007001
Bio::Tools::QRNA A Parser for qrna output     1.007001
Bio::Tools::RandomDistFunctions A set of routines useful for generating random data in different distributions     1.007001
Bio::Tools::RepeatMasker a parser for RepeatMasker output     1.007001
Bio::Tools::Run::GenericParameters An object for the parameters used to run programs     1.007001
Bio::Tools::Run::ParametersI A Base object for the parameters used to run programs     1.007001
Bio::Tools::Run::RemoteBlast Object for remote execution of the NCBI Blast via HTTP     1.007001
Bio::Tools::Seg parse seg output     1.007001
Bio::Tools::SeqPattern represent a sequence pattern or motif     1.007001
Bio::Tools::SeqPattern::Backtranslate     1.007001
Bio::Tools::SeqStats Object holding statistics for one particular sequence     1.007001
Bio::Tools::SeqWords Object holding n-mer statistics for a sequence     1.007001
Bio::Tools::SiRNA Perl object for designing small inhibitory RNAs.     1.007001
Bio::Tools::SiRNA::Ruleset::saigo Perl object implementing the Saigo group's rules for designing small inhibitory RNAs     1.007001
Bio::Tools::SiRNA::Ruleset::tuschl Perl object implementing the tuschl group's rules for designing small inhibitory RNAs     1.007001
Bio::Tools::Sigcleave Bioperl object for sigcleave analysis     1.007001
Bio::Tools::Signalp parser for Signalp output     1.007001
Bio::Tools::Signalp::ExtendedSignalp enhanced parser for Signalp output     1.007001
Bio::Tools::Sim4::Exon A single exon determined by an alignment     1.007001
Bio::Tools::Sim4::Results Results of one Sim4 run     1.007001
Bio::Tools::Spidey::Exon A single exon determined by an alignment     1.007001
Bio::Tools::Spidey::Results Results of a Spidey run     1.007001
Bio::Tools::TandemRepeatsFinder a parser for Tandem Repeats Finder output     1.007001
Bio::Tools::TargetP Results of one TargetP run     1.007001
Bio::Tools::Tmhmm parse TMHMM output (TransMembrane HMM)     1.007001
Bio::Tools::dpAlign Perl extension to do pairwise dynamic programming sequence alignment     1.007001
Bio::Tools::ipcress Parse ipcress output and make features     1.007001
Bio::Tools::isPcr Parse isPcr output and make features     1.007001
Bio::Tools::pICalculator calculate the isoelectric point of a protein     1.007001
Bio::Tools::pSW pairwise Smith Waterman object     1.007001
Bio::Tools::tRNAscanSE A parser for tRNAscan-SE output     1.007001
Bio::Tree::AlleleNode A Node with Alleles attached     1.007001
Bio::Tree::AnnotatableNode A Tree Node with support for annotation     1.007001
Bio::Tree::Compatible Testing compatibility of phylogenetic trees with nested taxa.     1.007001
Bio::Tree::DistanceFactory Construct a tree using distance based methods     1.007001
Bio::Tree::Draw::Cladogram Drawing phylogenetic trees in Encapsulated PostScript (EPS) format.     1.007001
Bio::Tree::Node A Simple Tree Node     1.007001
Bio::Tree::NodeI Interface describing a Tree Node     1.007001
Bio::Tree::NodeNHX A Simple Tree Node with support for NHX tags     1.007001
Bio::Tree::RandomFactory TreeFactory for generating Random Trees     1.007001
Bio::Tree::Statistics Calculate certain statistics for a Tree     1.007001
Bio::Tree::Tree An implementation of the TreeI interface.     1.007001
Bio::Tree::TreeFunctionsI Decorated Interface implementing basic Tree exploration methods     1.007001
Bio::Tree::TreeI A Tree object suitable for lots of things, designed originally for Phylogenetic Trees.     1.007001
Bio::TreeIO Parser for Tree files     1.007001
Bio::TreeIO::NewickParser which implements a newick string parser as a finite state machine which enables it to parse the full Newick specification.     1.007001
Bio::TreeIO::TreeEventBuilder Build Bio::Tree::Tree's and Bio::Tree::Node's from Events     1.007001
Bio::TreeIO::cluster A TreeIO driver module for parsing Algorithm::Cluster::treecluster() output     1.007001
Bio::TreeIO::lintree Parser for lintree output trees     1.007001
Bio::TreeIO::newick     1.007001
Bio::TreeIO::nexml A TreeIO driver module for parsing NeXML tree files     1.007001
Bio::TreeIO::nexus A TreeIO driver module for parsing Nexus tree output from PAUP     1.007001
Bio::TreeIO::nhx TreeIO implementation for parsing Newick/New Hampshire eXtendend (NHX) format.     1.007001
Bio::TreeIO::pag Bio::TreeIO driver for Pagel format     1.007001
Bio::TreeIO::phyloxml TreeIO implementation for parsing PhyloXML format.     1.007001
Bio::TreeIO::svggraph A simple output format that converts a Tree object to an SVG output     1.007001
Bio::TreeIO::tabtree A simple output format which displays a tree as an ASCII drawing     1.007001
Bio::UpdateableSeqI Descendant of Bio::SeqI that allows updates     1.007001
Bio::Variation::AAChange Sequence change class for polypeptides     1.007001
Bio::Variation::AAReverseMutate point mutation and codon information from single amino acid changes     1.007001
Bio::Variation::Allele Sequence object with allele-specific attributes     1.007001
Bio::Variation::DNAMutation DNA level mutation class     1.007001
Bio::Variation::IO Handler for sequence variation IO Formats     1.007001
Bio::Variation::IO::flat flat file sequence variation input/output stream     1.007001
Bio::Variation::IO::xml XML sequence variation input/output stream     1.007001
Bio::Variation::RNAChange Sequence change class for RNA level     1.007001
Bio::Variation::SNP submitted SNP     1.007001
Bio::Variation::SeqDiff Container class for mutation/variant descriptions     1.007001
Bio::Variation::VariantI Sequence Change SeqFeature abstract class     1.007001
Bio::WebAgent A base class for Web (any protocol) access     1.007001
BioPerl Perl Modules for Biology      
Deobfuscator get BioPerl method and package information from a Berkeley DB     0.0.3
FeatureStore     1.007001

Documentation

*bp_seqcut.pl*  
*bp_seqpart.pl* Takes one or more sequence files and splits them into a number of load balanced files.  
[[%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_find-blast-matches.pl extract DNA sequences based on BLAST hits  
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  
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
deobfuscator/Deobfuscator/README
deobfuscator/Deobfuscator/cgi-bin/deob_help.html
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