Christopher Fields / BioPerl-1.6.921

Modules

Bio::Align::AlignI	An interface for describing sequence alignments.	1.006921
Bio::Align::DNAStatistics	Calculate some statistics for a DNA alignment	1.006921
Bio::Align::Graphics	Graphic Rendering of Bio::Align::AlignI Objects	1.006921
Bio::Align::PairwiseStatistics	Base statistic object for Pairwise Alignments	1.006921
Bio::Align::ProteinStatistics	Calculate Protein Alignment statistics (mostly distances)	1.006921
Bio::Align::StatisticsI	Calculate some statistics for an alignment	1.006921
Bio::Align::Utilities	A collection of utilities regarding converting and manipulating alignment objects	1.006921
Bio::AlignIO	Handler for AlignIO Formats	1.006921
Bio::AlignIO::Handler::GenericAlignHandler	Bio::HandlerI-based generic data handler class for alignment-based data	1.006921
Bio::AlignIO::arp	ARP MSA Sequence input/output stream	1.006921
Bio::AlignIO::bl2seq	bl2seq sequence input/output stream	1.006921
Bio::AlignIO::clustalw	clustalw sequence input/output stream	1.006921
Bio::AlignIO::emboss	Parse EMBOSS alignment output (from applications water and needle)	1.006921
Bio::AlignIO::fasta	fasta MSA Sequence input/output stream	1.006921
Bio::AlignIO::largemultifasta	Largemultifasta MSA Sequence input/output stream	1.006921
Bio::AlignIO::maf	Multiple Alignment Format sequence input stream	1.006921
Bio::AlignIO::mase	mase sequence input/output stream	1.006921
Bio::AlignIO::mega	Parse and Create MEGA format data files	1.006921
Bio::AlignIO::meme	meme sequence input/output stream	1.006921
Bio::AlignIO::metafasta	Metafasta MSA Sequence input/output stream	1.006921
Bio::AlignIO::msf	msf sequence input/output stream	1.006921
Bio::AlignIO::nexml	NeXML format sequence alignment input/output stream driver	1.006921
Bio::AlignIO::nexus	NEXUS format sequence input/output stream	1.006921
Bio::AlignIO::pfam	pfam sequence input/output stream	1.006921
Bio::AlignIO::phylip	PHYLIP format sequence input/output stream	1.006921
Bio::AlignIO::po	po MSA Sequence input/output stream	1.006921
Bio::AlignIO::proda	proda sequence input/output stream	1.006921
Bio::AlignIO::prodom	prodom sequence input/output stream	1.006921
Bio::AlignIO::psi	Read/Write PSI-BLAST profile alignment files	1.006921
Bio::AlignIO::selex	selex sequence input/output stream	1.006921
Bio::AlignIO::stockholm	stockholm sequence input/output stream	1.006921
Bio::AlignIO::xmfa	XMFA MSA Sequence input/output stream	1.006921
Bio::AnalysisI	An interface to any (local or remote) analysis tool	1.006921
Bio::AnalysisI::JobI		1.006921
Bio::AnalysisParserI	Generic analysis output parser interface	1.006921
Bio::AnalysisResultI	Interface for analysis result objects	1.006921
Bio::AnnotatableI	the base interface an annotatable object must implement	1.006921
Bio::Annotation::AnnotationFactory	Instantiates a new Bio::AnnotationI (or derived class) through a factory	1.006921
Bio::Annotation::Collection	Default Perl implementation of AnnotationCollectionI	1.006921
Bio::Annotation::Comment	A comment object, holding text	1.006921
Bio::Annotation::DBLink	untyped links between databases	1.006921
Bio::Annotation::OntologyTerm	An ontology term adapted to AnnotationI	1.006921
Bio::Annotation::Reference	Specialised DBLink object for Literature References	1.006921
Bio::Annotation::Relation	Relationship (pairwise) with other objects SeqI and NodeI;	1.006921
Bio::Annotation::SimpleValue	A simple scalar	1.006921
Bio::Annotation::StructuredValue	A scalar with embedded structured information	1.006921
Bio::Annotation::TagTree	AnnotationI with tree-like hierarchal key-value relationships ('structured tags') that can be represented as simple text.	1.006921
Bio::Annotation::Target	Provides an object which represents a target (ie, a similarity hit) from one object to something in another database	1.006921
Bio::Annotation::Tree	Provide a tree as an annotation to a Bio::AnnotatableI object	1.006921
Bio::Annotation::TypeManager	Manages types for annotation collections	1.006921
Bio::AnnotationCollectionI	Interface for annotation collections	1.006921
Bio::AnnotationI	Annotation interface	1.006921
Bio::Assembly::Contig	Perl module to hold and manipulate sequence assembly contigs.	1.006921
Bio::Assembly::ContigAnalysis	Perform analysis on sequence assembly contigs.	1.006921
Bio::Assembly::IO	Handler for Assembly::IO Formats	1.006921
Bio::Assembly::IO::ace	module to load ACE files from various assembly programs	1.006921
Bio::Assembly::IO::bowtie	An IO module for assemblies in Bowtie format BETA	1.006921
Bio::Assembly::IO::maq	Driver to read assembly files in maq format BETA	1.006921
Bio::Assembly::IO::phrap	driver to load phrap.out files.	1.006921
Bio::Assembly::IO::sam	An IO module for assemblies in Sam format BETA	1.006921
Bio::Assembly::IO::tigr	Driver to read and write assembly files in the TIGR Assembler v2 default format.	1.006921
Bio::Assembly::Scaffold	Perl module to hold and manipulate sequence assembly data.	1.006921
Bio::Assembly::ScaffoldI	Abstract Inteface of Sequence Assemblies	1.006921
Bio::Assembly::Singlet	Perl module to hold and manipulate singlets from sequence assembly contigs.	1.006921
Bio::Assembly::Tools::ContigSpectrum	create and manipulate contig spectra	1.006921
Bio::Cluster::ClusterFactory	Instantiates a new Bio::ClusterI (or derived class) through a factory	1.006921
Bio::Cluster::FamilyI	Family Interface	1.006921
Bio::Cluster::SequenceFamily	Sequence Family object	1.006921
Bio::Cluster::UniGene	UniGene object	1.006921
Bio::Cluster::UniGeneI	abstract interface of UniGene object	1.006921
Bio::ClusterI	Cluster Interface	1.006921
Bio::ClusterIO	Handler for Cluster Formats	1.006921
Bio::ClusterIO::dbsnp	dbSNP input stream	1.006921
Bio::ClusterIO::unigene	UniGene input stream	1.006921
Bio::CodonUsage::IO	for reading and writing codon usage tables to file	1.006921
Bio::CodonUsage::Table	for access to the Codon usage Database at http://www.kazusa.or.jp/codon.	1.006921
Bio::Coordinate::Chain	Mapping locations through a chain of coordinate mappers	1.006921
Bio::Coordinate::Collection	Noncontinuous match between two coordinate sets	1.006921
Bio::Coordinate::ExtrapolatingPair	Continuous match between two coordinate sets	1.006921
Bio::Coordinate::GeneMapper	transformations between gene related coordinate systems	1.006921
Bio::Coordinate::Graph	Finds shortest path between nodes in a graph	1.006921
Bio::Coordinate::MapperI	Interface describing coordinate mappers	1.006921
Bio::Coordinate::Pair	Continuous match between two coordinate sets	1.006921
Bio::Coordinate::Result	Results from coordinate transformation	1.006921
Bio::Coordinate::Result::Gap	Another name for Bio::Location::Simple	1.006921
Bio::Coordinate::Result::Match	Another name for Bio::Location::Simple	1.006921
Bio::Coordinate::ResultI	Interface to identify coordinate mapper results	1.006921
Bio::Coordinate::Utils	Additional methods to create Bio::Coordinate objects	1.006921
Bio::DB::Ace	Database object interface to ACeDB servers	1.006921
Bio::DB::BioFetch	Database object interface to BioFetch retrieval	1.006921
Bio::DB::CUTG	for access to the Codon usage Database at http://www.kazusa.or.jp/codon.	1.006921
Bio::DB::DBFetch	Database object for retrieving using the dbfetch script	1.006921
Bio::DB::EMBL	Database object interface for EMBL entry retrieval	1.006921
Bio::DB::EntrezGene	Database object interface to Entrez Gene	1.006921
Bio::DB::Expression	DESCRIPTION of Object	1.006921
Bio::DB::Expression::geo	*** DESCRIPTION of Class	1.006921
Bio::DB::Failover	A Bio::DB::RandomAccessI compliant class which wraps a prioritized list of DBs	1.006921
Bio::DB::Fasta	Fast indexed access to fasta files	1.006921
Bio::DB::Fasta::Subdir		1.006921
Bio::DB::FileCache	In file cache for BioSeq objects	1.006921
Bio::DB::Flat	Interface for indexed flat files	1.006921
Bio::DB::Flat::BDB	Interface for BioHackathon standard BDB-indexed flat file	1.006921
Bio::DB::Flat::BDB::embl	embl adaptor for Open-bio standard BDB-indexed flat file	1.006921
Bio::DB::Flat::BDB::fasta	fasta adaptor for Open-bio standard BDB-indexed flat file	1.006921
Bio::DB::Flat::BDB::genbank	genbank adaptor for Open-bio standard BDB-indexed flat file	1.006921
Bio::DB::Flat::BDB::swiss	swissprot adaptor for Open-bio standard BDB-indexed flat file	1.006921
Bio::DB::Flat::BinarySearch	BinarySearch search indexing system for sequence files	1.006921
Bio::DB::GFF	Storage and retrieval of sequence annotation data	1.006921
Bio::DB::GFF::Adaptor::ace	ace interface (for multiple inheritance)	1.006921
Bio::DB::GFF::Adaptor::berkeleydb	Bio::DB::GFF database adaptor for in-memory databases	1.006921
Bio::DB::GFF::Adaptor::berkeleydb::iterator	iterator for Bio::DB::GFF::Adaptor::berkeleydb	1.006921
Bio::DB::GFF::Adaptor::biofetch	Cache BioFetch objects in a Bio::DB::GFF database	1.006921
Bio::DB::GFF::Adaptor::biofetch_oracle	Cache BioFetch objects in a Bio::DB::GFF database	1.006921
Bio::DB::GFF::Adaptor::dbi	Database adaptor for DBI (SQL) databases	1.006921
Bio::DB::GFF::Adaptor::dbi::caching_handle	Cache for database handles	1.006921
Bio::DB::GFF::Adaptor::dbi::faux_dbh		1.006921
Bio::DB::GFF::Adaptor::dbi::iterator	iterator for Bio::DB::GFF::Adaptor::dbi	1.006921
Bio::DB::GFF::Adaptor::dbi::mysql	Database adaptor for a specific mysql schema	1.006921
Bio::DB::GFF::Adaptor::dbi::mysqlace	Unholy union between mysql GFF database and acedb database	1.006921
Bio::DB::GFF::Adaptor::dbi::mysqlcmap	Database adaptor for an integraded CMap/GBrowse mysql schema	1.006921
Bio::DB::GFF::Adaptor::dbi::mysqlopt	Deprecated database adaptor	1.006921
Bio::DB::GFF::Adaptor::dbi::oracle	Database adaptor for a specific oracle schema	1.006921
Bio::DB::GFF::Adaptor::dbi::oracleace	Unholy union between oracle GFF database and acedb database	1.006921
Bio::DB::GFF::Adaptor::dbi::pg	Database adaptor for a specific postgres schema	1.006921
Bio::DB::GFF::Adaptor::dbi::pg_fts	Database adaptor for a specific postgres schema with a TSearch2 implementation	1.006921
Bio::DB::GFF::Adaptor::memory	Bio::DB::GFF database adaptor for in-memory databases	1.006921
Bio::DB::GFF::Adaptor::memory::feature_serializer	utility methods for serializing and deserializing GFF features	1.006921
Bio::DB::GFF::Adaptor::memory::iterator	iterator for Bio::DB::GFF::Adaptor::memory	1.006921
Bio::DB::GFF::Aggregator	Aggregate GFF groups into composite features	1.006921
Bio::DB::GFF::Aggregator::alignment	Alignment aggregator	1.006921
Bio::DB::GFF::Aggregator::clone	Clone aggregator	1.006921
Bio::DB::GFF::Aggregator::coding	The Coding Region Aggregator	1.006921
Bio::DB::GFF::Aggregator::gene	Sequence Ontology Geene	1.006921
Bio::DB::GFF::Aggregator::match	Match aggregator	1.006921
Bio::DB::GFF::Aggregator::none	No aggregation	1.006921
Bio::DB::GFF::Aggregator::orf	An aggregator for orf regions	1.006921
Bio::DB::GFF::Aggregator::processed_transcript	Sequence Ontology Transcript	1.006921
Bio::DB::GFF::Aggregator::so_transcript	Sequence Ontology Transcript	1.006921
Bio::DB::GFF::Aggregator::transcript	Transcript aggregator	1.006921
Bio::DB::GFF::Aggregator::ucsc_acembly	UCSC acembly aggregator	1.006921
Bio::DB::GFF::Aggregator::ucsc_ensgene	UCSC ensGene aggregator	1.006921
Bio::DB::GFF::Aggregator::ucsc_genscan	UCSC genscan aggregator	1.006921
Bio::DB::GFF::Aggregator::ucsc_refgene	UCSC refGene aggregator	1.006921
Bio::DB::GFF::Aggregator::ucsc_sanger22	UCSC sanger22 aggregator	1.006921
Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo	UCSC sanger22pseudo aggregator	1.006921
Bio::DB::GFF::Aggregator::ucsc_softberry	UCSC softberry aggregator	1.006921
Bio::DB::GFF::Aggregator::ucsc_twinscan	UCSC twinscan aggregator	1.006921
Bio::DB::GFF::Aggregator::ucsc_unigene	UCSC UniGene aggregator	1.006921
Bio::DB::GFF::Featname	The name of a feature	1.006921
Bio::DB::GFF::Feature	A relative segment identified by a feature type	1.006921
Bio::DB::GFF::FeatureIterator		1.006921
Bio::DB::GFF::Homol	A segment of DNA that is homologous to another	1.006921
Bio::DB::GFF::ID_Iterator		1.006921
Bio::DB::GFF::RelSegment	Sequence segment with relative coordinate support	1.006921
Bio::DB::GFF::Segment	Simple DNA segment object	1.006921
Bio::DB::GFF::Typename	The name of a feature type	1.006921
Bio::DB::GFF::Util::Binning	binning utility for Bio::DB::GFF index	1.006921
Bio::DB::GFF::Util::Rearrange	rearrange utility	1.006921
Bio::DB::GenBank	Database object interface to GenBank	1.006921
Bio::DB::GenPept	Database object interface to GenPept	1.006921
Bio::DB::GenericWebAgent	helper base class for parameter-based remote server access and response retrieval.	1.006921
Bio::DB::HIV	Database object interface to the Los Alamos HIV Sequence Database	1.006921
Bio::DB::HIV::HIVAnnotProcessor	Adds HIV-specific annotations to Bio::SeqIO streams	1.006921
Bio::DB::HIV::HIVQueryHelper	Routines and packages used by Bio::DB::HIV and Bio::DB::Query::HIVQuery	1.006921
Bio::DB::InMemoryCache	Abstract interface for a sequence database	1.006921
Bio::DB::Indexed::Stream		1.006921
Bio::DB::IndexedBase	Base class for modules using indexed sequence files	1.006921
Bio::DB::LocationI	A RandomAccessI-like abstract interface for retrieving location data from a sequence database and returning Bio::LocationI objects	1.006921
Bio::DB::MeSH	Term retrieval from a Web MeSH database	1.006921
Bio::DB::NCBIHelper	A collection of routines useful for queries to NCBI databases.	1.006921
Bio::DB::Qual	Fast indexed access to quality files	1.006921
Bio::DB::Query::GenBank	Build a GenBank Entrez Query	1.006921
Bio::DB::Query::HIVQuery	Query interface to the Los Alamos HIV Sequence Database	1.006921
Bio::DB::Query::WebQuery	Helper class for web-based sequence queryies	1.006921
Bio::DB::QueryI	Object Interface to queryable sequence databases	1.006921
Bio::DB::RandomAccessI	Abstract interface for a sequence database	1.006921
Bio::DB::RefSeq	Database object interface for RefSeq retrieval	1.006921
Bio::DB::ReferenceI	A RandomAccessI-like abstract interface for retrieving Reference data from a sequence database and returning Bio::Annotation::Reference objects	1.006921
Bio::DB::Registry	Access to the Open Bio Database Access registry scheme	1.006921
Bio::DB::SeqFeature	Normalized feature for use with Bio::DB::SeqFeature::Store	1.006921
Bio::DB::SeqFeature::NormalizedFeature	Normalized feature for use with Bio::DB::SeqFeature::Store	1.006921
Bio::DB::SeqFeature::NormalizedFeatureI	Interface for normalized features	1.006921
Bio::DB::SeqFeature::NormalizedTableFeatureI	Interface for normalized features whose hierarchy is stored in a table	1.006921
Bio::DB::SeqFeature::Segment	Location-based access to genome annotation data	1.006921
Bio::DB::SeqFeature::Store	Storage and retrieval of sequence annotation data	1.006921
Bio::DB::SeqFeature::Store::DBI::Iterator	utility methods for creating and iterating over SeqFeature records	1.006921
Bio::DB::SeqFeature::Store::DBI::Pg	PostgreSQL implementation of Bio::DB::SeqFeature::Store	1.006921
Bio::DB::SeqFeature::Store::DBI::SQLite	SQLite implementation of Bio::DB::SeqFeature::Store	1.006921
Bio::DB::SeqFeature::Store::DBI::mysql	Mysql implementation of Bio::DB::SeqFeature::Store	1.006921
Bio::DB::SeqFeature::Store::FeatureFileLoader	feature file loader for Bio::DB::SeqFeature::Store	1.006921
Bio::DB::SeqFeature::Store::FeatureIterator		1.006921
Bio::DB::SeqFeature::Store::GFF2Loader	GFF2 file loader for Bio::DB::SeqFeature::Store	1.006921
Bio::DB::SeqFeature::Store::GFF3Loader	GFF3 file loader for Bio::DB::SeqFeature::Store	1.006921
Bio::DB::SeqFeature::Store::LoadHelper	Internal utility for Bio::DB::SeqFeature::Store	1.006921
Bio::DB::SeqFeature::Store::Loader	Loader	1.006921
Bio::DB::SeqFeature::Store::bdb	fetch and store objects from a BerkeleyDB	1.006921
Bio::DB::SeqFeature::Store::berkeleydb	Storage and retrieval of sequence annotation data in Berkeleydb files	1.006921
Bio::DB::SeqFeature::Store::berkeleydb3	Storage and retrieval of sequence annotation data in Berkeleydb files	1.006921
Bio::DB::SeqFeature::Store::berkeleydb::Iterator		1.006921
Bio::DB::SeqFeature::Store::memory	In-memory implementation of Bio::DB::SeqFeature::Store	1.006921
Bio::DB::SeqFeature::Store::memory::Iterator		1.006921
Bio::DB::SeqHound	Database object interface to SeqHound	1.006921
Bio::DB::SeqI	Abstract Interface for Sequence databases	1.006921
Bio::DB::SeqVersion	front end to querying databases for identifier versions	1.006921
Bio::DB::SeqVersion::gi	interface to NCBI Sequence Revision History page	1.006921
Bio::DB::SwissProt	Database object interface to SwissProt retrieval	1.006921
Bio::DB::TFBS	Access to a Transcription Factor Binding Site database	1.006921
Bio::DB::TFBS::transfac_pro	An implementation of Bio::DB::TFBS which uses local flat files for transfac pro	1.006921
Bio::DB::Taxonomy	Access to a taxonomy database	1.006921
Bio::DB::Taxonomy::entrez	Taxonomy Entrez driver	1.006921
Bio::DB::Taxonomy::flatfile	Use the NCBI taxonomy from local indexed flat files	1.006921
Bio::DB::Taxonomy::greengenes	Use the Greengenes taxonomy	1.006921
Bio::DB::Taxonomy::list	An implementation of Bio::DB::Taxonomy that accepts lists of words to build a database	1.006921
Bio::DB::Taxonomy::silva	Use the Silva taxonomy	1.006921
Bio::DB::Universal	Artificial database that delegates to specific databases	1.006921
Bio::DB::UpdateableSeqI	An interface for writing to a database of sequences.	1.006921
Bio::DB::WebDBSeqI	Object Interface to generalize Web Databases for retrieving sequences	1.006921
Bio::DBLinkContainerI	Abstract interface for any object wanting to use database cross references	1.006921
Bio::Das::FeatureTypeI	Simple interface to Sequence Ontology feature types	1.006921
Bio::Das::SegmentI	DAS-style access to a feature database	1.006921
Bio::DasI	DAS-style access to a feature database	1.006921
Bio::DescribableI	interface for objects with human readable names and descriptions	1.006921
Bio::Draw::Pictogram	generate SVG output of Pictogram display for consensus motifs	1.006921
Bio::Event::EventGeneratorI	This interface describes the basic event generator class.	1.006921
Bio::Event::EventHandlerI	An Event Handler Interface	1.006921
Bio::Factory::AnalysisI	An interface to analysis tool factory	1.006921
Bio::Factory::ApplicationFactoryI	Interface class for Application Factories	1.006921
Bio::Factory::DriverFactory	Base class for factory classes loading drivers	1.006921
Bio::Factory::FTLocationFactory	A FeatureTable Location Parser	1.006921
Bio::Factory::LocationFactoryI	A factory interface for generating locations from a string	1.006921
Bio::Factory::MapFactoryI	A Factory for getting markers	1.006921
Bio::Factory::ObjectBuilderI	Interface for an object builder	1.006921
Bio::Factory::ObjectFactory	Instantiates a new Bio::Root::RootI (or derived class) through a factory	1.006921
Bio::Factory::ObjectFactoryI	A General object creator factory	1.006921
Bio::Factory::SeqAnalysisParserFactory	class capable of creating SeqAnalysisParserI compliant parsers	1.006921
Bio::Factory::SeqAnalysisParserFactoryI	interface describing objects capable of creating SeqAnalysisParserI compliant parsers	1.006921
Bio::Factory::SequenceFactoryI	This interface allows for generic building of sequences in factories which create sequences (like SeqIO)	1.006921
Bio::Factory::SequenceProcessorI	Interface for chained sequence processing algorithms	1.006921
Bio::Factory::SequenceStreamI	Interface describing the basics of a Sequence Stream.	1.006921
Bio::Factory::TreeFactoryI	Factory Interface for getting and writing trees from/to a data stream	1.006921
Bio::FeatureHolderI	the base interface an object with features must implement	1.006921
Bio::HandlerBaseI	Interface class for handler methods which interact with any event-driven parsers (drivers).	1.006921
Bio::IdCollectionI	interface for objects with multiple identifiers	1.006921
Bio::IdentifiableI	interface for objects with identifiers	1.006921
Bio::Index::Abstract	Abstract interface for indexing a flat file	1.006921
Bio::Index::AbstractSeq	base class for AbstractSeq	1.006921
Bio::Index::Blast	Indexes Blast reports and supports retrieval based on query accession(s)	1.006921
Bio::Index::BlastTable	Indexes tabular Blast reports (-m 8 or -m 9 format) and supports retrieval based on query accession(s)	1.006921
Bio::Index::EMBL	Interface for indexing (multiple) EMBL/Swissprot .dat files (i.e. flat file EMBL/Swissprot format).	1.006921
Bio::Index::Fasta	Interface for indexing (multiple) fasta files	1.006921
Bio::Index::Fastq	Interface for indexing (multiple) fastq files	1.006921
Bio::Index::GenBank	Interface for indexing one or more GenBank files (i.e. flat file GenBank format).	1.006921
Bio::Index::Hmmer	indexes HMMER reports and supports retreival based on query	1.006921
Bio::Index::Qual	Interface for indexing (multiple) fasta qual files	1.006921
Bio::Index::Stockholm		1.006921
Bio::Index::SwissPfam	Interface for indexing swisspfam files	1.006921
Bio::Index::Swissprot	Interface for indexing one or more Swissprot files.	1.006921
Bio::LiveSeq::AARange	AARange abstract class for LiveSeq	1.006921
Bio::LiveSeq::Chain	DoubleChain DataStructure for Perl	1.006921
Bio::LiveSeq::ChainI	Double linked chain data structure	1.006921
Bio::LiveSeq::DNA	DNA object for LiveSeq	1.006921
Bio::LiveSeq::Exon	Range abstract class for LiveSeq	1.006921
Bio::LiveSeq::Gene	Range abstract class for LiveSeq	1.006921
Bio::LiveSeq::IO::BioPerl	Loader for LiveSeq from EMBL entries with BioPerl	1.006921
Bio::LiveSeq::IO::Loader	Parent Loader for LiveSeq	1.006921
Bio::LiveSeq::Intron	Range abstract class for LiveSeq	1.006921
Bio::LiveSeq::Mutation	Mutation event descriptor class	1.006921
Bio::LiveSeq::Mutator	Package mutating LiveSequences	1.006921
Bio::LiveSeq::Prim_Transcript	Prim_Transcript class for LiveSeq	1.006921
Bio::LiveSeq::Range	Range abstract class for LiveSeq	1.006921
Bio::LiveSeq::Repeat_Region	Repeat_Region class for LiveSeq	1.006921
Bio::LiveSeq::Repeat_Unit	Repeat_Unit class for LiveSeq	1.006921
Bio::LiveSeq::SeqI	Abstract sequence interface class for LiveSeq	1.006921
Bio::LiveSeq::Transcript	Transcript class for LiveSeq	1.006921
Bio::LiveSeq::Translation	Translation class for LiveSeq	1.006921
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.	1.006921
Bio::Location::Atomic	Implementation of a Atomic Location on a Sequence	1.006921
Bio::Location::AvWithinCoordPolicy	class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise	1.006921
Bio::Location::CoordinatePolicyI	Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location	1.006921
Bio::Location::Fuzzy	Implementation of a Location on a Sequence which has unclear start and/or end locations	1.006921
Bio::Location::FuzzyLocationI	Abstract interface of a Location on a Sequence which has unclear start/end location	1.006921
Bio::Location::NarrowestCoordPolicy	class implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range	1.006921
Bio::Location::Simple	Implementation of a Simple Location on a Sequence	1.006921
Bio::Location::Split	Implementation of a Location on a Sequence which has multiple locations (start/end points)	1.006921
Bio::Location::SplitLocationI	Abstract interface of a Location on a Sequence which has multiple locations (start/end points)	1.006921
Bio::Location::WidestCoordPolicy	class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable range	1.006921
Bio::LocationI	Abstract interface of a Location on a Sequence	1.006921
Bio::Map::Clone	An central map object representing a clone	1.006921
Bio::Map::Contig	A MapI implementation handling the contigs of a Physical Map (such as FPC)	1.006921
Bio::Map::CytoMap	A Bio::MapI compliant map implementation handling cytogenic bands	1.006921
Bio::Map::CytoMarker	An object representing a marker.	1.006921
Bio::Map::CytoPosition	Marker class with cytogenetic band storing attributes	1.006921
Bio::Map::EntityI	An Entity Interface	1.006921
Bio::Map::FPCMarker	An central map object representing a marker	1.006921
Bio::Map::Gene	An gene modelled as a mappable element.	1.006921
Bio::Map::GeneMap	A MapI implementation to represent the area around a gene	1.006921
Bio::Map::GenePosition	A typed position, suitable for modelling the various regions of a gene.	1.006921
Bio::Map::GeneRelative	Represents being relative to named sub-regions of a gene.	1.006921
Bio::Map::LinkageMap	A representation of a genetic linkage map.	1.006921
Bio::Map::LinkagePosition	Create a Position for a Marker that will be placed on a Bio::Map::LinkageMap	1.006921
Bio::Map::MapI	Interface for describing Map objects in bioperl	1.006921
Bio::Map::Mappable	An object representing a generic map element that can have multiple locations in several maps.	1.006921
Bio::Map::MappableI	An object that can be placed in a map	1.006921
Bio::Map::Marker	An central map object representing a generic marker that can have multiple location in several maps.	1.006921
Bio::Map::MarkerI	Interface for basic marker functionality	1.006921
Bio::Map::Microsatellite	An object representing a Microsatellite marker.	1.006921
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.	1.006921
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.	1.006921
Bio::Map::Physical	A class for handling a Physical Map (such as FPC)	1.006921
Bio::Map::Position	A single position of a Marker, or the range over which that marker lies, in a Map	1.006921
Bio::Map::PositionHandler	A Position Handler Implementation	1.006921
Bio::Map::PositionHandlerI	A Position Handler Interface	1.006921
Bio::Map::PositionI	Abstracts the notion of a position having a value in the context of a marker and a Map	1.006921
Bio::Map::PositionWithSequence	A position with a sequence.	1.006921
Bio::Map::Prediction	An object representing the predictions of something that can have multiple locations in several maps.	1.006921
Bio::Map::Relative	Represents what a Position's coordiantes are relative to.	1.006921
Bio::Map::RelativeI	Interface for describing what a Position's coordiantes are relative to.	1.006921
Bio::Map::SimpleMap	A MapI implementation handling the basics of a Map	1.006921
Bio::Map::TranscriptionFactor	A transcription factor modelled as a mappable element	1.006921
Bio::MapIO	A Map Factory object	1.006921
Bio::MapIO::fpc	A FPC Map reader	1.006921
Bio::MapIO::mapmaker	A Mapmaker Map reader	1.006921
Bio::Matrix::Generic	A generic matrix implementation	1.006921
Bio::Matrix::IO	A factory for Matrix parsing	1.006921
Bio::Matrix::IO::mlagan	A parser for the mlagan substitution matrix	1.006921
Bio::Matrix::IO::phylip	A parser for PHYLIP distance matricies	1.006921
Bio::Matrix::IO::scoring	A parser for PAM/BLOSUM matricies	1.006921
Bio::Matrix::MatrixI	An interface for describing a Matrix	1.006921
Bio::Matrix::Mlagan	A generic matrix with mlagan fields	1.006921
Bio::Matrix::PSM::IO	PSM parser	1.006921
Bio::Matrix::PSM::IO::mast	PSM mast parser implementation	1.006921
Bio::Matrix::PSM::IO::masta	motif fasta format parser	1.006921
Bio::Matrix::PSM::IO::meme	PSM meme parser implementation	1.006921
Bio::Matrix::PSM::IO::psiblast	PSM psiblast parser	1.006921
Bio::Matrix::PSM::IO::transfac	PSM transfac parser	1.006921
Bio::Matrix::PSM::InstanceSite	A PSM site occurance	1.006921
Bio::Matrix::PSM::InstanceSiteI	InstanceSite interface, holds an instance of a PSM	1.006921
Bio::Matrix::PSM::ProtMatrix	SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) with log-odds scoring information.	1.006921
Bio::Matrix::PSM::ProtPsm	handle combination of site matricies	1.006921
Bio::Matrix::PSM::Psm	handle combination of site matricies	1.006921
Bio::Matrix::PSM::PsmHeader	PSM mast parser implementation	1.006921
Bio::Matrix::PSM::PsmHeaderI	handles the header data from a PSM file	1.006921
Bio::Matrix::PSM::PsmI	abstract interface to handler of site matricies	1.006921
Bio::Matrix::PSM::SiteMatrix	SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds	1.006921
Bio::Matrix::PSM::SiteMatrixI	SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds	1.006921
Bio::Matrix::PhylipDist	A Phylip Distance Matrix object	1.006921
Bio::Matrix::Scoring	Object which can hold scoring matrix information	1.006921
Bio::MolEvol::CodonModel	Codon Evolution Models	1.006921
Bio::Nexml::Factory	A factory module for creating BioPerl and Bio::Phylo objects from/to nexml documents	1.006921
Bio::NexmlIO	stream handler for NeXML documents	1.006921
Bio::Ontology::DocumentRegistry	Keep track of where to find ontologies. Allows lookups by name.	1.006921
Bio::Ontology::GOterm	representation of GO terms	1.006921
Bio::Ontology::InterProTerm	Implementation of InterProI term interface	1.006921
Bio::Ontology::OBOEngine	An Ontology Engine for OBO style flat file format from the Gene Ontology Consortium	1.006921
Bio::Ontology::OBOterm	representation of OBO terms	1.006921
Bio::Ontology::Ontology	standard implementation of an Ontology	1.006921
Bio::Ontology::OntologyEngineI	Interface a minimal Ontology implementation should satisfy	1.006921
Bio::Ontology::OntologyI	Interface for an ontology implementation	1.006921
Bio::Ontology::OntologyStore	A repository of ontologies	1.006921
Bio::Ontology::Path	a path for an ontology term graph	1.006921
Bio::Ontology::PathI	Interface for a path between ontology terms	1.006921
Bio::Ontology::Relationship	a relationship for an ontology	1.006921
Bio::Ontology::RelationshipFactory	Instantiates a new Bio::Ontology::RelationshipI (or derived class) through a factory	1.006921
Bio::Ontology::RelationshipI	Interface for a relationship between ontology terms	1.006921
Bio::Ontology::RelationshipType	a relationship type for an ontology	1.006921
Bio::Ontology::SimpleGOEngine::GraphAdaptor	Graph adaptor for Bio::Ontology::SimpleGOEngine	1.006921
Bio::Ontology::SimpleOntologyEngine	Implementation of OntologyEngineI interface	1.006921
Bio::Ontology::Term	implementation of the interface for ontology terms	1.006921
Bio::Ontology::TermFactory	Instantiates a new Bio::Ontology::TermI (or derived class) through a factory	1.006921
Bio::Ontology::TermI	interface for ontology terms	1.006921
Bio::OntologyIO	Parser factory for Ontology formats	1.006921
Bio::OntologyIO::Handlers::BaseSAXHandler	base class for SAX Handlers	1.006921
Bio::OntologyIO::Handlers::InterProHandler	XML handler class for InterProParser	1.006921
Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler	parse an InterPro XML file and persist the resulting terms to a Biosql database	1.006921
Bio::OntologyIO::InterProParser	Parser for InterPro xml files.	1.006921
Bio::OntologyIO::dagflat	a base class parser for GO flat-file type formats	1.006921
Bio::OntologyIO::goflat	a parser for the Gene Ontology flat-file format	1.006921
Bio::OntologyIO::obo	a parser for OBO flat-file format from Gene Ontology Consortium	1.006921
Bio::OntologyIO::simplehierarchy	a base class parser for simple hierarchy-by-indentation type formats	1.006921
Bio::OntologyIO::soflat	a parser for the Sequence Ontology flat-file format	1.006921
Bio::ParameterBaseI	Simple interface class for any parameter-related data such as IDs, database name, program arguments, and other odds and ends.	1.006921
Bio::Perl	Functional access to BioPerl for people who don't know objects	1.006921
Bio::Phenotype::Correlate	Representation of a correlating phenotype in a given species	1.006921
Bio::Phenotype::MeSH::Term	A MeSH term	1.006921
Bio::Phenotype::MeSH::Twig	Context for a MeSH term	1.006921
Bio::Phenotype::Measure	Representation of context/value(-range)/unit triplets	1.006921
Bio::Phenotype::OMIM::MiniMIMentry	Representation of a Mini MIM entry	1.006921
Bio::Phenotype::OMIM::OMIMentry	represents OMIM (Online Mendelian Inheritance in Man) database entries	1.006921
Bio::Phenotype::OMIM::OMIMentryAllelicVariant	Representation of a allelic variant of the OMIM database	1.006921
Bio::Phenotype::OMIM::OMIMparser	parser for the OMIM database	1.006921
Bio::Phenotype::Phenotype	A class for modeling phenotypes	1.006921
Bio::Phenotype::PhenotypeI	An interface for classes modeling phenotypes	1.006921
Bio::PhyloNetwork	Module to compute with Phylogenetic Networks	1.006921
Bio::PhyloNetwork::Factory	Module to sequentially generate Phylogenetic Networks	1.006921
Bio::PhyloNetwork::FactoryX	Module to sequentially generate Phylogenetic Networks	1.006921
Bio::PhyloNetwork::GraphViz	Interface between PhyloNetwork and GraphViz	1.006921
Bio::PhyloNetwork::RandomFactory	Module to generate random Phylogenetic Networks	1.006921
Bio::PhyloNetwork::TreeFactory	Module to sequentially generate Phylogenetic Trees	1.006921
Bio::PhyloNetwork::TreeFactoryMulti	Module to sequentially generate Phylogenetic Trees	1.006921
Bio::PhyloNetwork::TreeFactoryX	Module to sequentially generate Phylogenetic Trees	1.006921
Bio::PhyloNetwork::muVector	Module to compute with vectors of arbitrary dimension	1.006921
Bio::PopGen::Genotype	An implementation of GenotypeI which is just an allele container	1.006921
Bio::PopGen::GenotypeI	A marker and alleles for a specific individual	1.006921
Bio::PopGen::HtSNP	Select htSNP from a haplotype set	1.006921
Bio::PopGen::IO	Input individual,marker,allele information	1.006921
Bio::PopGen::IO::csv	Extract individual allele data from a CSV parser	1.006921
Bio::PopGen::IO::hapmap	A parser for HapMap output data	1.006921
Bio::PopGen::IO::phase	A parser for Phase format data	1.006921
Bio::PopGen::IO::prettybase	Extract individual allele data from PrettyBase format	1.006921
Bio::PopGen::Individual	An implementation of an Individual who has Genotype or Sequence Results	1.006921
Bio::PopGen::IndividualI	An individual who has Genotype or Sequence Results	1.006921
Bio::PopGen::Marker	A genetic marker which one uses to generate genotypes	1.006921
Bio::PopGen::MarkerI	A Population Genetic conceptual marker	1.006921
Bio::PopGen::PopStats	A collection of methods for calculating statistics about a population or sets of populations	1.006921
Bio::PopGen::Population	A population of individuals	1.006921
Bio::PopGen::PopulationI	Interface for Populations	1.006921
Bio::PopGen::Simulation::Coalescent	A Coalescent simulation factory	1.006921
Bio::PopGen::Simulation::GeneticDrift	A simple genetic drift simulation	1.006921
Bio::PopGen::Statistics	Population Genetics statistical tests	1.006921
Bio::PopGen::TagHaplotype	Haplotype tag object.	1.006921
Bio::PopGen::Utilities	Utilities for working with PopGen data and objects	1.006921
Bio::PrimarySeq	Bioperl lightweight sequence object	1.006921
Bio::PrimarySeq::Fasta		1.006921
Bio::PrimarySeqI	Interface definition for a Bio::PrimarySeq	1.006921
Bio::PullParserI	A base module for fast 'pull' parsing	1.006921
Bio::Range	Pure perl RangeI implementation	1.006921
Bio::RangeI	Range interface	1.006921
Bio::Restriction::Analysis	cutting sequences with restriction enzymes	1.006921
Bio::Restriction::Enzyme	A single restriction endonuclease (cuts DNA at specific locations)	1.006921
Bio::Restriction::Enzyme::MultiCut	A single restriction endonuclease	1.006921
Bio::Restriction::Enzyme::MultiSite	A single restriction endonuclease	1.006921
Bio::Restriction::EnzymeCollection	Set of restriction endonucleases	1.006921
Bio::Restriction::EnzymeI	Interface class for restriction endonuclease	1.006921
Bio::Restriction::IO	Handler for sequence variation IO Formats	1.006921
Bio::Restriction::IO::bairoch	bairoch enzyme set	1.006921
Bio::Restriction::IO::base	base enzyme set	1.006921
Bio::Restriction::IO::itype2	itype2 enzyme set	1.006921
Bio::Restriction::IO::prototype	prototype enzyme set	1.006921
Bio::Restriction::IO::withrefm	withrefm enzyme set	1.006921
Bio::Root::Build	A common Module::Build subclass base for BioPerl distributions	1.006921
Bio::Root::Exception	Generic exception objects for Bioperl	1.006921
Bio::Root::HTTPget	module for fallback HTTP get operations when LWP:: is unavailable	1.006921
Bio::Root::IO	module providing several methods often needed when dealing with file IO	1.006921
Bio::Root::Root	Hash-based implementation of Bio::Root::RootI	1.006921
Bio::Root::RootI	Abstract interface to root object code	1.006921
Bio::Root::Storable	object serialisation methods	1.006921
Bio::Root::Test	A common base for all Bioperl test scripts.	1.006921
Bio::Root::Utilities	General-purpose utility module	1.006921
Bio::Root::Version	provide global, distribution-level versioning	1.006921
Bio::Search::BlastStatistics	An object for Blast statistics	1.006921
Bio::Search::BlastUtils	Utility functions for Bio::Search:: BLAST objects	1.006921
Bio::Search::DatabaseI	Interface for a database used in a sequence search	1.006921
Bio::Search::GenericDatabase	Generic implementation of Bio::Search::DatabaseI	1.006921
Bio::Search::GenericStatistics	An object for statistics	1.006921
Bio::Search::HSP::BlastHSP	Bioperl BLAST High-Scoring Pair object	1.006921
Bio::Search::HSP::BlastPullHSP	A parser and HSP object for BlastN hsps	1.006921
Bio::Search::HSP::FastaHSP	HSP object for FASTA specific data	1.006921
Bio::Search::HSP::GenericHSP	A "Generic" implementation of a High Scoring Pair	1.006921
Bio::Search::HSP::HMMERHSP	A HSP object for HMMER results	1.006921
Bio::Search::HSP::HSPFactory	A factory to create Bio::Search::HSP::HSPI objects	1.006921
Bio::Search::HSP::HSPI	Interface for a High Scoring Pair in a similarity search result	1.006921
Bio::Search::HSP::HmmpfamHSP	A parser and HSP object for hmmpfam hsps	1.006921
Bio::Search::HSP::ModelHSP	A HSP object for model-based searches	1.006921
Bio::Search::HSP::PSLHSP	A HSP for PSL output	1.006921
Bio::Search::HSP::PsiBlastHSP	Bioperl BLAST High-Scoring Pair object	1.006921
Bio::Search::HSP::PullHSPI	Bio::Search::HSP::HSPI interface for pull parsers.	1.006921
Bio::Search::HSP::WABAHSP	HSP object suitable for describing WABA alignments	1.006921
Bio::Search::Hit::BlastHit	Blast-specific subclass of Bio::Search::Hit::GenericHit	1.006921
Bio::Search::Hit::BlastPullHit	A parser and hit object for BLASTN hits	1.006921
Bio::Search::Hit::Fasta	Hit object specific for Fasta-generated hits	1.006921
Bio::Search::Hit::GenericHit	A generic implementation of the Bio::Search::Hit::HitI interface	1.006921
Bio::Search::Hit::HMMERHit	A Hit module for HMMER hits	1.006921
Bio::Search::Hit::HitFactory	A factory to create Bio::Search::Hit::HitI objects	1.006921
Bio::Search::Hit::HitI	Interface for a hit in a similarity search result	1.006921
Bio::Search::Hit::HmmpfamHit	A parser and hit object for hmmpfam hits	1.006921
Bio::Search::Hit::ModelHit	A model-based implementation of the Bio::Search::Hit::HitI interface	1.006921
Bio::Search::Hit::PsiBlastHit	Bioperl BLAST Hit object	1.006921
Bio::Search::Hit::PullHitI	Bio::Search::Hit::HitI interface for pull parsers.	1.006921
Bio::Search::Hit::hmmer3Hit	DESCRIPTION of Object	1.006921
Bio::Search::Iteration::GenericIteration	A generic implementation of the Bio::Search::Iteration::IterationI interface.	1.006921
Bio::Search::Iteration::IterationI	Abstract interface to an iteration from an iterated search result, such as PSI-BLAST.	1.006921
Bio::Search::Processor	DESCRIPTION of Object	1.006921
Bio::Search::Result::BlastPullResult	A parser and result object for BLASTN results	1.006921
Bio::Search::Result::BlastResult	Blast-specific subclass of Bio::Search::Result::GenericResult	1.006921
Bio::Search::Result::CrossMatchResult	CrossMatch-specific subclass of Bio::Search::Result::GenericResult	1.006921
Bio::Search::Result::GenericResult	Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results.	1.006921
Bio::Search::Result::HMMERResult	A Result object for HMMER results	1.006921
Bio::Search::Result::HmmpfamResult	A parser and result object for hmmpfam results	1.006921
Bio::Search::Result::PullResultI	Bio::Search::Result::ResultI interface for 'pull' parsers	1.006921
Bio::Search::Result::ResultFactory	A factory to create Bio::Search::Result::ResultI objects	1.006921
Bio::Search::Result::ResultI	Abstract interface to Search Result objects	1.006921
Bio::Search::Result::WABAResult	Result object for WABA alignment output	1.006921
Bio::Search::Result::hmmer3Result	DESCRIPTION of Object	1.006921
Bio::Search::SearchUtils	Utility functions for Bio::Search:: objects	1.006921
Bio::Search::StatisticsI	A Base object for statistics	1.006921
Bio::Search::Tiling::MapTileUtils	utilities for manipulating closed intervals for an HSP tiling algorithm	1.006921
Bio::Search::Tiling::MapTiling	An implementation of an HSP tiling algorithm, with methods to obtain frequently-requested statistics	1.006921
Bio::Search::Tiling::TilingI	Abstract interface for an HSP tiling module	1.006921
Bio::SearchDist	A perl wrapper around Sean Eddy's histogram object	1.006921
Bio::SearchIO	Driver for parsing Sequence Database Searches (BLAST, FASTA, ...)	1.006921
Bio::SearchIO::EventHandlerI	An abstract Event Handler for Search Result parsing	1.006921
Bio::SearchIO::FastHitEventBuilder	Event Handler for SearchIO events.	1.006921
Bio::SearchIO::IteratedSearchResultEventBuilder	Event Handler for SearchIO events.	1.006921
Bio::SearchIO::SearchResultEventBuilder	Event Handler for SearchIO events.	1.006921
Bio::SearchIO::SearchWriterI	Interface for outputting parsed Search results	1.006921
Bio::SearchIO::Writer::BSMLResultWriter	BSML output writer	1.006921
Bio::SearchIO::Writer::GbrowseGFF	Interface for outputting parsed search results in Gbrowse GFF format	1.006921
Bio::SearchIO::Writer::HSPTableWriter	Tab-delimited data for Bio::Search::HSP::HSPI objects	1.006921
Bio::SearchIO::Writer::HTMLResultWriter	write a Bio::Search::ResultI in HTML	1.006921
Bio::SearchIO::Writer::HitTableWriter	Tab-delimited data for Bio::Search::Hit::HitI objects	1.006921
Bio::SearchIO::Writer::ResultTableWriter	Outputs tab-delimited data for each Bio::Search::Result::ResultI object.	1.006921
Bio::SearchIO::Writer::TextResultWriter	Object to implement writing a Bio::Search::ResultI in Text.	1.006921
Bio::SearchIO::XML::BlastHandler	XML Handler for NCBI Blast XML parsing.	1.006921
Bio::SearchIO::XML::PsiBlastHandler	XML Handler for NCBI Blast PSIBLAST XML parsing.	1.006921
Bio::SearchIO::axt	a parser for axt format reports	1.006921
Bio::SearchIO::blast	Event generator for event based parsing of blast reports	1.006921
Bio::SearchIO::blast_pull	A parser for BLAST output	1.006921
Bio::SearchIO::blasttable	Driver module for SearchIO for parsing NCBI -m 8/9 format	1.006921
Bio::SearchIO::blastxml	A SearchIO implementation of NCBI Blast XML parsing.	1.006921
Bio::SearchIO::cross_match	CrossMatch-specific subclass of Bio::SearchIO	1.006921
Bio::SearchIO::erpin	SearchIO-based ERPIN parser	1.006921
Bio::SearchIO::exonerate	parser for Exonerate	1.006921
Bio::SearchIO::fasta	A SearchIO parser for FASTA results	1.006921
Bio::SearchIO::gmap_f9	Event generator for parsing gmap reports (Z format)	1.006921
Bio::SearchIO::hmmer	A parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam)	1.006921
Bio::SearchIO::hmmer2	A parser for HMMER output (hmmpfam, hmmsearch)	1.006921
Bio::SearchIO::hmmer3		1.006921
Bio::SearchIO::hmmer_pull	A parser for HMMER output	1.006921
Bio::SearchIO::infernal	SearchIO-based Infernal parser	1.006921
Bio::SearchIO::megablast	a driver module for Bio::SearchIO to parse megablast reports (format 0)	1.006921
Bio::SearchIO::psl	A parser for PSL output (UCSC)	1.006921
Bio::SearchIO::rnamotif	SearchIO-based RNAMotif parser	1.006921
Bio::SearchIO::sim4	parser for Sim4 alignments	1.006921
Bio::SearchIO::waba	SearchIO parser for Jim Kent WABA program alignment output	1.006921
Bio::SearchIO::wise	Parsing of wise output as alignments	1.006921
Bio::Seq	Sequence object, with features	1.006921
Bio::Seq::BaseSeqProcessor	Base implementation for a SequenceProcessor	1.006921
Bio::Seq::EncodedSeq	subtype of Bio::LocatableSeq to store DNA that encodes a protein	1.006921
Bio::Seq::LargeLocatableSeq	LocatableSeq object that stores sequence as files in the tempdir	1.006921
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	1.006921
Bio::Seq::LargeSeq	SeqI compliant object that stores sequence as files in /tmp	1.006921
Bio::Seq::LargeSeqI	Interface class for sequences that cache their residues in a temporary file	1.006921
Bio::Seq::Meta	Generic superclass for sequence objects with residue-based meta information	1.006921
Bio::Seq::Meta::Array	array-based generic implementation of a sequence class with residue-based meta information	1.006921
Bio::Seq::MetaI	Interface for sequence objects with residue-based meta information	1.006921
Bio::Seq::PrimaryQual	Bioperl lightweight Quality Object	1.006921
Bio::Seq::PrimaryQual::Qual		1.006921
Bio::Seq::PrimedSeq	A sequence and a pair of primers matching on it	1.006921
Bio::Seq::QualI	Interface definition for a Bio::Seq::Qual	1.006921
Bio::Seq::Quality	Implementation of sequence with residue quality and trace values	1.006921
Bio::Seq::RichSeq	Module implementing a sequence created from a rich sequence database entry	1.006921
Bio::Seq::RichSeqI	interface for sequences from rich data sources, mostly databases	1.006921
Bio::Seq::SeqBuilder	Configurable object builder for sequence stream parsers	1.006921
Bio::Seq::SeqFactory	Instantiation of generic Bio::PrimarySeqI (or derived) objects through a factory	1.006921
Bio::Seq::SeqFastaSpeedFactory	Rapid creation of Bio::Seq objects through a factory	1.006921
Bio::Seq::SeqWithQuality	Bioperl object packaging a sequence with its quality. Deprecated class, use Bio::Seq::Quality instead!	1.006921
Bio::Seq::SequenceTrace	Bioperl object packaging a sequence with its trace	1.006921
Bio::Seq::SimulatedRead	Read with sequencing errors taken from a reference sequence	1.006921
Bio::Seq::TraceI	Interface definition for a Bio::Seq::Trace	1.006921
Bio::SeqAnalysisParserI	Sequence analysis output parser interface	1.006921
Bio::SeqEvolution::DNAPoint	evolve a sequence by point mutations	1.006921
Bio::SeqEvolution::EvolutionI	the interface for evolving sequences	1.006921
Bio::SeqEvolution::Factory	Factory object to instantiate sequence evolving classes	1.006921
Bio::SeqFeature::Amplicon	Amplicon feature	1.006921
Bio::SeqFeature::AnnotationAdaptor	integrates SeqFeatureIs annotation	1.006921
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.	1.006921
Bio::SeqFeature::CollectionI	An interface for a collection of SeqFeatureI objects.	1.006921
Bio::SeqFeature::Computation	Computation SeqFeature	1.006921
Bio::SeqFeature::FeaturePair	hold pair feature information e.g. blast hits	1.006921
Bio::SeqFeature::Gene::Exon	a feature representing an exon	1.006921
Bio::SeqFeature::Gene::ExonI	Interface for a feature representing an exon	1.006921
Bio::SeqFeature::Gene::GeneStructure	A feature representing an arbitrarily complex structure of a gene	1.006921
Bio::SeqFeature::Gene::GeneStructureI	A feature representing an arbitrarily complex structure of a gene	1.006921
Bio::SeqFeature::Gene::Intron	An intron feature	1.006921
Bio::SeqFeature::Gene::NC_Feature	superclass for non-coding features	1.006921
Bio::SeqFeature::Gene::Poly_A_site	poly A feature	1.006921
Bio::SeqFeature::Gene::Promoter	Describes a promoter	1.006921
Bio::SeqFeature::Gene::Transcript	A feature representing a transcript	1.006921
Bio::SeqFeature::Gene::TranscriptI	Interface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site.	1.006921
Bio::SeqFeature::Gene::UTR	A feature representing an untranslated region that is part of a transcriptional unit	1.006921
Bio::SeqFeature::Generic	Generic SeqFeature	1.006921
Bio::SeqFeature::Lite	Lightweight Bio::SeqFeatureI class	1.006921
Bio::SeqFeature::PositionProxy	handle features when truncation/revcom sequences span a feature	1.006921
Bio::SeqFeature::Primer	Primer Generic SeqFeature	1.006921
Bio::SeqFeature::SiRNA::Oligo	Perl object for small inhibitory RNAs.	1.006921
Bio::SeqFeature::SiRNA::Pair	Perl object for small inhibitory RNA (SiRNA) oligo pairs	1.006921
Bio::SeqFeature::Similarity	A sequence feature based on similarity	1.006921
Bio::SeqFeature::SimilarityPair	Sequence feature based on the similarity of two sequences.	1.006921
Bio::SeqFeature::SubSeq	Feature representing a subsequence	1.006921
Bio::SeqFeature::Tools::FeatureNamer	generates unique persistent names for features	1.006921
Bio::SeqFeature::Tools::IDHandler	maps $seq_feature->primary_tag	1.006921
Bio::SeqFeature::Tools::TypeMapper	maps $seq_feature->primary_tag	1.006921
Bio::SeqFeature::Tools::Unflattener	turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy	1.006921
Bio::SeqFeature::TypedSeqFeatureI	a strongly typed SeqFeature	1.006921
Bio::SeqFeatureI	Abstract interface of a Sequence Feature	1.006921
Bio::SeqI	[Developers] Abstract Interface of Sequence (with features)	1.006921
Bio::SeqIO	Handler for SeqIO Formats	1.006921
Bio::SeqIO::FTHelper	Helper class for Embl/Genbank feature tables	1.006921
Bio::SeqIO::Handler::GenericRichSeqHandler	Bio::HandlerI-based data handler for GenBank/EMBL/UniProt (and other) sequence data	1.006921
Bio::SeqIO::MultiFile	Treating a set of files as a single input stream	1.006921
Bio::SeqIO::abi	abi trace sequence input/output stream	1.006921
Bio::SeqIO::ace	ace sequence input/output stream	1.006921
Bio::SeqIO::agave	AGAVE sequence output stream.	1.006921
Bio::SeqIO::alf	alf trace sequence input/output stream	1.006921
Bio::SeqIO::asciitree	asciitree sequence input/output stream	1.006921
Bio::SeqIO::bsml	BSML sequence input/output stream	1.006921
Bio::SeqIO::bsml_sax	BSML sequence input/output stream using SAX	1.006921
Bio::SeqIO::chadoxml	chadoxml sequence output stream	1.006921
Bio::SeqIO::chaos	chaos sequence input/output stream	1.006921
Bio::SeqIO::chaosxml	chaosxml sequence input/output stream	1.006921
Bio::SeqIO::ctf	ctf trace sequence input/output stream	1.006921
Bio::SeqIO::embl	EMBL sequence input/output stream	1.006921
Bio::SeqIO::embldriver	EMBL sequence input/output stream	1.006921
Bio::SeqIO::entrezgene	Entrez Gene ASN1 parser	1.006921
Bio::SeqIO::excel	sequence input/output stream from a MSExcel-formatted table	1.006921
Bio::SeqIO::exp	exp trace sequence input/output stream	1.006921
Bio::SeqIO::fasta	fasta sequence input/output stream	1.006921
Bio::SeqIO::fastq	fastq sequence input/output stream	1.006921
Bio::SeqIO::flybase_chadoxml	FlyBase variant of chadoxml with sequence output stream	1.006921
Bio::SeqIO::game	a class for parsing and writing game-XML	1.006921
Bio::SeqIO::game::featHandler	a class for handling feature elements	1.006921
Bio::SeqIO::game::gameHandler	PerlSAX handler for game-XML	1.006921
Bio::SeqIO::game::gameSubs	a base class for game-XML parsing	1.006921
Bio::SeqIO::game::gameWriter	a class for writing game-XML	1.006921
Bio::SeqIO::game::seqHandler	a class for handling game-XML sequences	1.006921
Bio::SeqIO::gbdriver	GenBank handler-based push parser	1.006921
Bio::SeqIO::gbxml	GenBank sequence input/output stream using SAX	1.006921
Bio::SeqIO::gcg	GCG sequence input/output stream	1.006921
Bio::SeqIO::genbank	GenBank sequence input/output stream	1.006921
Bio::SeqIO::interpro	InterProScan XML input/output stream	1.006921
Bio::SeqIO::kegg	KEGG sequence input/output stream	1.006921
Bio::SeqIO::largefasta	method i/o on very large fasta sequence files	1.006921
Bio::SeqIO::lasergene	Lasergene sequence file input/output stream	1.006921
Bio::SeqIO::locuslink	LocusLink input/output stream	1.006921
Bio::SeqIO::mbsout	input stream for output by Teshima et al.'s mbs.	1.006921
Bio::SeqIO::metafasta	metafasta sequence input/output stream	1.006921
Bio::SeqIO::msout	input stream for output by Hudson's ms	1.006921
Bio::SeqIO::nexml	NeXML sequence input/output stream	1.006921
Bio::SeqIO::phd	phd file input/output stream	1.006921
Bio::SeqIO::pir	PIR sequence input/output stream	1.006921
Bio::SeqIO::pln	pln trace sequence input/output stream	1.006921
Bio::SeqIO::qual	.qual file input/output stream	1.006921
Bio::SeqIO::raw	raw sequence file input/output stream	1.006921
Bio::SeqIO::scf	.scf file input/output stream	1.006921
Bio::SeqIO::seqxml	SeqXML sequence input/output stream	1.006921
Bio::SeqIO::strider	DNA strider sequence input/output stream	1.006921
Bio::SeqIO::swiss	Swissprot sequence input/output stream	1.006921
Bio::SeqIO::swissdriver	SwissProt/UniProt handler-based push parser	1.006921
Bio::SeqIO::tab	nearly raw sequence file input/output stream. Reads/writes id"\t"sequence"\n"	1.006921
Bio::SeqIO::table	sequence input/output stream from a delimited table	1.006921
Bio::SeqIO::tigr	TIGR XML sequence input/output stream	1.006921
Bio::SeqIO::tigrxml	Parse TIGR (new) XML	1.006921
Bio::SeqIO::tinyseq	reading/writing sequences in NCBI TinySeq format	1.006921
Bio::SeqIO::tinyseq::tinyseqHandler	XML event handlers to support NCBI TinySeq XML parsing	1.006921
Bio::SeqIO::ztr	ztr trace sequence input/output stream	1.006921
Bio::SeqUtils	Additional methods for PrimarySeq objects	1.006921
Bio::SimpleAlign	Multiple alignments held as a set of sequences	1.006921
Bio::SimpleAnalysisI	A simple interface to any (local or remote) analysis tool	1.006921
Bio::Species	Generic species object.	1.006921
Bio::Structure::Atom	Bioperl structure Object, describes an Atom	1.006921
Bio::Structure::Chain	Bioperl structure Object, describes a chain	1.006921
Bio::Structure::Entry	Bioperl structure Object, describes the whole entry	1.006921
Bio::Structure::IO	Handler for Structure Formats	1.006921
Bio::Structure::IO::pdb	PDB input/output stream	1.006921
Bio::Structure::Model	Bioperl structure Object, describes a Model	1.006921
Bio::Structure::Residue	Bioperl structure Object, describes a Residue	1.006921
Bio::Structure::SecStr::DSSP::Res	Module for parsing/accessing dssp output	1.006921
Bio::Structure::SecStr::STRIDE::Res	Module for parsing/accessing stride output	1.006921
Bio::Structure::StructureI	Abstract Interface for a Structure objects	1.006921
Bio::Symbol::Alphabet	BSANE/BioCORBA compliant symbol list alphabet	1.006921
Bio::Symbol::AlphabetI	A Symbol Alphabet	1.006921
Bio::Symbol::DNAAlphabet	A ready made DNA alphabet	1.006921
Bio::Symbol::ProteinAlphabet	A ready made Protein alphabet	1.006921
Bio::Symbol::Symbol	A biological symbol	1.006921
Bio::Symbol::SymbolI	Interface for a Symbol	1.006921
Bio::Taxon	A node in a represented taxonomy	1.006921
Bio::Taxonomy	representing Taxonomy.	1.006921
Bio::Taxonomy::FactoryI	interface to define how to access NCBI Taxonoy	1.006921
Bio::Taxonomy::Node	A node in a represented taxonomy	1.006921
Bio::Taxonomy::Taxon	Generic Taxonomic Entity object	1.006921
Bio::Taxonomy::Tree	An Organism Level Implementation of TreeI interface.	1.006921
Bio::Tools::AlignFactory	Base object for alignment factories	1.006921
Bio::Tools::Alignment::Consed	A module to work with objects from consed .ace files	1.006921
Bio::Tools::Alignment::Trim	A kludge to do specialized trimming of sequence based on quality.	1.006921
Bio::Tools::AmpliconSearch	Find amplicons in a template using degenerate PCR primers	1.006921
Bio::Tools::Analysis::DNA::ESEfinder	a wrapper around ESEfinder server	1.006921
Bio::Tools::Analysis::Protein::Domcut	a wrapper around Domcut server	1.006921
Bio::Tools::Analysis::Protein::ELM	a wrapper around the ELM server which predicts short functional motifs on amino acid sequences	1.006921
Bio::Tools::Analysis::Protein::GOR4	a wrapper around GOR4 protein secondary structure prediction server	1.006921
Bio::Tools::Analysis::Protein::HNN	a wrapper around the HNN protein secondary structure prediction server	1.006921
Bio::Tools::Analysis::Protein::Mitoprot	a wrapper around Mitoprot server	1.006921
Bio::Tools::Analysis::Protein::NetPhos	a wrapper around NetPhos server	1.006921
Bio::Tools::Analysis::Protein::Scansite	a wrapper around the Scansite server	1.006921
Bio::Tools::Analysis::Protein::Sopma	a wrapper around the Sopma protein secondary structure prediction server	1.006921
Bio::Tools::Analysis::SimpleAnalysisBase	abstract superclass for SimpleAnalysis implementations	1.006921
Bio::Tools::AnalysisResult	Base class for analysis result objects and parsers	1.006921
Bio::Tools::Blat	parser for Blat program	1.006921
Bio::Tools::CodonTable	Codon table object	1.006921
Bio::Tools::Coil	parser for Coil output	1.006921
Bio::Tools::ECnumber	representation of EC numbers (Enzyme Classification)	1.006921
Bio::Tools::EMBOSS::Palindrome	parse EMBOSS palindrome output	1.006921
Bio::Tools::EPCR	Parse ePCR output and make features	1.006921
Bio::Tools::ERPIN	a parser for ERPIN output	1.006921
Bio::Tools::ESTScan	Results of one ESTScan run	1.006921
Bio::Tools::Eponine	Results of one Eponine run	1.006921
Bio::Tools::Est2Genome	Parse est2genome output, makes simple Bio::SeqFeature::Generic objects	1.006921
Bio::Tools::Fgenesh	parse results of one Fgenesh run	1.006921
Bio::Tools::FootPrinter	write sequence features in FootPrinter format	1.006921
Bio::Tools::GFF	A Bio::SeqAnalysisParserI compliant GFF format parser	1.006921
Bio::Tools::Gel	Calculates relative electrophoretic migration distances	1.006921
Bio::Tools::Geneid	Results of one geneid run	1.006921
Bio::Tools::Genemark	Results of one Genemark run	1.006921
Bio::Tools::Genewise	Results of one Genewise run	1.006921
Bio::Tools::Genomewise	Results of one Genomewise run	1.006921
Bio::Tools::Genscan	Results of one Genscan run	1.006921
Bio::Tools::Glimmer	parser for Glimmer 2.X/3.X prokaryotic and GlimmerM/GlimmerHMM eukaryotic gene predictions	1.006921
Bio::Tools::Grail	Results of one Grail run	1.006921
Bio::Tools::GuessSeqFormat	Module for determining the sequence format of the contents of a file, a string, or through a filehandle.	1.006921
Bio::Tools::HMMER::Domain	One particular domain hit from HMMER	1.006921
Bio::Tools::HMMER::Results	Object representing HMMER output results	1.006921
Bio::Tools::HMMER::Set	Set of identical domains from HMMER matches	1.006921
Bio::Tools::Hmmpfam	Parser for Hmmpfam program	1.006921
Bio::Tools::IUPAC	Generates unique sequence objects or regular expressions from an ambiguous IUPAC sequence	1.006921
Bio::Tools::Infernal	A parser for Infernal output	1.006921
Bio::Tools::Lucy	Object for analyzing the output from Lucy, a vector and quality trimming program from TIGR	1.006921
Bio::Tools::MZEF	Results of one MZEF run	1.006921
Bio::Tools::Match	Parses output from Transfac's match(TM)	1.006921
Bio::Tools::OddCodes	Object holding alternative alphabet coding for one protein sequence	1.006921
Bio::Tools::Phylo::Gerp	Parses output from GERP	1.006921
Bio::Tools::Phylo::Gumby	Parses output from gumby	1.006921
Bio::Tools::Phylo::Molphy	parser for Molphy output	1.006921
Bio::Tools::Phylo::Molphy::Result	container for data parsed from a ProtML run	1.006921
Bio::Tools::Phylo::PAML	Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00	1.006921
Bio::Tools::Phylo::PAML::Codeml	Parses output from the PAML program codeml.	1.006921
Bio::Tools::Phylo::PAML::ModelResult	A container for NSSite Model Result from PAML	1.006921
Bio::Tools::Phylo::PAML::Result	A PAML result set object	1.006921
Bio::Tools::Phylo::Phylip::ProtDist	parser for ProtDist output	1.006921
Bio::Tools::Prediction::Exon	A predicted exon feature	1.006921
Bio::Tools::Prediction::Gene	a predicted gene structure feature	1.006921
Bio::Tools::Primer3	Create input for and work with the output from the program primer3	1.006921
Bio::Tools::Primer::Assessor::Base	base class for common assessor things	1.006921
Bio::Tools::Primer::AssessorI	interface for assessing primer pairs	1.006921
Bio::Tools::Primer::Feature	position of a single primer	1.006921
Bio::Tools::Primer::Pair	two primers on left and right side	1.006921
Bio::Tools::Prints	Parser for FingerPRINTScanII program	1.006921
Bio::Tools::Profile	parse Profile output	1.006921
Bio::Tools::Promoterwise	parser for Promoterwise tab format output	1.006921
Bio::Tools::PrositeScan	Parser for ps_scan result	1.006921
Bio::Tools::Protparam	submit to and parse output from protparam ;	1.006921
Bio::Tools::Pseudowise	Results of one Pseudowise run	1.006921
Bio::Tools::QRNA	A Parser for qrna output	1.006921
Bio::Tools::RNAMotif	A parser for RNAMotif output	1.006921
Bio::Tools::RandomDistFunctions	A set of routines useful for generating random data in different distributions	1.006921
Bio::Tools::RepeatMasker	a parser for RepeatMasker output	1.006921
Bio::Tools::Run::GenericParameters	An object for the parameters used to run programs	1.006921
Bio::Tools::Run::ParametersI	A Base object for the parameters used to run programs	1.006921
Bio::Tools::Run::RemoteBlast	Object for remote execution of the NCBI Blast via HTTP	1.006921
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.	1.006921
Bio::Tools::Run::StandAloneNCBIBlast	Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). With experimental support for NCBI rpsblast.	1.006921
Bio::Tools::Run::StandAloneWUBlast	Object for the local execution of WU-Blast.	1.006921
Bio::Tools::Run::WrapperBase	Extensions to WrapperBase for handling programs with commands ALPHA	1.006921
Bio::Tools::Seg	parse seg output	1.006921
Bio::Tools::SeqPattern	represent a sequence pattern or motif	1.006921
Bio::Tools::SeqPattern::Backtranslate		1.006921
Bio::Tools::SeqStats	Object holding statistics for one particular sequence	1.006921
Bio::Tools::SeqWords	Object holding n-mer statistics for a sequence	1.006921
Bio::Tools::SiRNA	Perl object for designing small inhibitory RNAs.	1.006921
Bio::Tools::SiRNA::Ruleset::saigo	Perl object implementing the Saigo group's rules for designing small inhibitory RNAs	1.006921
Bio::Tools::SiRNA::Ruleset::tuschl	Perl object implementing the tuschl group's rules for designing small inhibitory RNAs	1.006921
Bio::Tools::Sigcleave	Bioperl object for sigcleave analysis	1.006921
Bio::Tools::Signalp	parser for Signalp output	1.006921
Bio::Tools::Signalp::ExtendedSignalp	enhanced parser for Signalp output	1.006921
Bio::Tools::Sim4::Exon	A single exon determined by an alignment	1.006921
Bio::Tools::Sim4::Results	Results of one Sim4 run	1.006921
Bio::Tools::Spidey::Exon	A single exon determined by an alignment	1.006921
Bio::Tools::Spidey::Results	Results of a Spidey run	1.006921
Bio::Tools::TandemRepeatsFinder	a parser for Tandem Repeats Finder output	1.006921
Bio::Tools::TargetP	Results of one TargetP run	1.006921
Bio::Tools::Tmhmm	parse TMHMM output (TransMembrane HMM)	1.006921
Bio::Tools::dpAlign	Perl extension to do pairwise dynamic programming sequence alignment	1.006921
Bio::Tools::ipcress	Parse ipcress output and make features	1.006921
Bio::Tools::isPcr	Parse isPcr output and make features	1.006921
Bio::Tools::pICalculator	calculate the isoelectric point of a protein	1.006921
Bio::Tools::pSW	pairwise Smith Waterman object	1.006921
Bio::Tools::tRNAscanSE	A parser for tRNAscan-SE output	1.006921
Bio::Tree::AlleleNode	A Node with Alleles attached	1.006921
Bio::Tree::AnnotatableNode	A Tree Node with support for annotation	1.006921
Bio::Tree::Compatible	Testing compatibility of phylogenetic trees with nested taxa.	1.006921
Bio::Tree::DistanceFactory	Construct a tree using distance based methods	1.006921
Bio::Tree::Draw::Cladogram	Drawing phylogenetic trees in Encapsulated PostScript (EPS) format.	1.006921
Bio::Tree::Node	A Simple Tree Node	1.006921
Bio::Tree::NodeI	Interface describing a Tree Node	1.006921
Bio::Tree::NodeNHX	A Simple Tree Node with support for NHX tags	1.006921
Bio::Tree::RandomFactory	TreeFactory for generating Random Trees	1.006921
Bio::Tree::Statistics	Calculate certain statistics for a Tree	1.006921
Bio::Tree::Tree	An implementation of the TreeI interface.	1.006921
Bio::Tree::TreeFunctionsI	Decorated Interface implementing basic Tree exploration methods	1.006921
Bio::Tree::TreeI	A Tree object suitable for lots of things, designed originally for Phylogenetic Trees.	1.006921
Bio::TreeIO	Parser for Tree files	1.006921
Bio::TreeIO::NewickParser	which implements a newick string parser as a finite state machine which enables it to parse the full Newick specification.	1.006921
Bio::TreeIO::TreeEventBuilder	Build Bio::Tree::Tree's and Bio::Tree::Node's from Events	1.006921
Bio::TreeIO::cluster	A TreeIO driver module for parsing Algorithm::Cluster::treecluster() output	1.006921
Bio::TreeIO::lintree	Parser for lintree output trees	1.006921
Bio::TreeIO::newick		1.006921
Bio::TreeIO::nexml	A TreeIO driver module for parsing NeXML tree files	1.006921
Bio::TreeIO::nexus	A TreeIO driver module for parsing Nexus tree output from PAUP	1.006921
Bio::TreeIO::nhx	TreeIO implementation for parsing Newick/New Hampshire eXtendend (NHX) format.	1.006921
Bio::TreeIO::pag	Bio::TreeIO driver for Pagel format	1.006921
Bio::TreeIO::phyloxml	TreeIO implementation for parsing PhyloXML format.	1.006921
Bio::TreeIO::svggraph	A simple output format that converts a Tree object to an SVG output	1.006921
Bio::TreeIO::tabtree	A simple output format which displays a tree as an ASCII drawing	1.006921
Bio::UpdateableSeqI	Descendant of Bio::SeqI that allows updates	1.006921
Bio::Variation::AAChange	Sequence change class for polypeptides	1.006921
Bio::Variation::AAReverseMutate	point mutation and codon information from single amino acid changes	1.006921
Bio::Variation::Allele	Sequence object with allele-specific attributes	1.006921
Bio::Variation::DNAMutation	DNA level mutation class	1.006921
Bio::Variation::IO	Handler for sequence variation IO Formats	1.006921
Bio::Variation::IO::flat	flat file sequence variation input/output stream	1.006921
Bio::Variation::IO::xml	XML sequence variation input/output stream	1.006921
Bio::Variation::RNAChange	Sequence change class for RNA level	1.006921
Bio::Variation::SNP	submitted SNP	1.006921
Bio::Variation::SeqDiff	Container class for mutation/variant descriptions	1.006921
Bio::Variation::VariantI	Sequence Change SeqFeature abstract class	1.006921
Bio::WebAgent	A base class for Web (any protocol) access	1.006921
BioPerl	Perl Modules for Biology
Deobfuscator	get BioPerl method and package information from a Berkeley DB	0.0.3
FeatureStore		1.006921

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

BioPerl-1.6.921

Modules

Documentation

Other Files