Christopher Fields > BioPerl-1.6.922

BioPerl-1.6.922

This Release BioPerl-1.6.922  [Download] [Browse 14 Sep 2013
Latest 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
README

Modules

Bio::Align::AlignI An interface for describing sequence alignments.     1.006922
Bio::Align::DNAStatistics Calculate some statistics for a DNA alignment     1.006922
Bio::Align::Graphics Graphic Rendering of Bio::Align::AlignI Objects     1.006922
Bio::Align::PairwiseStatistics Base statistic object for Pairwise Alignments     1.006922
Bio::Align::ProteinStatistics Calculate Protein Alignment statistics (mostly distances)     1.006922
Bio::Align::StatisticsI Calculate some statistics for an alignment     1.006922
Bio::Align::Utilities A collection of utilities regarding converting and manipulating alignment objects     1.006922
Bio::AlignIO Handler for AlignIO Formats     1.006922
Bio::AlignIO::Handler::GenericAlignHandler Bio::HandlerI-based generic data handler class for alignment-based data     1.006922
Bio::AlignIO::arp ARP MSA Sequence input/output stream     1.006922
Bio::AlignIO::bl2seq bl2seq sequence input/output stream     1.006922
Bio::AlignIO::clustalw clustalw sequence input/output stream     1.006922
Bio::AlignIO::emboss Parse EMBOSS alignment output (from applications water and needle)     1.006922
Bio::AlignIO::fasta fasta MSA Sequence input/output stream     1.006922
Bio::AlignIO::largemultifasta Largemultifasta MSA Sequence input/output stream     1.006922
Bio::AlignIO::maf Multiple Alignment Format sequence input stream     1.006922
Bio::AlignIO::mase mase sequence input/output stream     1.006922
Bio::AlignIO::mega Parse and Create MEGA format data files     1.006922
Bio::AlignIO::meme meme sequence input/output stream     1.006922
Bio::AlignIO::metafasta Metafasta MSA Sequence input/output stream     1.006922
Bio::AlignIO::msf msf sequence input/output stream     1.006922
Bio::AlignIO::nexml NeXML format sequence alignment input/output stream driver     1.006922
Bio::AlignIO::nexus NEXUS format sequence input/output stream     1.006922
Bio::AlignIO::pfam pfam sequence input/output stream     1.006922
Bio::AlignIO::phylip PHYLIP format sequence input/output stream     1.006922
Bio::AlignIO::po po MSA Sequence input/output stream     1.006922
Bio::AlignIO::proda proda sequence input/output stream     1.006922
Bio::AlignIO::prodom prodom sequence input/output stream     1.006922
Bio::AlignIO::psi Read/Write PSI-BLAST profile alignment files     1.006922
Bio::AlignIO::selex selex sequence input/output stream     1.006922
Bio::AlignIO::stockholm stockholm sequence input/output stream     1.006922
Bio::AlignIO::xmfa XMFA MSA Sequence input/output stream     1.006922
Bio::AnalysisI An interface to any (local or remote) analysis tool     1.006922
Bio::AnalysisI::JobI     1.006922
Bio::AnalysisParserI Generic analysis output parser interface     1.006922
Bio::AnalysisResultI Interface for analysis result objects     1.006922
Bio::AnnotatableI the base interface an annotatable object must implement     1.006922
Bio::Annotation::AnnotationFactory Instantiates a new Bio::AnnotationI (or derived class) through a factory     1.006922
Bio::Annotation::Collection Default Perl implementation of AnnotationCollectionI     1.006922
Bio::Annotation::Comment A comment object, holding text     1.006922
Bio::Annotation::DBLink untyped links between databases     1.006922
Bio::Annotation::OntologyTerm An ontology term adapted to AnnotationI     1.006922
Bio::Annotation::Reference Specialised DBLink object for Literature References     1.006922
Bio::Annotation::Relation Relationship (pairwise) with other objects SeqI and NodeI;     1.006922
Bio::Annotation::SimpleValue A simple scalar     1.006922
Bio::Annotation::StructuredValue A scalar with embedded structured information     1.006922
Bio::Annotation::TagTree AnnotationI with tree-like hierarchal key-value relationships ('structured tags') that can be represented as simple text.     1.006922
Bio::Annotation::Target Provides an object which represents a target (ie, a similarity hit) from one object to something in another database     1.006922
Bio::Annotation::Tree Provide a tree as an annotation to a Bio::AnnotatableI object     1.006922
Bio::Annotation::TypeManager Manages types for annotation collections     1.006922
Bio::AnnotationCollectionI Interface for annotation collections     1.006922
Bio::AnnotationI Annotation interface     1.006922
Bio::Assembly::Contig Perl module to hold and manipulate sequence assembly contigs.     1.006922
Bio::Assembly::ContigAnalysis Perform analysis on sequence assembly contigs.     1.006922
Bio::Assembly::IO Handler for Assembly::IO Formats     1.006922
Bio::Assembly::IO::ace module to load ACE files from various assembly programs     1.006922
Bio::Assembly::IO::bowtie An IO module for assemblies in Bowtie format *BETA*     1.006922
Bio::Assembly::IO::maq Driver to read assembly files in maq format *BETA*     1.006922
Bio::Assembly::IO::phrap driver to load phrap.out files.     1.006922
Bio::Assembly::IO::sam An IO module for assemblies in Sam format *BETA*     1.006922
Bio::Assembly::IO::tigr Driver to read and write assembly files in the TIGR Assembler v2 default format.     1.006922
Bio::Assembly::Scaffold Perl module to hold and manipulate sequence assembly data.     1.006922
Bio::Assembly::ScaffoldI Abstract Inteface of Sequence Assemblies     1.006922
Bio::Assembly::Singlet Perl module to hold and manipulate singlets from sequence assembly contigs.     1.006922
Bio::Assembly::Tools::ContigSpectrum create and manipulate contig spectra     1.006922
Bio::Cluster::ClusterFactory Instantiates a new Bio::ClusterI (or derived class) through a factory     1.006922
Bio::Cluster::FamilyI Family Interface     1.006922
Bio::Cluster::SequenceFamily Sequence Family object     1.006922
Bio::Cluster::UniGene UniGene object     1.006922
Bio::Cluster::UniGeneI abstract interface of UniGene object     1.006922
Bio::ClusterI Cluster Interface     1.006922
Bio::ClusterIO Handler for Cluster Formats     1.006922
Bio::ClusterIO::dbsnp dbSNP input stream     1.006922
Bio::ClusterIO::unigene UniGene input stream     1.006922
Bio::CodonUsage::IO for reading and writing codon usage tables to file     1.006922
Bio::CodonUsage::Table for access to the Codon usage Database at http://www.kazusa.or.jp/codon.     1.006922
Bio::Coordinate::Chain Mapping locations through a chain of coordinate mappers     1.006922
Bio::Coordinate::Collection Noncontinuous match between two coordinate sets     1.006922
Bio::Coordinate::ExtrapolatingPair Continuous match between two coordinate sets     1.006922
Bio::Coordinate::GeneMapper transformations between gene related coordinate systems     1.006922
Bio::Coordinate::Graph Finds shortest path between nodes in a graph     1.006922
Bio::Coordinate::MapperI Interface describing coordinate mappers     1.006922
Bio::Coordinate::Pair Continuous match between two coordinate sets     1.006922
Bio::Coordinate::Result Results from coordinate transformation     1.006922
Bio::Coordinate::Result::Gap Another name for Bio::Location::Simple     1.006922
Bio::Coordinate::Result::Match Another name for Bio::Location::Simple     1.006922
Bio::Coordinate::ResultI Interface to identify coordinate mapper results     1.006922
Bio::Coordinate::Utils Additional methods to create Bio::Coordinate objects     1.006922
Bio::DB::Ace Database object interface to ACeDB servers     1.006922
Bio::DB::BioFetch Database object interface to BioFetch retrieval     1.006922
Bio::DB::CUTG for access to the Codon usage Database at http://www.kazusa.or.jp/codon.     1.006922
Bio::DB::DBFetch Database object for retrieving using the dbfetch script     1.006922
Bio::DB::EMBL Database object interface for EMBL entry retrieval     1.006922
Bio::DB::EntrezGene Database object interface to Entrez Gene     1.006922
Bio::DB::Expression DESCRIPTION of Object     1.006922
Bio::DB::Expression::geo *** DESCRIPTION of Class     1.006922
Bio::DB::Failover A Bio::DB::RandomAccessI compliant class which wraps a prioritized list of DBs     1.006922
Bio::DB::Fasta Fast indexed access to fasta files     1.006922
Bio::DB::Fasta::Subdir     1.006922
Bio::DB::FileCache In file cache for BioSeq objects     1.006922
Bio::DB::Flat Interface for indexed flat files     1.006922
Bio::DB::Flat::BDB Interface for BioHackathon standard BDB-indexed flat file     1.006922
Bio::DB::Flat::BDB::embl embl adaptor for Open-bio standard BDB-indexed flat file     1.006922
Bio::DB::Flat::BDB::fasta fasta adaptor for Open-bio standard BDB-indexed flat file     1.006922
Bio::DB::Flat::BDB::genbank genbank adaptor for Open-bio standard BDB-indexed flat file     1.006922
Bio::DB::Flat::BDB::swiss swissprot adaptor for Open-bio standard BDB-indexed flat file     1.006922
Bio::DB::Flat::BinarySearch BinarySearch search indexing system for sequence files     1.006922
Bio::DB::GFF Storage and retrieval of sequence annotation data     1.006922
Bio::DB::GFF::Adaptor::ace ace interface (for multiple inheritance)     1.006922
Bio::DB::GFF::Adaptor::berkeleydb Bio::DB::GFF database adaptor for in-memory databases     1.006922
Bio::DB::GFF::Adaptor::berkeleydb::iterator iterator for Bio::DB::GFF::Adaptor::berkeleydb     1.006922
Bio::DB::GFF::Adaptor::biofetch Cache BioFetch objects in a Bio::DB::GFF database     1.006922
Bio::DB::GFF::Adaptor::biofetch_oracle Cache BioFetch objects in a Bio::DB::GFF database     1.006922
Bio::DB::GFF::Adaptor::dbi Database adaptor for DBI (SQL) databases     1.006922
Bio::DB::GFF::Adaptor::dbi::caching_handle Cache for database handles     1.006922
Bio::DB::GFF::Adaptor::dbi::faux_dbh     1.006922
Bio::DB::GFF::Adaptor::dbi::iterator iterator for Bio::DB::GFF::Adaptor::dbi     1.006922
Bio::DB::GFF::Adaptor::dbi::mysql Database adaptor for a specific mysql schema     1.006922
Bio::DB::GFF::Adaptor::dbi::mysqlace Unholy union between mysql GFF database and acedb database     1.006922
Bio::DB::GFF::Adaptor::dbi::mysqlcmap Database adaptor for an integraded CMap/GBrowse mysql schema     1.006922
Bio::DB::GFF::Adaptor::dbi::mysqlopt Deprecated database adaptor     1.006922
Bio::DB::GFF::Adaptor::dbi::oracle Database adaptor for a specific oracle schema     1.006922
Bio::DB::GFF::Adaptor::dbi::oracleace Unholy union between oracle GFF database and acedb database     1.006922
Bio::DB::GFF::Adaptor::dbi::pg Database adaptor for a specific postgres schema     1.006922
Bio::DB::GFF::Adaptor::dbi::pg_fts Database adaptor for a specific postgres schema with a TSearch2 implementation     1.006922
Bio::DB::GFF::Adaptor::memory Bio::DB::GFF database adaptor for in-memory databases     1.006922
Bio::DB::GFF::Adaptor::memory::feature_serializer utility methods for serializing and deserializing GFF features     1.006922
Bio::DB::GFF::Adaptor::memory::iterator iterator for Bio::DB::GFF::Adaptor::memory     1.006922
Bio::DB::GFF::Aggregator Aggregate GFF groups into composite features     1.006922
Bio::DB::GFF::Aggregator::alignment Alignment aggregator     1.006922
Bio::DB::GFF::Aggregator::clone Clone aggregator     1.006922
Bio::DB::GFF::Aggregator::coding The Coding Region Aggregator     1.006922
Bio::DB::GFF::Aggregator::gene Sequence Ontology Geene     1.006922
Bio::DB::GFF::Aggregator::match Match aggregator     1.006922
Bio::DB::GFF::Aggregator::none No aggregation     1.006922
Bio::DB::GFF::Aggregator::orf An aggregator for orf regions     1.006922
Bio::DB::GFF::Aggregator::processed_transcript Sequence Ontology Transcript     1.006922
Bio::DB::GFF::Aggregator::so_transcript Sequence Ontology Transcript     1.006922
Bio::DB::GFF::Aggregator::transcript Transcript aggregator     1.006922
Bio::DB::GFF::Aggregator::ucsc_acembly UCSC acembly aggregator     1.006922
Bio::DB::GFF::Aggregator::ucsc_ensgene UCSC ensGene aggregator     1.006922
Bio::DB::GFF::Aggregator::ucsc_genscan UCSC genscan aggregator     1.006922
Bio::DB::GFF::Aggregator::ucsc_refgene UCSC refGene aggregator     1.006922
Bio::DB::GFF::Aggregator::ucsc_sanger22 UCSC sanger22 aggregator     1.006922
Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo UCSC sanger22pseudo aggregator     1.006922
Bio::DB::GFF::Aggregator::ucsc_softberry UCSC softberry aggregator     1.006922
Bio::DB::GFF::Aggregator::ucsc_twinscan UCSC twinscan aggregator     1.006922
Bio::DB::GFF::Aggregator::ucsc_unigene UCSC UniGene aggregator     1.006922
Bio::DB::GFF::Featname The name of a feature     1.006922
Bio::DB::GFF::Feature A relative segment identified by a feature type     1.006922
Bio::DB::GFF::FeatureIterator     1.006922
Bio::DB::GFF::Homol A segment of DNA that is homologous to another     1.006922
Bio::DB::GFF::ID_Iterator     1.006922
Bio::DB::GFF::RelSegment Sequence segment with relative coordinate support     1.006922
Bio::DB::GFF::Segment Simple DNA segment object     1.006922
Bio::DB::GFF::Typename The name of a feature type     1.006922
Bio::DB::GFF::Util::Binning binning utility for Bio::DB::GFF index     1.006922
Bio::DB::GFF::Util::Rearrange rearrange utility     1.006922
Bio::DB::GenBank Database object interface to GenBank     1.006922
Bio::DB::GenPept Database object interface to GenPept     1.006922
Bio::DB::GenericWebAgent helper base class for parameter-based remote server access and response retrieval.     1.006922
Bio::DB::HIV Database object interface to the Los Alamos HIV Sequence Database     1.006922
Bio::DB::HIV::HIVAnnotProcessor Adds HIV-specific annotations to Bio::SeqIO streams     1.006922
Bio::DB::HIV::HIVQueryHelper Routines and packages used by Bio::DB::HIV and Bio::DB::Query::HIVQuery     1.006922
Bio::DB::InMemoryCache Abstract interface for a sequence database     1.006922
Bio::DB::Indexed::Stream     1.006922
Bio::DB::IndexedBase Base class for modules using indexed sequence files     1.006922
Bio::DB::LocationI A RandomAccessI-like abstract interface for retrieving location data from a sequence database and returning Bio::LocationI objects     1.006922
Bio::DB::MeSH Term retrieval from a Web MeSH database     1.006922
Bio::DB::NCBIHelper A collection of routines useful for queries to NCBI databases.     1.006922
Bio::DB::Qual Fast indexed access to quality files     1.006922
Bio::DB::Query::GenBank Build a GenBank Entrez Query     1.006922
Bio::DB::Query::HIVQuery Query interface to the Los Alamos HIV Sequence Database     1.006922
Bio::DB::Query::WebQuery Helper class for web-based sequence queryies     1.006922
Bio::DB::QueryI Object Interface to queryable sequence databases     1.006922
Bio::DB::RandomAccessI Abstract interface for a sequence database     1.006922
Bio::DB::RefSeq Database object interface for RefSeq retrieval     1.006922
Bio::DB::ReferenceI A RandomAccessI-like abstract interface for retrieving Reference data from a sequence database and returning Bio::Annotation::Reference objects     1.006922
Bio::DB::Registry Access to the Open Bio Database Access registry scheme     1.006922
Bio::DB::SeqFeature Normalized feature for use with Bio::DB::SeqFeature::Store     1.006922
Bio::DB::SeqFeature::NormalizedFeature Normalized feature for use with Bio::DB::SeqFeature::Store     1.006922
Bio::DB::SeqFeature::NormalizedFeatureI Interface for normalized features     1.006922
Bio::DB::SeqFeature::NormalizedTableFeatureI Interface for normalized features whose hierarchy is stored in a table     1.006922
Bio::DB::SeqFeature::Segment Location-based access to genome annotation data     1.006922
Bio::DB::SeqFeature::Store Storage and retrieval of sequence annotation data     1.006922
Bio::DB::SeqFeature::Store::DBI::Iterator utility methods for creating and iterating over SeqFeature records     1.006922
Bio::DB::SeqFeature::Store::DBI::Pg PostgreSQL implementation of Bio::DB::SeqFeature::Store     1.006922
Bio::DB::SeqFeature::Store::DBI::SQLite SQLite implementation of Bio::DB::SeqFeature::Store     1.006922
Bio::DB::SeqFeature::Store::DBI::mysql Mysql implementation of Bio::DB::SeqFeature::Store     1.006922
Bio::DB::SeqFeature::Store::FeatureFileLoader feature file loader for Bio::DB::SeqFeature::Store     1.006922
Bio::DB::SeqFeature::Store::FeatureIterator     1.006922
Bio::DB::SeqFeature::Store::GFF2Loader GFF2 file loader for Bio::DB::SeqFeature::Store     1.006922
Bio::DB::SeqFeature::Store::GFF3Loader GFF3 file loader for Bio::DB::SeqFeature::Store     1.006922
Bio::DB::SeqFeature::Store::LoadHelper Internal utility for Bio::DB::SeqFeature::Store     1.006922
Bio::DB::SeqFeature::Store::Loader Loader     1.006922
Bio::DB::SeqFeature::Store::bdb fetch and store objects from a BerkeleyDB     1.006922
Bio::DB::SeqFeature::Store::berkeleydb Storage and retrieval of sequence annotation data in Berkeleydb files     1.006922
Bio::DB::SeqFeature::Store::berkeleydb3 Storage and retrieval of sequence annotation data in Berkeleydb files     1.006922
Bio::DB::SeqFeature::Store::berkeleydb::Iterator     1.006922
Bio::DB::SeqFeature::Store::memory In-memory implementation of Bio::DB::SeqFeature::Store     1.006922
Bio::DB::SeqFeature::Store::memory::Iterator     1.006922
Bio::DB::SeqHound Database object interface to SeqHound     1.006922
Bio::DB::SeqI Abstract Interface for Sequence databases     1.006922
Bio::DB::SeqVersion front end to querying databases for identifier versions     1.006922
Bio::DB::SeqVersion::gi interface to NCBI Sequence Revision History page     1.006922
Bio::DB::SwissProt Database object interface to SwissProt retrieval     1.006922
Bio::DB::TFBS Access to a Transcription Factor Binding Site database     1.006922
Bio::DB::TFBS::transfac_pro An implementation of Bio::DB::TFBS which uses local flat files for transfac pro     1.006922
Bio::DB::Taxonomy Access to a taxonomy database     1.006922
Bio::DB::Taxonomy::entrez Taxonomy Entrez driver     1.006922
Bio::DB::Taxonomy::flatfile Use the NCBI taxonomy from local indexed flat files     1.006922
Bio::DB::Taxonomy::greengenes Use the Greengenes taxonomy     1.006922
Bio::DB::Taxonomy::list An implementation of Bio::DB::Taxonomy that accepts lists of words to build a database     1.006922
Bio::DB::Taxonomy::silva Use the Silva taxonomy     1.006922
Bio::DB::Universal Artificial database that delegates to specific databases     1.006922
Bio::DB::UpdateableSeqI An interface for writing to a database of sequences.     1.006922
Bio::DB::WebDBSeqI Object Interface to generalize Web Databases for retrieving sequences     1.006922
Bio::DBLinkContainerI Abstract interface for any object wanting to use database cross references     1.006922
Bio::Das::FeatureTypeI Simple interface to Sequence Ontology feature types     1.006922
Bio::Das::SegmentI DAS-style access to a feature database     1.006922
Bio::DasI DAS-style access to a feature database     1.006922
Bio::DescribableI interface for objects with human readable names and descriptions     1.006922
Bio::Draw::Pictogram generate SVG output of Pictogram display for consensus motifs     1.006922
Bio::Event::EventGeneratorI This interface describes the basic event generator class.     1.006922
Bio::Event::EventHandlerI An Event Handler Interface     1.006922
Bio::Factory::AnalysisI An interface to analysis tool factory     1.006922
Bio::Factory::ApplicationFactoryI Interface class for Application Factories     1.006922
Bio::Factory::DriverFactory Base class for factory classes loading drivers     1.006922
Bio::Factory::FTLocationFactory A FeatureTable Location Parser     1.006922
Bio::Factory::LocationFactoryI A factory interface for generating locations from a string     1.006922
Bio::Factory::MapFactoryI A Factory for getting markers     1.006922
Bio::Factory::ObjectBuilderI Interface for an object builder     1.006922
Bio::Factory::ObjectFactory Instantiates a new Bio::Root::RootI (or derived class) through a factory     1.006922
Bio::Factory::ObjectFactoryI A General object creator factory     1.006922
Bio::Factory::SeqAnalysisParserFactory class capable of creating SeqAnalysisParserI compliant parsers     1.006922
Bio::Factory::SeqAnalysisParserFactoryI interface describing objects capable of creating SeqAnalysisParserI compliant parsers     1.006922
Bio::Factory::SequenceFactoryI This interface allows for generic building of sequences in factories which create sequences (like SeqIO)     1.006922
Bio::Factory::SequenceProcessorI Interface for chained sequence processing algorithms     1.006922
Bio::Factory::SequenceStreamI Interface describing the basics of a Sequence Stream.     1.006922
Bio::Factory::TreeFactoryI Factory Interface for getting and writing trees from/to a data stream     1.006922
Bio::FeatureHolderI the base interface an object with features must implement     1.006922
Bio::HandlerBaseI Interface class for handler methods which interact with any event-driven parsers (drivers).     1.006922
Bio::IdCollectionI interface for objects with multiple identifiers     1.006922
Bio::IdentifiableI interface for objects with identifiers     1.006922
Bio::Index::Abstract Abstract interface for indexing a flat file     1.006922
Bio::Index::AbstractSeq base class for AbstractSeq     1.006922
Bio::Index::Blast Indexes Blast reports and supports retrieval based on query accession(s)     1.006922
Bio::Index::BlastTable Indexes tabular Blast reports (-m 8 or -m 9 format) and supports retrieval based on query accession(s)     1.006922
Bio::Index::EMBL Interface for indexing (multiple) EMBL/Swissprot .dat files (i.e. flat file EMBL/Swissprot format).     1.006922
Bio::Index::Fasta Interface for indexing (multiple) fasta files     1.006922
Bio::Index::Fastq Interface for indexing (multiple) fastq files     1.006922
Bio::Index::GenBank Interface for indexing one or more GenBank files (i.e. flat file GenBank format).     1.006922
Bio::Index::Hmmer indexes HMMER reports and supports retreival based on query     1.006922
Bio::Index::Qual Interface for indexing (multiple) fasta qual files     1.006922
Bio::Index::Stockholm     1.006922
Bio::Index::SwissPfam Interface for indexing swisspfam files     1.006922
Bio::Index::Swissprot Interface for indexing one or more Swissprot files.     1.006922
Bio::LiveSeq::AARange AARange abstract class for LiveSeq     1.006922
Bio::LiveSeq::Chain DoubleChain DataStructure for Perl     1.006922
Bio::LiveSeq::ChainI Double linked chain data structure     1.006922
Bio::LiveSeq::DNA DNA object for LiveSeq     1.006922
Bio::LiveSeq::Exon Range abstract class for LiveSeq     1.006922
Bio::LiveSeq::Gene Range abstract class for LiveSeq     1.006922
Bio::LiveSeq::IO::BioPerl Loader for LiveSeq from EMBL entries with BioPerl     1.006922
Bio::LiveSeq::IO::Loader Parent Loader for LiveSeq     1.006922
Bio::LiveSeq::Intron Range abstract class for LiveSeq     1.006922
Bio::LiveSeq::Mutation Mutation event descriptor class     1.006922
Bio::LiveSeq::Mutator Package mutating LiveSequences     1.006922
Bio::LiveSeq::Prim_Transcript Prim_Transcript class for LiveSeq     1.006922
Bio::LiveSeq::Range Range abstract class for LiveSeq     1.006922
Bio::LiveSeq::Repeat_Region Repeat_Region class for LiveSeq     1.006922
Bio::LiveSeq::Repeat_Unit Repeat_Unit class for LiveSeq     1.006922
Bio::LiveSeq::SeqI Abstract sequence interface class for LiveSeq     1.006922
Bio::LiveSeq::Transcript Transcript class for LiveSeq     1.006922
Bio::LiveSeq::Translation Translation class for LiveSeq     1.006922
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.     1.006922
Bio::Location::Atomic Implementation of a Atomic Location on a Sequence     1.006922
Bio::Location::AvWithinCoordPolicy class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise     1.006922
Bio::Location::CoordinatePolicyI Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location     1.006922
Bio::Location::Fuzzy Implementation of a Location on a Sequence which has unclear start and/or end locations     1.006922
Bio::Location::FuzzyLocationI Abstract interface of a Location on a Sequence which has unclear start/end location     1.006922
Bio::Location::NarrowestCoordPolicy class implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range     1.006922
Bio::Location::Simple Implementation of a Simple Location on a Sequence     1.006922
Bio::Location::Split Implementation of a Location on a Sequence which has multiple locations (start/end points)     1.006922
Bio::Location::SplitLocationI Abstract interface of a Location on a Sequence which has multiple locations (start/end points)     1.006922
Bio::Location::WidestCoordPolicy class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable range     1.006922
Bio::LocationI Abstract interface of a Location on a Sequence     1.006922
Bio::Map::Clone An central map object representing a clone     1.006922
Bio::Map::Contig A MapI implementation handling the contigs of a Physical Map (such as FPC)     1.006922
Bio::Map::CytoMap A Bio::MapI compliant map implementation handling cytogenic bands     1.006922
Bio::Map::CytoMarker An object representing a marker.     1.006922
Bio::Map::CytoPosition Marker class with cytogenetic band storing attributes     1.006922
Bio::Map::EntityI An Entity Interface     1.006922
Bio::Map::FPCMarker An central map object representing a marker     1.006922
Bio::Map::Gene An gene modelled as a mappable element.     1.006922
Bio::Map::GeneMap A MapI implementation to represent the area around a gene     1.006922
Bio::Map::GenePosition A typed position, suitable for modelling the various regions of a gene.     1.006922
Bio::Map::GeneRelative Represents being relative to named sub-regions of a gene.     1.006922
Bio::Map::LinkageMap A representation of a genetic linkage map.     1.006922
Bio::Map::LinkagePosition Create a Position for a Marker that will be placed on a Bio::Map::LinkageMap     1.006922
Bio::Map::MapI Interface for describing Map objects in bioperl     1.006922
Bio::Map::Mappable An object representing a generic map element that can have multiple locations in several maps.     1.006922
Bio::Map::MappableI An object that can be placed in a map     1.006922
Bio::Map::Marker An central map object representing a generic marker that can have multiple location in several maps.     1.006922
Bio::Map::MarkerI Interface for basic marker functionality     1.006922
Bio::Map::Microsatellite An object representing a Microsatellite marker.     1.006922
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.     1.006922
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.     1.006922
Bio::Map::Physical A class for handling a Physical Map (such as FPC)     1.006922
Bio::Map::Position A single position of a Marker, or the range over which that marker lies, in a Map     1.006922
Bio::Map::PositionHandler A Position Handler Implementation     1.006922
Bio::Map::PositionHandlerI A Position Handler Interface     1.006922
Bio::Map::PositionI Abstracts the notion of a position having a value in the context of a marker and a Map     1.006922
Bio::Map::PositionWithSequence A position with a sequence.     1.006922
Bio::Map::Prediction An object representing the predictions of something that can have multiple locations in several maps.     1.006922
Bio::Map::Relative Represents what a Position's coordiantes are relative to.     1.006922
Bio::Map::RelativeI Interface for describing what a Position's coordiantes are relative to.     1.006922
Bio::Map::SimpleMap A MapI implementation handling the basics of a Map     1.006922
Bio::Map::TranscriptionFactor A transcription factor modelled as a mappable element     1.006922
Bio::MapIO A Map Factory object     1.006922
Bio::MapIO::fpc A FPC Map reader     1.006922
Bio::MapIO::mapmaker A Mapmaker Map reader     1.006922
Bio::Matrix::Generic A generic matrix implementation     1.006922
Bio::Matrix::IO A factory for Matrix parsing     1.006922
Bio::Matrix::IO::mlagan A parser for the mlagan substitution matrix     1.006922
Bio::Matrix::IO::phylip A parser for PHYLIP distance matricies     1.006922
Bio::Matrix::IO::scoring A parser for PAM/BLOSUM matricies     1.006922
Bio::Matrix::MatrixI An interface for describing a Matrix     1.006922
Bio::Matrix::Mlagan A generic matrix with mlagan fields     1.006922
Bio::Matrix::PSM::IO PSM parser     1.006922
Bio::Matrix::PSM::IO::mast PSM mast parser implementation     1.006922
Bio::Matrix::PSM::IO::masta motif fasta format parser     1.006922
Bio::Matrix::PSM::IO::meme PSM meme parser implementation     1.006922
Bio::Matrix::PSM::IO::psiblast PSM psiblast parser     1.006922
Bio::Matrix::PSM::IO::transfac PSM transfac parser     1.006922
Bio::Matrix::PSM::InstanceSite A PSM site occurance     1.006922
Bio::Matrix::PSM::InstanceSiteI InstanceSite interface, holds an instance of a PSM     1.006922
Bio::Matrix::PSM::ProtMatrix SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) with log-odds scoring information.     1.006922
Bio::Matrix::PSM::ProtPsm handle combination of site matricies     1.006922
Bio::Matrix::PSM::Psm handle combination of site matricies     1.006922
Bio::Matrix::PSM::PsmHeader PSM mast parser implementation     1.006922
Bio::Matrix::PSM::PsmHeaderI handles the header data from a PSM file     1.006922
Bio::Matrix::PSM::PsmI abstract interface to handler of site matricies     1.006922
Bio::Matrix::PSM::SiteMatrix SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds     1.006922
Bio::Matrix::PSM::SiteMatrixI SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds     1.006922
Bio::Matrix::PhylipDist A Phylip Distance Matrix object     1.006922
Bio::Matrix::Scoring Object which can hold scoring matrix information     1.006922
Bio::MolEvol::CodonModel Codon Evolution Models     1.006922
Bio::Nexml::Factory A factory module for creating BioPerl and Bio::Phylo objects from/to nexml documents     1.006922
Bio::NexmlIO stream handler for NeXML documents     1.006922
Bio::Ontology::DocumentRegistry Keep track of where to find ontologies. Allows lookups by name.     1.006922
Bio::Ontology::GOterm representation of GO terms     1.006922
Bio::Ontology::InterProTerm Implementation of InterProI term interface     1.006922
Bio::Ontology::OBOEngine An Ontology Engine for OBO style flat file format from the Gene Ontology Consortium     1.006922
Bio::Ontology::OBOterm representation of OBO terms     1.006922
Bio::Ontology::Ontology standard implementation of an Ontology     1.006922
Bio::Ontology::OntologyEngineI Interface a minimal Ontology implementation should satisfy     1.006922
Bio::Ontology::OntologyI Interface for an ontology implementation     1.006922
Bio::Ontology::OntologyStore A repository of ontologies     1.006922
Bio::Ontology::Path a path for an ontology term graph     1.006922
Bio::Ontology::PathI Interface for a path between ontology terms     1.006922
Bio::Ontology::Relationship a relationship for an ontology     1.006922
Bio::Ontology::RelationshipFactory Instantiates a new Bio::Ontology::RelationshipI (or derived class) through a factory     1.006922
Bio::Ontology::RelationshipI Interface for a relationship between ontology terms     1.006922
Bio::Ontology::RelationshipType a relationship type for an ontology     1.006922
Bio::Ontology::SimpleGOEngine::GraphAdaptor Graph adaptor for Bio::Ontology::SimpleGOEngine     1.006922
Bio::Ontology::SimpleOntologyEngine Implementation of OntologyEngineI interface     1.006922
Bio::Ontology::Term implementation of the interface for ontology terms     1.006922
Bio::Ontology::TermFactory Instantiates a new Bio::Ontology::TermI (or derived class) through a factory     1.006922
Bio::Ontology::TermI interface for ontology terms     1.006922
Bio::OntologyIO Parser factory for Ontology formats     1.006922
Bio::OntologyIO::Handlers::BaseSAXHandler base class for SAX Handlers     1.006922
Bio::OntologyIO::Handlers::InterProHandler XML handler class for InterProParser     1.006922
Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler parse an InterPro XML file and persist the resulting terms to a Biosql database     1.006922
Bio::OntologyIO::InterProParser Parser for InterPro xml files.     1.006922
Bio::OntologyIO::dagflat a base class parser for GO flat-file type formats     1.006922
Bio::OntologyIO::goflat a parser for the Gene Ontology flat-file format     1.006922
Bio::OntologyIO::obo a parser for OBO flat-file format from Gene Ontology Consortium     1.006922
Bio::OntologyIO::simplehierarchy a base class parser for simple hierarchy-by-indentation type formats     1.006922
Bio::OntologyIO::soflat a parser for the Sequence Ontology flat-file format     1.006922
Bio::ParameterBaseI Simple interface class for any parameter-related data such as IDs, database name, program arguments, and other odds and ends.     1.006922
Bio::Perl Functional access to BioPerl for people who don't know objects     1.006922
Bio::Phenotype::Correlate Representation of a correlating phenotype in a given species     1.006922
Bio::Phenotype::MeSH::Term A MeSH term     1.006922
Bio::Phenotype::MeSH::Twig Context for a MeSH term     1.006922
Bio::Phenotype::Measure Representation of context/value(-range)/unit triplets     1.006922
Bio::Phenotype::OMIM::MiniMIMentry Representation of a Mini MIM entry     1.006922
Bio::Phenotype::OMIM::OMIMentry represents OMIM (Online Mendelian Inheritance in Man) database entries     1.006922
Bio::Phenotype::OMIM::OMIMentryAllelicVariant Representation of a allelic variant of the OMIM database     1.006922
Bio::Phenotype::OMIM::OMIMparser parser for the OMIM database     1.006922
Bio::Phenotype::Phenotype A class for modeling phenotypes     1.006922
Bio::Phenotype::PhenotypeI An interface for classes modeling phenotypes     1.006922
Bio::PhyloNetwork Module to compute with Phylogenetic Networks     1.006922
Bio::PhyloNetwork::Factory Module to sequentially generate Phylogenetic Networks     1.006922
Bio::PhyloNetwork::FactoryX Module to sequentially generate Phylogenetic Networks     1.006922
Bio::PhyloNetwork::GraphViz Interface between PhyloNetwork and GraphViz     1.006922
Bio::PhyloNetwork::RandomFactory Module to generate random Phylogenetic Networks     1.006922
Bio::PhyloNetwork::TreeFactory Module to sequentially generate Phylogenetic Trees     1.006922
Bio::PhyloNetwork::TreeFactoryMulti Module to sequentially generate Phylogenetic Trees     1.006922
Bio::PhyloNetwork::TreeFactoryX Module to sequentially generate Phylogenetic Trees     1.006922
Bio::PhyloNetwork::muVector Module to compute with vectors of arbitrary dimension     1.006922
Bio::PopGen::Genotype An implementation of GenotypeI which is just an allele container     1.006922
Bio::PopGen::GenotypeI A marker and alleles for a specific individual     1.006922
Bio::PopGen::HtSNP Select htSNP from a haplotype set     1.006922
Bio::PopGen::IO Input individual,marker,allele information     1.006922
Bio::PopGen::IO::csv Extract individual allele data from a CSV parser     1.006922
Bio::PopGen::IO::hapmap A parser for HapMap output data     1.006922
Bio::PopGen::IO::phase A parser for Phase format data     1.006922
Bio::PopGen::IO::prettybase Extract individual allele data from PrettyBase format     1.006922
Bio::PopGen::Individual An implementation of an Individual who has Genotype or Sequence Results     1.006922
Bio::PopGen::IndividualI An individual who has Genotype or Sequence Results     1.006922
Bio::PopGen::Marker A genetic marker which one uses to generate genotypes     1.006922
Bio::PopGen::MarkerI A Population Genetic conceptual marker     1.006922
Bio::PopGen::PopStats A collection of methods for calculating statistics about a population or sets of populations     1.006922
Bio::PopGen::Population A population of individuals     1.006922
Bio::PopGen::PopulationI Interface for Populations     1.006922
Bio::PopGen::Simulation::Coalescent A Coalescent simulation factory     1.006922
Bio::PopGen::Simulation::GeneticDrift A simple genetic drift simulation     1.006922
Bio::PopGen::Statistics Population Genetics statistical tests     1.006922
Bio::PopGen::TagHaplotype Haplotype tag object.     1.006922
Bio::PopGen::Utilities Utilities for working with PopGen data and objects     1.006922
Bio::PrimarySeq Bioperl lightweight sequence object     1.006922
Bio::PrimarySeq::Fasta     1.006922
Bio::PrimarySeqI Interface definition for a Bio::PrimarySeq     1.006922
Bio::PullParserI A base module for fast 'pull' parsing     1.006922
Bio::Range Pure perl RangeI implementation     1.006922
Bio::RangeI Range interface     1.006922
Bio::Restriction::Analysis cutting sequences with restriction enzymes     1.006922
Bio::Restriction::Enzyme A single restriction endonuclease (cuts DNA at specific locations)     1.006922
Bio::Restriction::Enzyme::MultiCut A single restriction endonuclease     1.006922
Bio::Restriction::Enzyme::MultiSite A single restriction endonuclease     1.006922
Bio::Restriction::EnzymeCollection Set of restriction endonucleases     1.006922
Bio::Restriction::EnzymeI Interface class for restriction endonuclease     1.006922
Bio::Restriction::IO Handler for sequence variation IO Formats     1.006922
Bio::Restriction::IO::bairoch bairoch enzyme set     1.006922
Bio::Restriction::IO::base base enzyme set     1.006922
Bio::Restriction::IO::itype2 itype2 enzyme set     1.006922
Bio::Restriction::IO::prototype prototype enzyme set     1.006922
Bio::Restriction::IO::withrefm withrefm enzyme set     1.006922
Bio::Root::Build A common Module::Build subclass base for BioPerl distributions     1.006922
Bio::Root::Exception Generic exception objects for Bioperl     1.006922
Bio::Root::HTTPget module for fallback HTTP get operations when LWP:: is unavailable     1.006922
Bio::Root::IO module providing several methods often needed when dealing with file IO     1.006922
Bio::Root::Root Hash-based implementation of Bio::Root::RootI     1.006922
Bio::Root::RootI Abstract interface to root object code     1.006922
Bio::Root::Storable object serialisation methods     1.006922
Bio::Root::Test A common base for all Bioperl test scripts.     1.006922
Bio::Root::Utilities General-purpose utility module     1.006922
Bio::Root::Version provide global, distribution-level versioning     1.006922
Bio::Search::BlastStatistics An object for Blast statistics     1.006922
Bio::Search::BlastUtils Utility functions for Bio::Search:: BLAST objects     1.006922
Bio::Search::DatabaseI Interface for a database used in a sequence search     1.006922
Bio::Search::GenericDatabase Generic implementation of Bio::Search::DatabaseI     1.006922
Bio::Search::GenericStatistics An object for statistics     1.006922
Bio::Search::HSP::BlastHSP Bioperl BLAST High-Scoring Pair object     1.006922
Bio::Search::HSP::BlastPullHSP A parser and HSP object for BlastN hsps     1.006922
Bio::Search::HSP::FastaHSP HSP object for FASTA specific data     1.006922
Bio::Search::HSP::GenericHSP A "Generic" implementation of a High Scoring Pair     1.006922
Bio::Search::HSP::HMMERHSP A HSP object for HMMER results     1.006922
Bio::Search::HSP::HSPFactory A factory to create Bio::Search::HSP::HSPI objects     1.006922
Bio::Search::HSP::HSPI Interface for a High Scoring Pair in a similarity search result     1.006922
Bio::Search::HSP::HmmpfamHSP A parser and HSP object for hmmpfam hsps     1.006922
Bio::Search::HSP::ModelHSP A HSP object for model-based searches     1.006922
Bio::Search::HSP::PSLHSP A HSP for PSL output     1.006922
Bio::Search::HSP::PsiBlastHSP Bioperl BLAST High-Scoring Pair object     1.006922
Bio::Search::HSP::PullHSPI Bio::Search::HSP::HSPI interface for pull parsers.     1.006922
Bio::Search::HSP::WABAHSP HSP object suitable for describing WABA alignments     1.006922
Bio::Search::Hit::BlastHit Blast-specific subclass of Bio::Search::Hit::GenericHit     1.006922
Bio::Search::Hit::BlastPullHit A parser and hit object for BLASTN hits     1.006922
Bio::Search::Hit::Fasta Hit object specific for Fasta-generated hits     1.006922
Bio::Search::Hit::GenericHit A generic implementation of the Bio::Search::Hit::HitI interface     1.006922
Bio::Search::Hit::HMMERHit A Hit module for HMMER hits     1.006922
Bio::Search::Hit::HitFactory A factory to create Bio::Search::Hit::HitI objects     1.006922
Bio::Search::Hit::HitI Interface for a hit in a similarity search result     1.006922
Bio::Search::Hit::HmmpfamHit A parser and hit object for hmmpfam hits     1.006922
Bio::Search::Hit::ModelHit A model-based implementation of the Bio::Search::Hit::HitI interface     1.006922
Bio::Search::Hit::PsiBlastHit Bioperl BLAST Hit object     1.006922
Bio::Search::Hit::PullHitI Bio::Search::Hit::HitI interface for pull parsers.     1.006922
Bio::Search::Hit::hmmer3Hit DESCRIPTION of Object     1.006922
Bio::Search::Iteration::GenericIteration A generic implementation of the Bio::Search::Iteration::IterationI interface.     1.006922
Bio::Search::Iteration::IterationI Abstract interface to an iteration from an iterated search result, such as PSI-BLAST.     1.006922
Bio::Search::Processor DESCRIPTION of Object     1.006922
Bio::Search::Result::BlastPullResult A parser and result object for BLASTN results     1.006922
Bio::Search::Result::BlastResult Blast-specific subclass of Bio::Search::Result::GenericResult     1.006922
Bio::Search::Result::CrossMatchResult CrossMatch-specific subclass of Bio::Search::Result::GenericResult     1.006922
Bio::Search::Result::GenericResult Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results.     1.006922
Bio::Search::Result::HMMERResult A Result object for HMMER results     1.006922
Bio::Search::Result::HmmpfamResult A parser and result object for hmmpfam results     1.006922
Bio::Search::Result::PullResultI Bio::Search::Result::ResultI interface for 'pull' parsers     1.006922
Bio::Search::Result::ResultFactory A factory to create Bio::Search::Result::ResultI objects     1.006922
Bio::Search::Result::ResultI Abstract interface to Search Result objects     1.006922
Bio::Search::Result::WABAResult Result object for WABA alignment output     1.006922
Bio::Search::Result::hmmer3Result DESCRIPTION of Object     1.006922
Bio::Search::SearchUtils Utility functions for Bio::Search:: objects     1.006922
Bio::Search::StatisticsI A Base object for statistics     1.006922
Bio::Search::Tiling::MapTileUtils utilities for manipulating closed intervals for an HSP tiling algorithm     1.006922
Bio::Search::Tiling::MapTiling An implementation of an HSP tiling algorithm, with methods to obtain frequently-requested statistics     1.006922
Bio::Search::Tiling::TilingI Abstract interface for an HSP tiling module     1.006922
Bio::SearchDist A perl wrapper around Sean Eddy's histogram object     1.006922
Bio::SearchIO Driver for parsing Sequence Database Searches (BLAST, FASTA, ...)     1.006922
Bio::SearchIO::EventHandlerI An abstract Event Handler for Search Result parsing     1.006922
Bio::SearchIO::FastHitEventBuilder Event Handler for SearchIO events.     1.006922
Bio::SearchIO::IteratedSearchResultEventBuilder Event Handler for SearchIO events.     1.006922
Bio::SearchIO::SearchResultEventBuilder Event Handler for SearchIO events.     1.006922
Bio::SearchIO::SearchWriterI Interface for outputting parsed Search results     1.006922
Bio::SearchIO::Writer::BSMLResultWriter BSML output writer     1.006922
Bio::SearchIO::Writer::GbrowseGFF Interface for outputting parsed search results in Gbrowse GFF format     1.006922
Bio::SearchIO::Writer::HSPTableWriter Tab-delimited data for Bio::Search::HSP::HSPI objects     1.006922
Bio::SearchIO::Writer::HTMLResultWriter write a Bio::Search::ResultI in HTML     1.006922
Bio::SearchIO::Writer::HitTableWriter Tab-delimited data for Bio::Search::Hit::HitI objects     1.006922
Bio::SearchIO::Writer::ResultTableWriter Outputs tab-delimited data for each Bio::Search::Result::ResultI object.     1.006922
Bio::SearchIO::Writer::TextResultWriter Object to implement writing a Bio::Search::ResultI in Text.     1.006922
Bio::SearchIO::XML::BlastHandler XML Handler for NCBI Blast XML parsing.     1.006922
Bio::SearchIO::XML::PsiBlastHandler XML Handler for NCBI Blast PSIBLAST XML parsing.     1.006922
Bio::SearchIO::axt a parser for axt format reports     1.006922
Bio::SearchIO::blast Event generator for event based parsing of blast reports     1.006922
Bio::SearchIO::blast_pull A parser for BLAST output     1.006922
Bio::SearchIO::blasttable Driver module for SearchIO for parsing NCBI -m 8/9 format     1.006922
Bio::SearchIO::blastxml A SearchIO implementation of NCBI Blast XML parsing.     1.006922
Bio::SearchIO::cross_match CrossMatch-specific subclass of Bio::SearchIO     1.006922
Bio::SearchIO::erpin SearchIO-based ERPIN parser     1.006922
Bio::SearchIO::exonerate parser for Exonerate     1.006922
Bio::SearchIO::fasta A SearchIO parser for FASTA results     1.006922
Bio::SearchIO::gmap_f9 Event generator for parsing gmap reports (Z format)     1.006922
Bio::SearchIO::hmmer A parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam)     1.006922
Bio::SearchIO::hmmer2 A parser for HMMER output (hmmpfam, hmmsearch)     1.006922
Bio::SearchIO::hmmer3     1.006922
Bio::SearchIO::hmmer_pull A parser for HMMER output     1.006922
Bio::SearchIO::infernal SearchIO-based Infernal parser     1.006922
Bio::SearchIO::megablast a driver module for Bio::SearchIO to parse megablast reports (format 0)     1.006922
Bio::SearchIO::psl A parser for PSL output (UCSC)     1.006922
Bio::SearchIO::rnamotif SearchIO-based RNAMotif parser     1.006922
Bio::SearchIO::sim4 parser for Sim4 alignments     1.006922
Bio::SearchIO::waba SearchIO parser for Jim Kent WABA program alignment output     1.006922
Bio::SearchIO::wise Parsing of wise output as alignments     1.006922
Bio::Seq Sequence object, with features     1.006922
Bio::Seq::BaseSeqProcessor Base implementation for a SequenceProcessor     1.006922
Bio::Seq::EncodedSeq subtype of Bio::LocatableSeq to store DNA that encodes a protein     1.006922
Bio::Seq::LargeLocatableSeq LocatableSeq object that stores sequence as files in the tempdir     1.006922
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     1.006922
Bio::Seq::LargeSeq SeqI compliant object that stores sequence as files in /tmp     1.006922
Bio::Seq::LargeSeqI Interface class for sequences that cache their residues in a temporary file     1.006922
Bio::Seq::Meta Generic superclass for sequence objects with residue-based meta information     1.006922
Bio::Seq::Meta::Array array-based generic implementation of a sequence class with residue-based meta information     1.006922
Bio::Seq::MetaI Interface for sequence objects with residue-based meta information     1.006922
Bio::Seq::PrimaryQual Bioperl lightweight Quality Object     1.006922
Bio::Seq::PrimaryQual::Qual     1.006922
Bio::Seq::PrimedSeq A sequence and a pair of primers matching on it     1.006922
Bio::Seq::QualI Interface definition for a Bio::Seq::Qual     1.006922
Bio::Seq::Quality Implementation of sequence with residue quality and trace values     1.006922
Bio::Seq::RichSeq Module implementing a sequence created from a rich sequence database entry     1.006922
Bio::Seq::RichSeqI interface for sequences from rich data sources, mostly databases     1.006922
Bio::Seq::SeqBuilder Configurable object builder for sequence stream parsers     1.006922
Bio::Seq::SeqFactory Instantiation of generic Bio::PrimarySeqI (or derived) objects through a factory     1.006922
Bio::Seq::SeqFastaSpeedFactory Rapid creation of Bio::Seq objects through a factory     1.006922
Bio::Seq::SeqWithQuality Bioperl object packaging a sequence with its quality. Deprecated class, use Bio::Seq::Quality instead!     1.006922
Bio::Seq::SequenceTrace Bioperl object packaging a sequence with its trace     1.006922
Bio::Seq::SimulatedRead Read with sequencing errors taken from a reference sequence     1.006922
Bio::Seq::TraceI Interface definition for a Bio::Seq::Trace     1.006922
Bio::SeqAnalysisParserI Sequence analysis output parser interface     1.006922
Bio::SeqEvolution::DNAPoint evolve a sequence by point mutations     1.006922
Bio::SeqEvolution::EvolutionI the interface for evolving sequences     1.006922
Bio::SeqEvolution::Factory Factory object to instantiate sequence evolving classes     1.006922
Bio::SeqFeature::Amplicon Amplicon feature     1.006922
Bio::SeqFeature::AnnotationAdaptor integrates SeqFeatureIs annotation     1.006922
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.     1.006922
Bio::SeqFeature::CollectionI An interface for a collection of SeqFeatureI objects.     1.006922
Bio::SeqFeature::Computation Computation SeqFeature     1.006922
Bio::SeqFeature::FeaturePair hold pair feature information e.g. blast hits     1.006922
Bio::SeqFeature::Gene::Exon a feature representing an exon     1.006922
Bio::SeqFeature::Gene::ExonI Interface for a feature representing an exon     1.006922
Bio::SeqFeature::Gene::GeneStructure A feature representing an arbitrarily complex structure of a gene     1.006922
Bio::SeqFeature::Gene::GeneStructureI A feature representing an arbitrarily complex structure of a gene     1.006922
Bio::SeqFeature::Gene::Intron An intron feature     1.006922
Bio::SeqFeature::Gene::NC_Feature superclass for non-coding features     1.006922
Bio::SeqFeature::Gene::Poly_A_site poly A feature     1.006922
Bio::SeqFeature::Gene::Promoter Describes a promoter     1.006922
Bio::SeqFeature::Gene::Transcript A feature representing a transcript     1.006922
Bio::SeqFeature::Gene::TranscriptI Interface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site.     1.006922
Bio::SeqFeature::Gene::UTR A feature representing an untranslated region that is part of a transcriptional unit     1.006922
Bio::SeqFeature::Generic Generic SeqFeature     1.006922
Bio::SeqFeature::Lite Lightweight Bio::SeqFeatureI class     1.006922
Bio::SeqFeature::PositionProxy handle features when truncation/revcom sequences span a feature     1.006922
Bio::SeqFeature::Primer Primer Generic SeqFeature     1.006922
Bio::SeqFeature::SiRNA::Oligo Perl object for small inhibitory RNAs.     1.006922
Bio::SeqFeature::SiRNA::Pair Perl object for small inhibitory RNA (SiRNA) oligo pairs     1.006922
Bio::SeqFeature::Similarity A sequence feature based on similarity     1.006922
Bio::SeqFeature::SimilarityPair Sequence feature based on the similarity of two sequences.     1.006922
Bio::SeqFeature::SubSeq Feature representing a subsequence     1.006922
Bio::SeqFeature::Tools::FeatureNamer generates unique persistent names for features     1.006922
Bio::SeqFeature::Tools::IDHandler maps $seq_feature->primary_tag     1.006922
Bio::SeqFeature::Tools::TypeMapper maps $seq_feature->primary_tag     1.006922
Bio::SeqFeature::Tools::Unflattener turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy     1.006922
Bio::SeqFeature::TypedSeqFeatureI a strongly typed SeqFeature     1.006922
Bio::SeqFeatureI Abstract interface of a Sequence Feature     1.006922
Bio::SeqI [Developers] Abstract Interface of Sequence (with features)     1.006922
Bio::SeqIO Handler for SeqIO Formats     1.006922
Bio::SeqIO::FTHelper Helper class for Embl/Genbank feature tables     1.006922
Bio::SeqIO::Handler::GenericRichSeqHandler Bio::HandlerI-based data handler for GenBank/EMBL/UniProt (and other) sequence data     1.006922
Bio::SeqIO::MultiFile Treating a set of files as a single input stream     1.006922
Bio::SeqIO::abi abi trace sequence input/output stream     1.006922
Bio::SeqIO::ace ace sequence input/output stream     1.006922
Bio::SeqIO::agave AGAVE sequence output stream.     1.006922
Bio::SeqIO::alf alf trace sequence input/output stream     1.006922
Bio::SeqIO::asciitree asciitree sequence input/output stream     1.006922
Bio::SeqIO::bsml BSML sequence input/output stream     1.006922
Bio::SeqIO::bsml_sax BSML sequence input/output stream using SAX     1.006922
Bio::SeqIO::chadoxml chadoxml sequence output stream     1.006922
Bio::SeqIO::chaos chaos sequence input/output stream     1.006922
Bio::SeqIO::chaosxml chaosxml sequence input/output stream     1.006922
Bio::SeqIO::ctf ctf trace sequence input/output stream     1.006922
Bio::SeqIO::embl EMBL sequence input/output stream     1.006922
Bio::SeqIO::embldriver EMBL sequence input/output stream     1.006922
Bio::SeqIO::entrezgene Entrez Gene ASN1 parser     1.006922
Bio::SeqIO::excel sequence input/output stream from a MSExcel-formatted table     1.006922
Bio::SeqIO::exp exp trace sequence input/output stream     1.006922
Bio::SeqIO::fasta fasta sequence input/output stream     1.006922
Bio::SeqIO::fastq fastq sequence input/output stream     1.006922
Bio::SeqIO::flybase_chadoxml FlyBase variant of chadoxml with sequence output stream     1.006922
Bio::SeqIO::game a class for parsing and writing game-XML     1.006922
Bio::SeqIO::game::featHandler a class for handling feature elements     1.006922
Bio::SeqIO::game::gameHandler PerlSAX handler for game-XML     1.006922
Bio::SeqIO::game::gameSubs a base class for game-XML parsing     1.006922
Bio::SeqIO::game::gameWriter a class for writing game-XML     1.006922
Bio::SeqIO::game::seqHandler a class for handling game-XML sequences     1.006922
Bio::SeqIO::gbdriver GenBank handler-based push parser     1.006922
Bio::SeqIO::gbxml GenBank sequence input/output stream using SAX     1.006922
Bio::SeqIO::gcg GCG sequence input/output stream     1.006922
Bio::SeqIO::genbank GenBank sequence input/output stream     1.006922
Bio::SeqIO::interpro InterProScan XML input/output stream     1.006922
Bio::SeqIO::kegg KEGG sequence input/output stream     1.006922
Bio::SeqIO::largefasta method i/o on very large fasta sequence files     1.006922
Bio::SeqIO::lasergene Lasergene sequence file input/output stream     1.006922
Bio::SeqIO::locuslink LocusLink input/output stream     1.006922
Bio::SeqIO::mbsout input stream for output by Teshima et al.'s mbs.     1.006922
Bio::SeqIO::metafasta metafasta sequence input/output stream     1.006922
Bio::SeqIO::msout input stream for output by Hudson's ms     1.006922
Bio::SeqIO::nexml NeXML sequence input/output stream     1.006922
Bio::SeqIO::phd phd file input/output stream     1.006922
Bio::SeqIO::pir PIR sequence input/output stream     1.006922
Bio::SeqIO::pln pln trace sequence input/output stream     1.006922
Bio::SeqIO::qual .qual file input/output stream     1.006922
Bio::SeqIO::raw raw sequence file input/output stream     1.006922
Bio::SeqIO::scf .scf file input/output stream     1.006922
Bio::SeqIO::seqxml SeqXML sequence input/output stream     1.006922
Bio::SeqIO::strider DNA strider sequence input/output stream     1.006922
Bio::SeqIO::swiss Swissprot sequence input/output stream     1.006922
Bio::SeqIO::swissdriver SwissProt/UniProt handler-based push parser     1.006922
Bio::SeqIO::tab nearly raw sequence file input/output stream. Reads/writes id"\t"sequence"\n"     1.006922
Bio::SeqIO::table sequence input/output stream from a delimited table     1.006922
Bio::SeqIO::tigr TIGR XML sequence input/output stream     1.006922
Bio::SeqIO::tigrxml Parse TIGR (new) XML     1.006922
Bio::SeqIO::tinyseq reading/writing sequences in NCBI TinySeq format     1.006922
Bio::SeqIO::tinyseq::tinyseqHandler XML event handlers to support NCBI TinySeq XML parsing     1.006922
Bio::SeqIO::ztr ztr trace sequence input/output stream     1.006922
Bio::SeqUtils Additional methods for PrimarySeq objects     1.006922
Bio::SimpleAlign Multiple alignments held as a set of sequences     1.006922
Bio::SimpleAnalysisI A simple interface to any (local or remote) analysis tool     1.006922
Bio::Species Generic species object.     1.006922
Bio::Structure::Atom Bioperl structure Object, describes an Atom     1.006922
Bio::Structure::Chain Bioperl structure Object, describes a chain     1.006922
Bio::Structure::Entry Bioperl structure Object, describes the whole entry     1.006922
Bio::Structure::IO Handler for Structure Formats     1.006922
Bio::Structure::IO::pdb PDB input/output stream     1.006922
Bio::Structure::Model Bioperl structure Object, describes a Model     1.006922
Bio::Structure::Residue Bioperl structure Object, describes a Residue     1.006922
Bio::Structure::SecStr::DSSP::Res Module for parsing/accessing dssp output     1.006922
Bio::Structure::SecStr::STRIDE::Res Module for parsing/accessing stride output     1.006922
Bio::Structure::StructureI Abstract Interface for a Structure objects     1.006922
Bio::Symbol::Alphabet BSANE/BioCORBA compliant symbol list alphabet     1.006922
Bio::Symbol::AlphabetI A Symbol Alphabet     1.006922
Bio::Symbol::DNAAlphabet A ready made DNA alphabet     1.006922
Bio::Symbol::ProteinAlphabet A ready made Protein alphabet     1.006922
Bio::Symbol::Symbol A biological symbol     1.006922
Bio::Symbol::SymbolI Interface for a Symbol     1.006922
Bio::Taxon A node in a represented taxonomy     1.006922
Bio::Taxonomy representing Taxonomy.     1.006922
Bio::Taxonomy::FactoryI interface to define how to access NCBI Taxonoy     1.006922
Bio::Taxonomy::Node A node in a represented taxonomy     1.006922
Bio::Taxonomy::Taxon Generic Taxonomic Entity object     1.006922
Bio::Taxonomy::Tree An Organism Level Implementation of TreeI interface.     1.006922
Bio::Tools::AlignFactory Base object for alignment factories     1.006922
Bio::Tools::Alignment::Consed A module to work with objects from consed .ace files     1.006922
Bio::Tools::Alignment::Trim A kludge to do specialized trimming of sequence based on quality.     1.006922
Bio::Tools::AmpliconSearch Find amplicons in a template using degenerate PCR primers     1.006922
Bio::Tools::Analysis::DNA::ESEfinder a wrapper around ESEfinder server     1.006922
Bio::Tools::Analysis::Protein::Domcut a wrapper around Domcut server     1.006922
Bio::Tools::Analysis::Protein::ELM a wrapper around the ELM server which predicts short functional motifs on amino acid sequences     1.006922
Bio::Tools::Analysis::Protein::GOR4 a wrapper around GOR4 protein secondary structure prediction server     1.006922
Bio::Tools::Analysis::Protein::HNN a wrapper around the HNN protein secondary structure prediction server     1.006922
Bio::Tools::Analysis::Protein::Mitoprot a wrapper around Mitoprot server     1.006922
Bio::Tools::Analysis::Protein::NetPhos a wrapper around NetPhos server     1.006922
Bio::Tools::Analysis::Protein::Scansite a wrapper around the Scansite server     1.006922
Bio::Tools::Analysis::Protein::Sopma a wrapper around the Sopma protein secondary structure prediction server     1.006922
Bio::Tools::Analysis::SimpleAnalysisBase abstract superclass for SimpleAnalysis implementations     1.006922
Bio::Tools::AnalysisResult Base class for analysis result objects and parsers     1.006922
Bio::Tools::Blat parser for Blat program     1.006922
Bio::Tools::CodonTable Codon table object     1.006922
Bio::Tools::Coil parser for Coil output     1.006922
Bio::Tools::ECnumber representation of EC numbers (Enzyme Classification)     1.006922
Bio::Tools::EMBOSS::Palindrome parse EMBOSS palindrome output     1.006922
Bio::Tools::EPCR Parse ePCR output and make features     1.006922
Bio::Tools::ERPIN a parser for ERPIN output     1.006922
Bio::Tools::ESTScan Results of one ESTScan run     1.006922
Bio::Tools::Eponine Results of one Eponine run     1.006922
Bio::Tools::Est2Genome Parse est2genome output, makes simple Bio::SeqFeature::Generic objects     1.006922
Bio::Tools::Fgenesh parse results of one Fgenesh run     1.006922
Bio::Tools::FootPrinter write sequence features in FootPrinter format     1.006922
Bio::Tools::GFF A Bio::SeqAnalysisParserI compliant GFF format parser     1.006922
Bio::Tools::Gel Calculates relative electrophoretic migration distances     1.006922
Bio::Tools::Geneid Results of one geneid run     1.006922
Bio::Tools::Genemark Results of one Genemark run     1.006922
Bio::Tools::Genewise Results of one Genewise run     1.006922
Bio::Tools::Genomewise Results of one Genomewise run     1.006922
Bio::Tools::Genscan Results of one Genscan run     1.006922
Bio::Tools::Glimmer parser for Glimmer 2.X/3.X prokaryotic and GlimmerM/GlimmerHMM eukaryotic gene predictions     1.006922
Bio::Tools::Grail Results of one Grail run     1.006922
Bio::Tools::GuessSeqFormat Module for determining the sequence format of the contents of a file, a string, or through a filehandle.     1.006922
Bio::Tools::HMMER::Domain One particular domain hit from HMMER     1.006922
Bio::Tools::HMMER::Results Object representing HMMER output results     1.006922
Bio::Tools::HMMER::Set Set of identical domains from HMMER matches     1.006922
Bio::Tools::Hmmpfam Parser for Hmmpfam program     1.006922
Bio::Tools::IUPAC Generates unique sequence objects or regular expressions from an ambiguous IUPAC sequence     1.006922
Bio::Tools::Infernal A parser for Infernal output     1.006922
Bio::Tools::Lucy Object for analyzing the output from Lucy, a vector and quality trimming program from TIGR     1.006922
Bio::Tools::MZEF Results of one MZEF run     1.006922
Bio::Tools::Match Parses output from Transfac's match(TM)     1.006922
Bio::Tools::OddCodes Object holding alternative alphabet coding for one protein sequence     1.006922
Bio::Tools::Phylo::Gerp Parses output from GERP     1.006922
Bio::Tools::Phylo::Gumby Parses output from gumby     1.006922
Bio::Tools::Phylo::Molphy parser for Molphy output     1.006922
Bio::Tools::Phylo::Molphy::Result container for data parsed from a ProtML run     1.006922
Bio::Tools::Phylo::PAML Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00     1.006922
Bio::Tools::Phylo::PAML::Codeml Parses output from the PAML program codeml.     1.006922
Bio::Tools::Phylo::PAML::ModelResult A container for NSSite Model Result from PAML     1.006922
Bio::Tools::Phylo::PAML::Result A PAML result set object     1.006922
Bio::Tools::Phylo::Phylip::ProtDist parser for ProtDist output     1.006922
Bio::Tools::Prediction::Exon A predicted exon feature     1.006922
Bio::Tools::Prediction::Gene a predicted gene structure feature     1.006922
Bio::Tools::Primer3 Create input for and work with the output from the program primer3     1.006922
Bio::Tools::Primer::Assessor::Base base class for common assessor things     1.006922
Bio::Tools::Primer::AssessorI interface for assessing primer pairs     1.006922
Bio::Tools::Primer::Feature position of a single primer     1.006922
Bio::Tools::Primer::Pair two primers on left and right side     1.006922
Bio::Tools::Prints Parser for FingerPRINTScanII program     1.006922
Bio::Tools::Profile parse Profile output     1.006922
Bio::Tools::Promoterwise parser for Promoterwise tab format output     1.006922
Bio::Tools::PrositeScan Parser for ps_scan result     1.006922
Bio::Tools::Protparam submit to and parse output from protparam ;     1.006922
Bio::Tools::Pseudowise Results of one Pseudowise run     1.006922
Bio::Tools::QRNA A Parser for qrna output     1.006922
Bio::Tools::RNAMotif A parser for RNAMotif output     1.006922
Bio::Tools::RandomDistFunctions A set of routines useful for generating random data in different distributions     1.006922
Bio::Tools::RepeatMasker a parser for RepeatMasker output     1.006922
Bio::Tools::Run::GenericParameters An object for the parameters used to run programs     1.006922
Bio::Tools::Run::ParametersI A Base object for the parameters used to run programs     1.006922
Bio::Tools::Run::RemoteBlast Object for remote execution of the NCBI Blast via HTTP     1.006922
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.     1.006922
Bio::Tools::Run::StandAloneNCBIBlast Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). With experimental support for NCBI rpsblast.     1.006922
Bio::Tools::Run::StandAloneWUBlast Object for the local execution of WU-Blast.     1.006922
Bio::Tools::Run::WrapperBase Extensions to WrapperBase for handling programs with commands *ALPHA*     1.006922
Bio::Tools::Seg parse seg output     1.006922
Bio::Tools::SeqPattern represent a sequence pattern or motif     1.006922
Bio::Tools::SeqPattern::Backtranslate     1.006922
Bio::Tools::SeqStats Object holding statistics for one particular sequence     1.006922
Bio::Tools::SeqWords Object holding n-mer statistics for a sequence     1.006922
Bio::Tools::SiRNA Perl object for designing small inhibitory RNAs.     1.006922
Bio::Tools::SiRNA::Ruleset::saigo Perl object implementing the Saigo group's rules for designing small inhibitory RNAs     1.006922
Bio::Tools::SiRNA::Ruleset::tuschl Perl object implementing the tuschl group's rules for designing small inhibitory RNAs     1.006922
Bio::Tools::Sigcleave Bioperl object for sigcleave analysis     1.006922
Bio::Tools::Signalp parser for Signalp output     1.006922
Bio::Tools::Signalp::ExtendedSignalp enhanced parser for Signalp output     1.006922
Bio::Tools::Sim4::Exon A single exon determined by an alignment     1.006922
Bio::Tools::Sim4::Results Results of one Sim4 run     1.006922
Bio::Tools::Spidey::Exon A single exon determined by an alignment     1.006922
Bio::Tools::Spidey::Results Results of a Spidey run     1.006922
Bio::Tools::TandemRepeatsFinder a parser for Tandem Repeats Finder output     1.006922
Bio::Tools::TargetP Results of one TargetP run     1.006922
Bio::Tools::Tmhmm parse TMHMM output (TransMembrane HMM)     1.006922
Bio::Tools::dpAlign Perl extension to do pairwise dynamic programming sequence alignment     1.006922
Bio::Tools::ipcress Parse ipcress output and make features     1.006922
Bio::Tools::isPcr Parse isPcr output and make features     1.006922
Bio::Tools::pICalculator calculate the isoelectric point of a protein     1.006922
Bio::Tools::pSW pairwise Smith Waterman object     1.006922
Bio::Tools::tRNAscanSE A parser for tRNAscan-SE output     1.006922
Bio::Tree::AlleleNode A Node with Alleles attached     1.006922
Bio::Tree::AnnotatableNode A Tree Node with support for annotation     1.006922
Bio::Tree::Compatible Testing compatibility of phylogenetic trees with nested taxa.     1.006922
Bio::Tree::DistanceFactory Construct a tree using distance based methods     1.006922
Bio::Tree::Draw::Cladogram Drawing phylogenetic trees in Encapsulated PostScript (EPS) format.     1.006922
Bio::Tree::Node A Simple Tree Node     1.006922
Bio::Tree::NodeI Interface describing a Tree Node     1.006922
Bio::Tree::NodeNHX A Simple Tree Node with support for NHX tags     1.006922
Bio::Tree::RandomFactory TreeFactory for generating Random Trees     1.006922
Bio::Tree::Statistics Calculate certain statistics for a Tree     1.006922
Bio::Tree::Tree An implementation of the TreeI interface.     1.006922
Bio::Tree::TreeFunctionsI Decorated Interface implementing basic Tree exploration methods     1.006922
Bio::Tree::TreeI A Tree object suitable for lots of things, designed originally for Phylogenetic Trees.     1.006922
Bio::TreeIO Parser for Tree files     1.006922
Bio::TreeIO::NewickParser which implements a newick string parser as a finite state machine which enables it to parse the full Newick specification.     1.006922
Bio::TreeIO::TreeEventBuilder Build Bio::Tree::Tree's and Bio::Tree::Node's from Events     1.006922
Bio::TreeIO::cluster A TreeIO driver module for parsing Algorithm::Cluster::treecluster() output     1.006922
Bio::TreeIO::lintree Parser for lintree output trees     1.006922
Bio::TreeIO::newick     1.006922
Bio::TreeIO::nexml A TreeIO driver module for parsing NeXML tree files     1.006922
Bio::TreeIO::nexus A TreeIO driver module for parsing Nexus tree output from PAUP     1.006922
Bio::TreeIO::nhx TreeIO implementation for parsing Newick/New Hampshire eXtendend (NHX) format.     1.006922
Bio::TreeIO::pag Bio::TreeIO driver for Pagel format     1.006922
Bio::TreeIO::phyloxml TreeIO implementation for parsing PhyloXML format.     1.006922
Bio::TreeIO::svggraph A simple output format that converts a Tree object to an SVG output     1.006922
Bio::TreeIO::tabtree A simple output format which displays a tree as an ASCII drawing     1.006922
Bio::UpdateableSeqI Descendant of Bio::SeqI that allows updates     1.006922
Bio::Variation::AAChange Sequence change class for polypeptides     1.006922
Bio::Variation::AAReverseMutate point mutation and codon information from single amino acid changes     1.006922
Bio::Variation::Allele Sequence object with allele-specific attributes     1.006922
Bio::Variation::DNAMutation DNA level mutation class     1.006922
Bio::Variation::IO Handler for sequence variation IO Formats     1.006922
Bio::Variation::IO::flat flat file sequence variation input/output stream     1.006922
Bio::Variation::IO::xml XML sequence variation input/output stream     1.006922
Bio::Variation::RNAChange Sequence change class for RNA level     1.006922
Bio::Variation::SNP submitted SNP     1.006922
Bio::Variation::SeqDiff Container class for mutation/variant descriptions     1.006922
Bio::Variation::VariantI Sequence Change SeqFeature abstract class     1.006922
Bio::WebAgent A base class for Web (any protocol) access     1.006922
BioPerl Perl Modules for Biology      
Deobfuscator get BioPerl method and package information from a Berkeley DB     0.0.3
FeatureStore     1.006922

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_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