Christopher Fields / BioPerl

Modules

Bio::Align::AlignI	An interface for describing sequence alignments.	1.006000
Bio::Align::DNAStatistics	Calculate some statistics for a DNA alignment	1.006000
Bio::Align::PairwiseStatistics	Base statistic object for Pairwise Alignments	1.006000
Bio::Align::ProteinStatistics	Calculate Protein Alignment statistics (mostly distances)	1.006000
Bio::Align::StatisticsI	Calculate some statistics for an alignment	1.006000
Bio::Align::Utilities	A collection of utilities regarding converting and manipulating alignment objects	1.006000
Bio::AlignIO	Handler for AlignIO Formats	1.006000
Bio::AlignIO::Handler::GenericAlignHandler	Bio::HandlerI-based generic data handler class for alignment-based data	1.006000
Bio::AlignIO::arp	ARP MSA Sequence input/output stream	1.006000
Bio::AlignIO::bl2seq	bl2seq sequence input/output stream	1.006000
Bio::AlignIO::clustalw	clustalw sequence input/output stream	1.006000
Bio::AlignIO::emboss	Parse EMBOSS alignment output (from applications water and needle)	1.006000
Bio::AlignIO::fasta	fasta MSA Sequence input/output stream	1.006000
Bio::AlignIO::largemultifasta	Largemultifasta MSA Sequence input/output stream	1.006000
Bio::AlignIO::maf	Multiple Alignment Format sequence input stream	1.006000
Bio::AlignIO::mase	mase sequence input/output stream	1.006000
Bio::AlignIO::mega	Parse and Create MEGA format data files	1.006000
Bio::AlignIO::meme	meme sequence input/output stream	1.006000
Bio::AlignIO::metafasta	Metafasta MSA Sequence input/output stream	1.006000
Bio::AlignIO::msf	msf sequence input/output stream	1.006000
Bio::AlignIO::nexus	NEXUS format sequence input/output stream	1.006000
Bio::AlignIO::pfam	pfam sequence input/output stream	1.006000
Bio::AlignIO::phylip	PHYLIP format sequence input/output stream	1.006000
Bio::AlignIO::po	po MSA Sequence input/output stream	1.006000
Bio::AlignIO::proda	proda sequence input/output stream	1.006000
Bio::AlignIO::prodom	prodom sequence input/output stream	1.006000
Bio::AlignIO::psi	Read/Write PSI-BLAST profile alignment files	1.006000
Bio::AlignIO::selex	selex sequence input/output stream	1.006000
Bio::AlignIO::stockholm	stockholm sequence input/output stream	1.006000
Bio::AlignIO::xmfa	XMFA MSA Sequence input/output stream	1.006000
Bio::AnalysisI::JobI	An interface to any (local or remote) analysis tool	1.006000
Bio::AnalysisParserI	Generic analysis output parser interface	1.006000
Bio::AnalysisResultI	Interface for analysis result objects	1.006000
Bio::AnnotatableI	the base interface an annotatable object must implement	1.006000
Bio::Annotation::AnnotationFactory	Instantiates a new Bio::AnnotationI (or derived class) through a factory	1.006000
Bio::Annotation::Collection	Default Perl implementation of AnnotationCollectionI	1.006000
Bio::Annotation::Comment	A comment object, holding text	1.006000
Bio::Annotation::DBLink	untyped links between databases	1.006000
Bio::Annotation::OntologyTerm	An ontology term adapted to AnnotationI	1.006000
Bio::Annotation::Reference	Specialised DBLink object for Literature References	1.006000
Bio::Annotation::Relation	Relationship (pairwise) with other objects SeqI and NodeI;	1.006000
Bio::Annotation::SimpleValue	A simple scalar	1.006000
Bio::Annotation::StructuredValue	A scalar with embedded structured information	1.006000
Bio::Annotation::TagTree	AnnotationI with tree-like hierarchal key-value relationships ('structured tags') that can be represented as simple text.	1.006000
Bio::Annotation::Target	Provides an object which represents a target (ie, a similarity hit) from one object to something in another database	1.006000
Bio::Annotation::Tree	Provide a tree as an annotation to a Bio::AnnotatableI object	1.006000
Bio::Annotation::TypeManager	Manages types for annotation collections	1.006000
Bio::AnnotationCollectionI	Interface for annotation collections	1.006000
Bio::AnnotationI	Annotation interface	1.006000
Bio::Assembly::Contig	Perl module to hold and manipulate sequence assembly contigs.	1.006000
Bio::Assembly::ContigAnalysis	Perform analysis on sequence assembly contigs.	1.006000
Bio::Assembly::IO	Handler for Assembly::IO Formats	1.006000
Bio::Assembly::IO::ace	module to load ACE files from various assembly programs	1.006000
Bio::Assembly::IO::phrap	driver to load phrap.out files.	1.006000
Bio::Assembly::IO::tigr	Driver to read and write assembly files in the TIGR Assembler v2 default format.	1.006000
Bio::Assembly::Scaffold	Perl module to hold and manipulate sequence assembly data.	1.006000
Bio::Assembly::ScaffoldI	Abstract Inteface of Sequence Assemblies	1.006000
Bio::Assembly::Singlet	Perl module to hold and manipulate singlets from sequence assembly contigs.	1.006000
Bio::Assembly::Tools::ContigSpectrum		1.006000
Bio::Biblio	A Bibliographic Query Service module	1.006000
Bio::Biblio::Article	Representation of a general article	1.006000
Bio::Biblio::BiblioBase	An abstract base for other biblio classes	1.006000
Bio::Biblio::Book	Representation of a book	1.006000
Bio::Biblio::BookArticle	Representation of a book article	1.006000
Bio::Biblio::IO	Handling the bibliographic references	1.006000
Bio::Biblio::IO::medline2ref	A converter of a raw hash to MEDLINE citations	1.006000
Bio::Biblio::IO::medlinexml	A converter of XML files with MEDLINE citations	1.006000
Bio::Biblio::IO::pubmed2ref	A converter of a raw hash to PUBMED citations	1.006000
Bio::Biblio::IO::pubmedxml	A converter of XML files with PUBMED citations	1.006000
Bio::Biblio::Journal	Representation of a journal	1.006000
Bio::Biblio::JournalArticle	Representation of a journal article	1.006000
Bio::Biblio::MedlineArticle	Representation of a MEDLINE article	1.006000
Bio::Biblio::MedlineBook	Representation of a MEDLINE book	1.006000
Bio::Biblio::MedlineBookArticle	Representation of a MEDLINE book article	1.006000
Bio::Biblio::MedlineJournal	Representation of a MEDLINE journal	1.006000
Bio::Biblio::MedlineJournalArticle	Representation of a MEDLINE journal article	1.006000
Bio::Biblio::Organisation	Representation of an organisation	1.006000
Bio::Biblio::Patent	Representation of a patent	1.006000
Bio::Biblio::Person	Representation of a person	1.006000
Bio::Biblio::Proceeding	Representation of a conference proceeding	1.006000
Bio::Biblio::Provider	Representation of a general provider	1.006000
Bio::Biblio::PubmedArticle	Representation of a PUBMED article	1.006000
Bio::Biblio::PubmedBookArticle	Representation of a PUBMED book article	1.006000
Bio::Biblio::PubmedJournalArticle	Representation of a PUBMED journal article	1.006000
Bio::Biblio::Ref	Representation of a bibliographic reference	1.006000
Bio::Biblio::Service	Representation of a provider of type service	1.006000
Bio::Biblio::TechReport	Representation of a technical report	1.006000
Bio::Biblio::Thesis	Representation of thesis	1.006000
Bio::Biblio::WebResource	Representation of a web resource	1.006000
Bio::Cluster::ClusterFactory	Instantiates a new Bio::ClusterI (or derived class) through a factory	1.006000
Bio::Cluster::FamilyI	Family Interface	1.006000
Bio::Cluster::SequenceFamily	Sequence Family object	1.006000
Bio::Cluster::UniGene	UniGene object	1.006000
Bio::Cluster::UniGeneI	abstract interface of UniGene object	1.006000
Bio::ClusterI	Cluster Interface	1.006000
Bio::ClusterIO	Handler for Cluster Formats	1.006000
Bio::ClusterIO::dbsnp	dbSNP input stream	1.006000
Bio::ClusterIO::unigene	UniGene input stream	1.006000
Bio::CodonUsage::IO	for reading and writing codon usage tables to file	1.006000
Bio::CodonUsage::Table	for access to the Codon usage Database at http://www.kazusa.or.jp/codon.	1.006000
Bio::Coordinate::Chain	Mapping locations through a chain of coordinate mappers	1.006000
Bio::Coordinate::Collection	Noncontinuous match between two coordinate sets	1.006000
Bio::Coordinate::ExtrapolatingPair	Continuous match between two coordinate sets	1.006000
Bio::Coordinate::GeneMapper	transformations between gene related coordinate systems	1.006000
Bio::Coordinate::Graph	Finds shortest path between nodes in a graph	1.006000
Bio::Coordinate::MapperI	Interface describing coordinate mappers	1.006000
Bio::Coordinate::Pair	Continuous match between two coordinate sets	1.006000
Bio::Coordinate::Result	Results from coordinate transformation	1.006000
Bio::Coordinate::Result::Gap	Another name for Bio::Location::Simple	1.006000
Bio::Coordinate::Result::Match	Another name for Bio::Location::Simple	1.006000
Bio::Coordinate::ResultI	Interface to identify coordinate mapper results	1.006000
Bio::Coordinate::Utils	Additional methods to create Bio::Coordinate objects	1.006000
Bio::DB::Ace	Database object interface to ACeDB servers	1.006000
Bio::DB::Biblio::biofetch	A BioFetch-based access to a bibliographic citation retrieval	1.006000
Bio::DB::Biblio::eutils	Access to PubMed's bibliographic query service	1.006000
Bio::DB::Biblio::soap	A SOAP-based access to a bibliographic query service	1.006000
Bio::DB::BiblioI	An interface to a Bibliographic Query Service	1.006000
Bio::DB::BioFetch	Database object interface to BioFetch retrieval	1.006000
Bio::DB::CUTG	for access to the Codon usage Database at http://www.kazusa.or.jp/codon.	1.006000
Bio::DB::DBFetch	Database object for retrieving using the dbfetch script	1.006000
Bio::DB::EMBL	Database object interface for EMBL entry retrieval	1.006000
Bio::DB::EUtilities	webagent which interacts with and retrieves data from NCBI's eUtils	1.006000
Bio::DB::EntrezGene	Database object interface to Entrez Gene	1.006000
Bio::DB::Expression	DESCRIPTION of Object	1.006000
Bio::DB::Expression::geo	*** DESCRIPTION of Class	1.006000
Bio::DB::Failover	A Bio::DB::RandomAccessI compliant class which wraps a prioritized list of DBs	1.006000
Bio::DB::Fasta::Stream	Fast indexed access to a directory of fasta files	1.006000
Bio::DB::FileCache	In file cache for BioSeq objects	1.006000
Bio::DB::Flat	Interface for indexed flat files	1.006000
Bio::DB::Flat::BDB	Interface for BioHackathon standard BDB-indexed flat file	1.006000
Bio::DB::Flat::BDB::embl	embl adaptor for Open-bio standard BDB-indexed flat file	1.006000
Bio::DB::Flat::BDB::fasta	fasta adaptor for Open-bio standard BDB-indexed flat file	1.006000
Bio::DB::Flat::BDB::genbank	genbank adaptor for Open-bio standard BDB-indexed flat file	1.006000
Bio::DB::Flat::BDB::swiss	swissprot adaptor for Open-bio standard BDB-indexed flat file	1.006000
Bio::DB::Flat::BinarySearch	BinarySearch search indexing system for sequence files	1.006000
Bio::DB::GFF::Adaptor::ace	ace interface (for multiple inheritance)	1.006000
Bio::DB::GFF::Adaptor::berkeleydb::iterator	iterator for Bio::DB::GFF::Adaptor::berkeleydb	1.006000
Bio::DB::GFF::Adaptor::biofetch	Cache BioFetch objects in a Bio::DB::GFF database	1.006000
Bio::DB::GFF::Adaptor::biofetch_oracle	Cache BioFetch objects in a Bio::DB::GFF database	1.006000
Bio::DB::GFF::Adaptor::dbi	Database adaptor for DBI (SQL) databases	1.006000
Bio::DB::GFF::Adaptor::dbi::faux_dbh	Cache for database handles	1.006000
Bio::DB::GFF::Adaptor::dbi::iterator	iterator for Bio::DB::GFF::Adaptor::dbi	1.006000
Bio::DB::GFF::Adaptor::dbi::mysql	Database adaptor for a specific mysql schema	1.006000
Bio::DB::GFF::Adaptor::dbi::mysqlace	Unholy union between mysql GFF database and acedb database	1.006000
Bio::DB::GFF::Adaptor::dbi::mysqlcmap	Database adaptor for an integraded CMap/GBrowse mysql schema	1.006000
Bio::DB::GFF::Adaptor::dbi::mysqlopt	Deprecated database adaptor	1.006000
Bio::DB::GFF::Adaptor::dbi::oracle	Database adaptor for a specific oracle schema	1.006000
Bio::DB::GFF::Adaptor::dbi::oracleace	Unholy union between oracle GFF database and acedb database	1.006000
Bio::DB::GFF::Adaptor::dbi::pg	Database adaptor for a specific postgres schema	1.006000
Bio::DB::GFF::Adaptor::dbi::pg_fts	Database adaptor for a specific postgres schema with a TSearch2 implementation	1.006000
Bio::DB::GFF::Adaptor::memory	Bio::DB::GFF database adaptor for in-memory databases	1.006000
Bio::DB::GFF::Adaptor::memory::feature_serializer		1.006000
Bio::DB::GFF::Adaptor::memory::iterator	iterator for Bio::DB::GFF::Adaptor::memory	1.006000
Bio::DB::GFF::Aggregator	Aggregate GFF groups into composite features	1.006000
Bio::DB::GFF::Aggregator::alignment	Alignment aggregator	1.006000
Bio::DB::GFF::Aggregator::clone	Clone aggregator	1.006000
Bio::DB::GFF::Aggregator::coding	The Coding Region Aggregator	1.006000
Bio::DB::GFF::Aggregator::gene	Sequence Ontology Geene	1.006000
Bio::DB::GFF::Aggregator::match	Match aggregator	1.006000
Bio::DB::GFF::Aggregator::none	No aggregation	1.006000
Bio::DB::GFF::Aggregator::orf	An aggregator for orf regions	1.006000
Bio::DB::GFF::Aggregator::processed_transcript	Sequence Ontology Transcript	1.006000
Bio::DB::GFF::Aggregator::so_transcript	Sequence Ontology Transcript	1.006000
Bio::DB::GFF::Aggregator::transcript	Transcript aggregator	1.006000
Bio::DB::GFF::Aggregator::ucsc_acembly	UCSC acembly aggregator	1.006000
Bio::DB::GFF::Aggregator::ucsc_ensgene	UCSC ensGene aggregator	1.006000
Bio::DB::GFF::Aggregator::ucsc_genscan	UCSC genscan aggregator	1.006000
Bio::DB::GFF::Aggregator::ucsc_refgene	UCSC refGene aggregator	1.006000
Bio::DB::GFF::Aggregator::ucsc_sanger22	UCSC sanger22 aggregator	1.006000
Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo	UCSC sanger22pseudo aggregator	1.006000
Bio::DB::GFF::Aggregator::ucsc_softberry	UCSC softberry aggregator	1.006000
Bio::DB::GFF::Aggregator::ucsc_twinscan	UCSC twinscan aggregator	1.006000
Bio::DB::GFF::Aggregator::ucsc_unigene	UCSC UniGene aggregator	1.006000
Bio::DB::GFF::Featname	The name of a feature	1.006000
Bio::DB::GFF::Feature	A relative segment identified by a feature type	1.006000
Bio::DB::GFF::Homol	A segment of DNA that is homologous to another	1.006000
Bio::DB::GFF::ID_Iterator	Storage and retrieval of sequence annotation data	1.006000
Bio::DB::GFF::RelSegment	Sequence segment with relative coordinate support	1.006000
Bio::DB::GFF::Segment	Simple DNA segment object	1.006000
Bio::DB::GFF::Typename	The name of a feature type	1.006000
Bio::DB::GFF::Util::Binning	binning utility for Bio::DB::GFF index	1.006000
Bio::DB::GFF::Util::Rearrange	rearrange utility	1.006000
Bio::DB::GenBank	Database object interface to GenBank	1.006000
Bio::DB::GenPept	Database object interface to GenPept	1.006000
Bio::DB::GenericWebAgent	helper base class for parameter-based remote server access and response retrieval.	1.006000
Bio::DB::HIV	Database object interface to the Los Alamos HIV Sequence Database	1.006000
Bio::DB::HIV::HIVAnnotProcessor	Adds HIV-specific annotations to Bio::SeqIO streams	1.006000
Bio::DB::InMemoryCache	Abstract interface for a sequence database	1.006000
Bio::DB::LocationI	A RandomAccessI-like abstract interface for retrieving location data from a sequence database and returning Bio::LocationI objects	1.006000
Bio::DB::MeSH	Term retrieval from a Web MeSH database	1.006000
Bio::DB::NCBIHelper	A collection of routines useful for queries to NCBI databases.	1.006000
Bio::DB::Qual::Stream	Fast indexed access to a directory of quality files	1.006000
Bio::DB::Query::GenBank	Build a GenBank Entrez Query	1.006000
Bio::DB::Query::HIVQuery	Query interface to the Los Alamos HIV Sequence Database	1.006000
Bio::DB::Query::WebQuery	Helper class for web-based sequence queryies	1.006000
Bio::DB::QueryI	Object Interface to queryable sequence databases	1.006000
Bio::DB::RandomAccessI	Abstract interface for a sequence database	1.006000
Bio::DB::RefSeq	Database object interface for RefSeq retrieval	1.006000
Bio::DB::ReferenceI	A RandomAccessI-like abstract interface for retrieving Reference data from a sequence database and returning Bio::Annotation::Reference objects	1.006000
Bio::DB::Registry	Access to the Open Bio Database Access registry scheme	1.006000
Bio::DB::SeqFeature	Normalized feature for use with Bio::DB::SeqFeature::Store	1.006000
Bio::DB::SeqFeature::NormalizedFeature	Normalized feature for use with Bio::DB::SeqFeature::Store	1.006000
Bio::DB::SeqFeature::NormalizedFeatureI	Interface for normalized features	1.006000
Bio::DB::SeqFeature::NormalizedTableFeatureI	Interface for normalized features whose hierarchy is stored in a table	1.006000
Bio::DB::SeqFeature::Segment	Location-based access to genome annotation data	1.006000
Bio::DB::SeqFeature::Store	Storage and retrieval of sequence annotation data	1.006000
Bio::DB::SeqFeature::Store::DBI::Iterator		1.006000
Bio::DB::SeqFeature::Store::DBI::mysql	Mysql implementation of Bio::DB::SeqFeature::Store	1.006000
Bio::DB::SeqFeature::Store::FeatureFileLoader	feature file loader for Bio::DB::SeqFeature::Store	1.006000
Bio::DB::SeqFeature::Store::GFF2Loader	GFF2 file loader for Bio::DB::SeqFeature::Store	1.006000
Bio::DB::SeqFeature::Store::GFF3Loader	GFF3 file loader for Bio::DB::SeqFeature::Store	1.006000
Bio::DB::SeqFeature::Store::LoadHelper	Internal utility for Bio::DB::SeqFeature::Store	1.006000
Bio::DB::SeqFeature::Store::Loader	Loader	1.006000
Bio::DB::SeqFeature::Store::bdb	fetch and store objects from a BerkeleyDB	1.006000
Bio::DB::SeqFeature::Store::berkeleydb::Iterator	Storage and retrieval of sequence annotation data in Berkeleydb files	1.006000
Bio::DB::SeqFeature::Store::memory	In-memory implementation of Bio::DB::SeqFeature::Store	1.006000
Bio::DB::SeqHound	Database object interface to SeqHound	1.006000
Bio::DB::SeqI	Abstract Interface for Sequence databases	1.006000
Bio::DB::SeqVersion	front end to querying databases for identifier versions	1.006000
Bio::DB::SeqVersion::gi	interface to NCBI Sequence Revision History page	1.006000
Bio::DB::SwissProt	Database object interface to SwissProt retrieval	1.006000
Bio::DB::TFBS	Access to a Transcription Factor Binding Site database	1.006000
Bio::DB::TFBS::transfac_pro	An implementation of Bio::DB::TFBS which uses local flat files for transfac pro	1.006000
Bio::DB::Taxonomy	Access to a taxonomy database	1.006000
Bio::DB::Taxonomy::entrez	Taxonomy Entrez driver	1.006000
Bio::DB::Taxonomy::flatfile	An implementation of Bio::DB::Taxonomy which uses local flat files	1.006000
Bio::DB::Taxonomy::list	An implementation of Bio::DB::Taxonomy that accepts lists of words to build a database	1.006000
Bio::DB::Universal	Artificial database that delegates to specific databases	1.006000
Bio::DB::UpdateableSeqI	An interface for writing to a database of sequences.	1.006000
Bio::DB::WebDBSeqI	Object Interface to generalize Web Databases for retrieving sequences	1.006000
Bio::DBLinkContainerI	Abstract interface for any object wanting to use database cross references	1.006000
Bio::Das::FeatureTypeI	Simple interface to Sequence Ontology feature types	1.006000
Bio::Das::SegmentI	DAS-style access to a feature database	1.006000
Bio::DasI	DAS-style access to a feature database	1.006000
Bio::DescribableI	interface for objects with human readable names and descriptions	1.006000
Bio::Event::EventGeneratorI	This interface describes the basic event generator class.	1.006000
Bio::Event::EventHandlerI	An Event Handler Interface	1.006000
Bio::Expression::Contact	DESCRIPTION of Object	1.006000
Bio::Expression::DataSet	DESCRIPTION of Object	1.006000
Bio::Expression::FeatureGroup	a set of DNA/RNA features. ISA Bio::Expression::FeatureI	1.006000
Bio::Expression::FeatureGroup::FeatureGroupMas50		1.006000
Bio::Expression::FeatureI	an interface class for DNA/RNA features	1.006000
Bio::Expression::FeatureSet::FeatureSetMas50		1.006000
Bio::Expression::Platform	DESCRIPTION of Object	1.006000
Bio::Expression::ProbeI	an interface class for DNA/RNA probes	1.006000
Bio::Expression::Sample	DESCRIPTION of Object	1.006000
Bio::Factory::AnalysisI	An interface to analysis tool factory	1.006000
Bio::Factory::ApplicationFactoryI	Interface class for Application Factories	1.006000
Bio::Factory::DriverFactory	Base class for factory classes loading drivers	1.006000
Bio::Factory::FTLocationFactory	A FeatureTable Location Parser	1.006000
Bio::Factory::LocationFactoryI	A factory interface for generating locations from a string	1.006000
Bio::Factory::MapFactoryI	A Factory for getting markers	1.006000
Bio::Factory::ObjectBuilderI	Interface for an object builder	1.006000
Bio::Factory::ObjectFactory	Instantiates a new Bio::Root::RootI (or derived class) through a factory	1.006000
Bio::Factory::ObjectFactoryI	A General object creator factory	1.006000
Bio::Factory::SeqAnalysisParserFactory	class capable of creating SeqAnalysisParserI compliant parsers	1.006000
Bio::Factory::SeqAnalysisParserFactoryI	interface describing objects capable of creating SeqAnalysisParserI compliant parsers	1.006000
Bio::Factory::SequenceFactoryI	This interface allows for generic building of sequences in factories which create sequences (like SeqIO)	1.006000
Bio::Factory::SequenceProcessorI	Interface for chained sequence processing algorithms	1.006000
Bio::Factory::SequenceStreamI	Interface describing the basics of a Sequence Stream.	1.006000
Bio::Factory::TreeFactoryI	Factory Interface for getting and writing trees from/to a data stream	1.006000
Bio::FeatureHolderI	the base interface an object with features must implement	1.006000
Bio::FeatureIO	Handler for FeatureIO	1.006000
Bio::FeatureIO::bed	read/write features from UCSC BED format	1.006000
Bio::FeatureIO::gff	read/write GFF feature files	1.006000
Bio::FeatureIO::gtf	read write features in GTF format	1.006000
Bio::FeatureIO::interpro	read features from InterPro XML	1.006000
Bio::FeatureIO::ptt	read/write features in PTT format	1.006000
Bio::FeatureIO::vecscreen_simple	read/write features from NCBI vecscreen -f 3 output	1.006000
Bio::HandlerBaseI	Interface class for handler methods which interact with any event-driven parsers (drivers).	1.006000
Bio::IdCollectionI	interface for objects with multiple identifiers	1.006000
Bio::IdentifiableI	interface for objects with identifiers	1.006000
Bio::Index::Abstract	Abstract interface for indexing a flat file	1.006000
Bio::Index::AbstractSeq	base class for AbstractSeq	1.006000
Bio::Index::Blast	Indexes Blast reports and supports retrieval based on query accession(s)	1.006000
Bio::Index::BlastTable	Indexes tabular Blast reports (-m 9 format) and supports retrieval based on query accession(s)	1.006000
Bio::Index::EMBL	Interface for indexing (multiple) EMBL/Swissprot .dat files (i.e. flat file EMBL/Swissprot format).	1.006000
Bio::Index::Fasta	Interface for indexing (multiple) fasta files	1.006000
Bio::Index::Fastq	Interface for indexing (multiple) fastq files	1.006000
Bio::Index::GenBank	Interface for indexing one or more GenBank files (i.e. flat file GenBank format).	1.006000
Bio::Index::Hmmer	Indexes HMMER reports and supports retreival based on query	1.006000
Bio::Index::Qual	Interface for indexing (multiple) fasta qual files	1.006000
Bio::Index::Stockholm	Indexes Stockholm format alignments (such as those from Pfam and Rfam. Retrieves raw stream data using the ID or a Bio::SimpleAlign (via Bio::AlignIO)	1.006000
Bio::Index::SwissPfam	Interface for indexing swisspfam files	1.006000
Bio::Index::Swissprot	Interface for indexing one or more Swissprot files.	1.006000
Bio::LiveSeq::AARange	AARange abstract class for LiveSeq	1.006000
Bio::LiveSeq::Chain	DoubleChain DataStructure for Perl	1.006000
Bio::LiveSeq::ChainI	Double linked chain data structure	1.006000
Bio::LiveSeq::DNA	DNA object for LiveSeq	1.006000
Bio::LiveSeq::Exon	Range abstract class for LiveSeq	1.006000
Bio::LiveSeq::Gene	Range abstract class for LiveSeq	1.006000
Bio::LiveSeq::IO::BioPerl	Loader for LiveSeq from EMBL entries with BioPerl	1.006000
Bio::LiveSeq::IO::Loader	Parent Loader for LiveSeq	1.006000
Bio::LiveSeq::Intron	Range abstract class for LiveSeq	1.006000
Bio::LiveSeq::Mutation	Mutation event descriptor class	1.006000
Bio::LiveSeq::Mutator	Package mutating LiveSequences	1.006000
Bio::LiveSeq::Prim_Transcript	Prim_Transcript class for LiveSeq	1.006000
Bio::LiveSeq::Range	Range abstract class for LiveSeq	1.006000
Bio::LiveSeq::Repeat_Region	Repeat_Region class for LiveSeq	1.006000
Bio::LiveSeq::Repeat_Unit	Repeat_Unit class for LiveSeq	1.006000
Bio::LiveSeq::SeqI	Abstract sequence interface class for LiveSeq	1.006000
Bio::LiveSeq::Transcript	Transcript class for LiveSeq	1.006000
Bio::LiveSeq::Translation	Translation class for LiveSeq	1.006000
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.	1.006000
Bio::Location::Atomic	Implementation of a Atomic Location on a Sequence	1.006000
Bio::Location::AvWithinCoordPolicy	class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise	1.006000
Bio::Location::CoordinatePolicyI	Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location	1.006000
Bio::Location::Fuzzy	Implementation of a Location on a Sequence which has unclear start and/or end locations	1.006000
Bio::Location::FuzzyLocationI	Abstract interface of a Location on a Sequence which has unclear start/end location	1.006000
Bio::Location::NarrowestCoordPolicy	class implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range	1.006000
Bio::Location::Simple	Implementation of a Simple Location on a Sequence	1.006000
Bio::Location::Split	Implementation of a Location on a Sequence which has multiple locations (start/end points)	1.006000
Bio::Location::SplitLocationI	Abstract interface of a Location on a Sequence which has multiple locations (start/end points)	1.006000
Bio::Location::WidestCoordPolicy	class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable range	1.006000
Bio::LocationI	Abstract interface of a Location on a Sequence	1.006000
Bio::Map::Clone	An central map object representing a clone	1.006000
Bio::Map::Contig	A MapI implementation handling the contigs of a Physical Map (such as FPC)	1.006000
Bio::Map::CytoMap	A Bio::MapI compliant map implementation handling cytogenic bands	1.006000
Bio::Map::CytoMarker	An object representing a marker.	1.006000
Bio::Map::CytoPosition	Marker class with cytogenetic band storing attributes	1.006000
Bio::Map::EntityI	An Entity Interface	1.006000
Bio::Map::FPCMarker	An central map object representing a marker	1.006000
Bio::Map::Gene	An gene modelled as a mappable element.	1.006000
Bio::Map::GeneMap	A MapI implementation to represent the area around a gene	1.006000
Bio::Map::GenePosition	A typed position, suitable for modelling the various regions of a gene.	1.006000
Bio::Map::GeneRelative	Represents being relative to named sub-regions of a gene.	1.006000
Bio::Map::LinkageMap	A representation of a genetic linkage map.	1.006000
Bio::Map::LinkagePosition	Create a Position for a Marker that will be placed on a Bio::Map::LinkageMap	1.006000
Bio::Map::MapI	Interface for describing Map objects in bioperl	1.006000
Bio::Map::Mappable	An object representing a generic map element that can have multiple locations in several maps.	1.006000
Bio::Map::MappableI	An object that can be placed in a map	1.006000
Bio::Map::Marker	An central map object representing a generic marker that can have multiple location in several maps.	1.006000
Bio::Map::MarkerI	Interface for basic marker functionality	1.006000
Bio::Map::Microsatellite	An object representing a Microsatellite marker.	1.006000
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.	1.006000
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.	1.006000
Bio::Map::Physical	A class for handling a Physical Map (such as FPC)	1.006000
Bio::Map::Position	A single position of a Marker, or the range over which that marker lies, in a Map	1.006000
Bio::Map::PositionHandler	A Position Handler Implementation	1.006000
Bio::Map::PositionHandlerI	A Position Handler Interface	1.006000
Bio::Map::PositionI	Abstracts the notion of a position having a value in the context of a marker and a Map	1.006000
Bio::Map::PositionWithSequence	A position with a sequence.	1.006000
Bio::Map::Prediction	An object representing the predictions of something that can have multiple locations in several maps.	1.006000
Bio::Map::Relative	Represents what a Position's coordiantes are relative to.	1.006000
Bio::Map::RelativeI	Interface for describing what a Position's coordiantes are relative to.	1.006000
Bio::Map::SimpleMap	A MapI implementation handling the basics of a Map	1.006000
Bio::Map::TranscriptionFactor	A transcription factor modelled as a mappable element	1.006000
Bio::MapIO	A Map Factory object	1.006000
Bio::MapIO::fpc	A FPC Map reader	1.006000
Bio::MapIO::mapmaker	A Mapmaker Map reader	1.006000
Bio::Matrix::Generic	A generic matrix implementation	1.006000
Bio::Matrix::IO	A factory for Matrix parsing	1.006000
Bio::Matrix::IO::mlagan	A parser for the mlagan substitution matrix	1.006000
Bio::Matrix::IO::phylip	A parser for PHYLIP distance matricies	1.006000
Bio::Matrix::IO::scoring	A parser for PAM/BLOSUM matricies	1.006000
Bio::Matrix::MatrixI	An interface for describing a Matrix	1.006000
Bio::Matrix::Mlagan	A generic matrix with mlagan fields	1.006000
Bio::Matrix::PSM::IO	PSM parser	1.006000
Bio::Matrix::PSM::IO::mast	PSM mast parser implementation	1.006000
Bio::Matrix::PSM::IO::masta	motif fasta format parser	1.006000
Bio::Matrix::PSM::IO::meme	PSM meme parser implementation	1.006000
Bio::Matrix::PSM::IO::psiblast	PSM psiblast parser	1.006000
Bio::Matrix::PSM::IO::transfac	PSM transfac parser	1.006000
Bio::Matrix::PSM::InstanceSite	A PSM site occurance	1.006000
Bio::Matrix::PSM::InstanceSiteI	InstanceSite interface, holds an instance of a PSM	1.006000
Bio::Matrix::PSM::ProtMatrix	SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) with log-odds scoring information.	1.006000
Bio::Matrix::PSM::ProtPsm	handle combination of site matricies	1.006000
Bio::Matrix::PSM::Psm	handle combination of site matricies	1.006000
Bio::Matrix::PSM::PsmHeader	PSM mast parser implementation	1.006000
Bio::Matrix::PSM::PsmHeaderI		1.006000
Bio::Matrix::PSM::PsmI	abstract interface to handler of site matricies	1.006000
Bio::Matrix::PSM::SiteMatrix	SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds	1.006000
Bio::Matrix::PSM::SiteMatrixI	SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds	1.006000
Bio::Matrix::PhylipDist	A Phylip Distance Matrix object	1.006000
Bio::Matrix::Scoring	Object which can hold scoring matrix information	1.006000
Bio::MolEvol::CodonModel	Codon Evolution Models	1.006000
Bio::Ontology::DocumentRegistry	Keep track of where to find ontologies. Allows lookups by name.	1.006000
Bio::Ontology::GOterm	representation of GO terms	1.006000
Bio::Ontology::InterProTerm	Implementation of InterProI term interface	1.006000
Bio::Ontology::OBOEngine	An Ontology Engine for OBO style flat file format from the Gene Ontology Consortium	1.006000
Bio::Ontology::OBOterm	representation of OBO terms	1.006000
Bio::Ontology::Ontology	standard implementation of an Ontology	1.006000
Bio::Ontology::OntologyEngineI	Interface a minimal Ontology implementation should satisfy	1.006000
Bio::Ontology::OntologyI	Interface for an ontology implementation	1.006000
Bio::Ontology::OntologyStore	A repository of ontologies	1.006000
Bio::Ontology::Path	a path for an ontology term graph	1.006000
Bio::Ontology::PathI	Interface for a path between ontology terms	1.006000
Bio::Ontology::Relationship	a relationship for an ontology	1.006000
Bio::Ontology::RelationshipFactory	Instantiates a new Bio::Ontology::RelationshipI (or derived class) through a factory	1.006000
Bio::Ontology::RelationshipI	Interface for a relationship between ontology terms	1.006000
Bio::Ontology::RelationshipType	a relationship type for an ontology	1.006000
Bio::Ontology::SimpleGOEngine::GraphAdaptor	Graph adaptor for Bio::Ontology::SimpleGOEngine	1.006000
Bio::Ontology::SimpleGOEngine::GraphAdaptor02	Graph adaptor (v02.x) for Bio::Ontology::SimpleGOEngine	1.006000
Bio::Ontology::SimpleOntologyEngine	Implementation of OntologyEngineI interface	1.006000
Bio::Ontology::Term	implementation of the interface for ontology terms	1.006000
Bio::Ontology::TermFactory	Instantiates a new Bio::Ontology::TermI (or derived class) through a factory	1.006000
Bio::Ontology::TermI	interface for ontology terms	1.006000
Bio::OntologyIO	Parser factory for Ontology formats	1.006000
Bio::OntologyIO::Handlers::BaseSAXHandler		1.006000
Bio::OntologyIO::Handlers::InterProHandler	XML handler class for InterProParser	1.006000
Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler	parse an InterPro XML file and persist the resulting terms to a Biosql database	1.006000
Bio::OntologyIO::InterProParser	Parser for InterPro xml files.	1.006000
Bio::OntologyIO::dagflat	a base class parser for GO flat-file type formats	1.006000
Bio::OntologyIO::goflat	a parser for the Gene Ontology flat-file format	1.006000
Bio::OntologyIO::obo	a parser for OBO flat-file format from Gene Ontology Consortium	1.006000
Bio::OntologyIO::simplehierarchy	a base class parser for simple hierarchy-by-indentation type formats	1.006000
Bio::OntologyIO::soflat	a parser for the Sequence Ontology flat-file format	1.006000
Bio::ParameterBaseI	Simple interface class for any parameter-related data such as IDs, database name, program arguments, and other odds and ends.	1.006000
Bio::Perl	Functional access to BioPerl for people who don't know objects	1.006000
Bio::Phenotype::Correlate	Representation of a correlating phenotype in a given species	1.006000
Bio::Phenotype::MeSH::Term	A MeSH term	1.006000
Bio::Phenotype::MeSH::Twig	Context for a MeSH term	1.006000
Bio::Phenotype::Measure	Representation of context/value(-range)/unit triplets	1.006000
Bio::Phenotype::OMIM::MiniMIMentry	Representation of a Mini MIM entry	1.006000
Bio::Phenotype::OMIM::OMIMentry	represents OMIM (Online Mendelian Inheritance in Man) database entries	1.006000
Bio::Phenotype::OMIM::OMIMentryAllelicVariant	Representation of a allelic variant of the OMIM database	1.006000
Bio::Phenotype::OMIM::OMIMparser	parser for the OMIM database	1.006000
Bio::Phenotype::Phenotype	A class for modeling phenotypes	1.006000
Bio::Phenotype::PhenotypeI	An interface for classes modeling phenotypes	1.006000
Bio::PhyloNetwork	Module to compute with Phylogenetic Networks	1.006000
Bio::PhyloNetwork::Factory	Module to sequentially generate Phylogenetic Networks	1.006000
Bio::PhyloNetwork::FactoryX	Module to sequentially generate Phylogenetic Networks	1.006000
Bio::PhyloNetwork::GraphViz	Interface between PhyloNetwork and GraphViz	1.006000
Bio::PhyloNetwork::RandomFactory	Module to generate random Phylogenetic Networks	1.006000
Bio::PhyloNetwork::TreeFactory	Module to sequentially generate Phylogenetic Trees	1.006000
Bio::PhyloNetwork::TreeFactoryMulti	Module to sequentially generate Phylogenetic Trees	1.006000
Bio::PhyloNetwork::TreeFactoryX	Module to sequentially generate Phylogenetic Trees	1.006000
Bio::PhyloNetwork::muVector	Module to compute with vectors of arbitrary dimension	1.006000
Bio::PopGen::Genotype	An implementation of GenotypeI which is just an allele container	1.006000
Bio::PopGen::GenotypeI	A marker and alleles for a specific individual	1.006000
Bio::PopGen::HtSNP	Select htSNP from a haplotype set	1.006000
Bio::PopGen::IO	Input individual,marker,allele information	1.006000
Bio::PopGen::IO::csv	Extract individual allele data from a CSV parser	1.006000
Bio::PopGen::IO::hapmap	A parser for HapMap output data	1.006000
Bio::PopGen::IO::phase	A parser for Phase format data	1.006000
Bio::PopGen::IO::prettybase	Extract individual allele data from PrettyBase format	1.006000
Bio::PopGen::Individual	An implementation of an Individual who has Genotype or Sequence Results	1.006000
Bio::PopGen::IndividualI	An individual who has Genotype or Sequence Results	1.006000
Bio::PopGen::Marker	A genetic marker which one uses to generate genotypes	1.006000
Bio::PopGen::MarkerI	A Population Genetic conceptual marker	1.006000
Bio::PopGen::PopStats	A collection of methods for calculating statistics about a population or sets of populations	1.006000
Bio::PopGen::Population	A population of individuals	1.006000
Bio::PopGen::PopulationI	Interface for Populations	1.006000
Bio::PopGen::Simulation::Coalescent	A Coalescent simulation factory	1.006000
Bio::PopGen::Simulation::GeneticDrift	A simple genetic drift simulation	1.006000
Bio::PopGen::Statistics	Population Genetics statistical tests	1.006000
Bio::PopGen::TagHaplotype	Haplotype tag object.	1.006000
Bio::PopGen::Utilities	Utilities for working with PopGen data and objects	1.006000
Bio::PrimarySeq	Bioperl lightweight Sequence Object	1.006000
Bio::PrimarySeqI	Interface definition for a Bio::PrimarySeq	1.006000
Bio::PullParserI	A base module for fast 'pull' parsing	1.006000
Bio::Range	Pure perl RangeI implementation	1.006000
Bio::RangeI	Range interface	1.006000
Bio::Restriction::Analysis	cutting sequences with restriction enzymes	1.006000
Bio::Restriction::Enzyme	A single restriction endonuclease (cuts DNA at specific locations)	1.006000
Bio::Restriction::Enzyme::MultiCut	A single restriction endonuclease	1.006000
Bio::Restriction::Enzyme::MultiSite	A single restriction endonuclease	1.006000
Bio::Restriction::EnzymeCollection	Set of restriction endonucleases	1.006000
Bio::Restriction::EnzymeI	Interface class for restriction endonuclease	1.006000
Bio::Restriction::IO	Handler for sequence variation IO Formats	1.006000
Bio::Restriction::IO::bairoch	bairoch enzyme set	1.006000
Bio::Restriction::IO::base	base enzyme set	1.006000
Bio::Restriction::IO::itype2	itype2 enzyme set	1.006000
Bio::Restriction::IO::prototype	prototype enzyme set	1.006000
Bio::Restriction::IO::withrefm	withrefm enzyme set	1.006000
Bio::Root::Build	A common Module::Build subclass base for Bioperl distributions	1.006000
Bio::Root::Exception	Generic exception objects for Bioperl	1.006000
Bio::Root::HTTPget	module for fallback HTTP get operations when LWP:: is unavailable	1.006000
Bio::Root::IO	module providing several methods often needed when dealing with file IO	1.006000
Bio::Root::Root	Hash-based implementation of Bio::Root::RootI	1.006000
Bio::Root::RootI	Abstract interface to root object code	1.006000
Bio::Root::Storable	object serialisation methods	1.006000
Bio::Root::Test	A common base for all Bioperl test scripts.	1.006000
Bio::Root::Test::Warn	Perl extension to test Bioperl methods for warnings	1.006000
Bio::Root::Utilities	General-purpose utility module	1.006000
Bio::Root::Version	provide global, distribution-level versioning	1.006000
Bio::Search::BlastStatistics	An object for Blast statistics	1.006000
Bio::Search::BlastUtils	Utility functions for Bio::Search:: BLAST objects	1.006000
Bio::Search::DatabaseI	Interface for a database used in a sequence search	1.006000
Bio::Search::GenericDatabase	Generic implementation of Bio::Search::DatabaseI	1.006000
Bio::Search::GenericStatistics	An object for statistics	1.006000
Bio::Search::HSP::BlastHSP	Bioperl BLAST High-Scoring Pair object	1.006000
Bio::Search::HSP::BlastPullHSP	A parser and HSP object for BlastN hsps	1.006000
Bio::Search::HSP::FastaHSP	HSP object for FASTA specific data	1.006000
Bio::Search::HSP::GenericHSP	A "Generic" implementation of a High Scoring Pair	1.006000
Bio::Search::HSP::HMMERHSP	A HSP object for HMMER results	1.006000
Bio::Search::HSP::HSPFactory	A factory to create Bio::Search::HSP::HSPI objects	1.006000
Bio::Search::HSP::HSPI	Interface for a High Scoring Pair in a similarity search result	1.006000
Bio::Search::HSP::HmmpfamHSP	A parser and HSP object for hmmpfam hsps	1.006000
Bio::Search::HSP::ModelHSP	A HSP object for model-based searches	1.006000
Bio::Search::HSP::PSLHSP	A HSP for PSL output	1.006000
Bio::Search::HSP::PsiBlastHSP	Bioperl BLAST High-Scoring Pair object	1.006000
Bio::Search::HSP::PullHSPI	Bio::Search::HSP::HSPI interface for pull parsers.	1.006000
Bio::Search::HSP::WABAHSP	HSP object suitable for describing WABA alignments	1.006000
Bio::Search::Hit::BlastHit	Blast-specific subclass of Bio::Search::Hit::GenericHit	1.006000
Bio::Search::Hit::BlastPullHit	A parser and hit object for BLASTN hits	1.006000
Bio::Search::Hit::Fasta	Hit object specific for Fasta-generated hits	1.006000
Bio::Search::Hit::GenericHit	A generic implementation of the Bio::Search::Hit::HitI interface	1.006000
Bio::Search::Hit::HMMERHit	A Hit module for HMMER hits	1.006000
Bio::Search::Hit::HitFactory	A factory to create Bio::Search::Hit::HitI objects	1.006000
Bio::Search::Hit::HitI	Interface for a hit in a similarity search result	1.006000
Bio::Search::Hit::HmmpfamHit	A parser and hit object for hmmpfam hits	1.006000
Bio::Search::Hit::ModelHit	A model-based implementation of the Bio::Search::Hit::HitI interface	1.006000
Bio::Search::Hit::PsiBlastHit	Bioperl BLAST Hit object	1.006000
Bio::Search::Hit::PullHitI	Bio::Search::Hit::HitI interface for pull parsers.	1.006000
Bio::Search::Iteration::GenericIteration	A generic implementation of the Bio::Search::Iteration::IterationI interface.	1.006000
Bio::Search::Iteration::IterationI	Abstract interface to an iteration from an iterated search result, such as PSI-BLAST.	1.006000
Bio::Search::Processor	DESCRIPTION of Object	1.006000
Bio::Search::Result::BlastPullResult	A parser and result object for BLASTN results	1.006000
Bio::Search::Result::BlastResult	Blast-specific subclass of Bio::Search::Result::GenericResult	1.006000
Bio::Search::Result::CrossMatchResult	CrossMatch-specific subclass of Bio::Search::Result::GenericResult	1.006000
Bio::Search::Result::GenericResult	Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results.	1.006000
Bio::Search::Result::HMMERResult	A Result object for HMMER results	1.006000
Bio::Search::Result::HmmpfamResult	A parser and result object for hmmpfam results	1.006000
Bio::Search::Result::PullResultI	Bio::Search::Result::ResultI interface for 'pull' parsers	1.006000
Bio::Search::Result::ResultFactory	A factory to create Bio::Search::Result::ResultI objects	1.006000
Bio::Search::Result::ResultI	Abstract interface to Search Result objects	1.006000
Bio::Search::Result::WABAResult	Result object for WABA alignment output	1.006000
Bio::Search::SearchUtils	Utility functions for Bio::Search:: objects	1.006000
Bio::Search::StatisticsI	A Base object for statistics	1.006000
Bio::SearchDist	A perl wrapper around Sean Eddy's histogram object	1.006000
Bio::SearchIO	Driver for parsing Sequence Database Searches (BLAST, FASTA, ...)	1.006000
Bio::SearchIO::EventHandlerI	An abstract Event Handler for Search Result parsing	1.006000
Bio::SearchIO::FastHitEventBuilder	Event Handler for SearchIO events.	1.006000
Bio::SearchIO::IteratedSearchResultEventBuilder	Event Handler for SearchIO events.	1.006000
Bio::SearchIO::SearchResultEventBuilder	Event Handler for SearchIO events.	1.006000
Bio::SearchIO::SearchWriterI	Interface for outputting parsed Search results	1.006000
Bio::SearchIO::Writer::BSMLResultWriter	BSML output writer	1.006000
Bio::SearchIO::Writer::GbrowseGFF	Interface for outputting parsed search results in Gbrowse GFF format	1.006000
Bio::SearchIO::Writer::HSPTableWriter	Tab-delimited data for Bio::Search::HSP::HSPI objects	1.006000
Bio::SearchIO::Writer::HTMLResultWriter	write a Bio::Search::ResultI in HTML	1.006000
Bio::SearchIO::Writer::HitTableWriter	Tab-delimited data for Bio::Search::Hit::HitI objects	1.006000
Bio::SearchIO::Writer::ResultTableWriter	Outputs tab-delimited data for each Bio::Search::Result::ResultI object.	1.006000
Bio::SearchIO::Writer::TextResultWriter	Object to implement writing a Bio::Search::ResultI in Text.	1.006000
Bio::SearchIO::XML::BlastHandler	XML Handler for NCBI Blast XML parsing.	1.006000
Bio::SearchIO::XML::PsiBlastHandler	XML Handler for NCBI Blast PSIBLAST XML parsing.	1.006000
Bio::SearchIO::axt	a parser for axt format reports	1.006000
Bio::SearchIO::blast	Event generator for event based parsing of blast reports	1.006000
Bio::SearchIO::blast_pull	A parser for BLAST output	1.006000
Bio::SearchIO::blasttable	Driver module for SearchIO for parsing NCBI -m 8/9 format	1.006000
Bio::SearchIO::blastxml	A SearchIO implementation of NCBI Blast XML parsing.	1.006000
Bio::SearchIO::cross_match	CrossMatch-specific subclass of Bio::SearchIO	1.006000
Bio::SearchIO::erpin	SearchIO-based ERPIN parser	1.006000
Bio::SearchIO::exonerate	parser for Exonerate	1.006000
Bio::SearchIO::fasta	A SearchIO parser for FASTA results	1.006000
Bio::SearchIO::hmmer	A parser for HMMER output (hmmpfam, hmmsearch)	1.006000
Bio::SearchIO::hmmer_pull	A parser for HMMER output	1.006000
Bio::SearchIO::infernal	SearchIO-based Infernal parser	1.006000
Bio::SearchIO::megablast	a driver module for Bio::SearchIO to parse megablast reports (format 0)	1.006000
Bio::SearchIO::psl	A parser for PSL output (UCSC)	1.006000
Bio::SearchIO::rnamotif	SearchIO-based RNAMotif parser	1.006000
Bio::SearchIO::sim4	parser for Sim4 alignments	1.006000
Bio::SearchIO::waba	SearchIO parser for Jim Kent WABA program alignment output	1.006000
Bio::SearchIO::wise	Parsing of wise output as alignments	1.006000
Bio::Seq	Sequence object, with features	1.006000
Bio::Seq::BaseSeqProcessor	Base implementation for a SequenceProcessor	1.006000
Bio::Seq::EncodedSeq	subtype of Bio::LocatableSeq to store DNA that encodes a protein	1.006000
Bio::Seq::LargeLocatableSeq	LocatableSeq object that stores sequence as files in the tempdir	1.006000
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	1.006000
Bio::Seq::LargeSeq	SeqI compliant object that stores sequence as files in /tmp	1.006000
Bio::Seq::LargeSeqI	Interface class for sequences that cache their residues in a temporary file	1.006000
Bio::Seq::Meta	Generic superclass for sequence objects with residue-based meta information	1.006000
Bio::Seq::Meta::Array	array-based generic implementation of a sequence class with residue-based meta information	1.006000
Bio::Seq::MetaI	Interface for sequence objects with residue-based meta information	1.006000
Bio::Seq::PrimaryQual	Bioperl lightweight Quality Object	1.006000
Bio::Seq::PrimedSeq	A representation of a sequence and two primers flanking a target region	1.006000
Bio::Seq::QualI	Interface definition for a Bio::Seq::Qual	1.006000
Bio::Seq::Quality	Implementation of sequence with residue quality and trace values	1.006000
Bio::Seq::RichSeq	Module implementing a sequence created from a rich sequence database entry	1.006000
Bio::Seq::RichSeqI	interface for sequences from rich data sources, mostly databases	1.006000
Bio::Seq::SeqBuilder	Configurable object builder for sequence stream parsers	1.006000
Bio::Seq::SeqFactory	Instantiates a new Bio::PrimarySeqI (or derived class) through a factory	1.006000
Bio::Seq::SeqFastaSpeedFactory	Instantiates a new Bio::PrimarySeqI (or derived class) through a factory	1.006000
Bio::Seq::SeqWithQuality	Bioperl object packaging a sequence with its quality. Deprecated class, use Bio::Seq::Quality instead!	1.006000
Bio::Seq::SequenceTrace	Bioperl object packaging a sequence with its trace	1.006000
Bio::Seq::TraceI	Interface definition for a Bio::Seq::Trace	1.006000
Bio::SeqAnalysisParserI	Sequence analysis output parser interface	1.006000
Bio::SeqEvolution::DNAPoint	evolve a sequence by point mutations	1.006000
Bio::SeqEvolution::EvolutionI	the interface for evolving sequences	1.006000
Bio::SeqEvolution::Factory	Factory object to instantiate sequence evolving classes	1.006000
Bio::SeqFeature::Annotated	PLEASE PUT SOMETHING HERE	1.006000
Bio::SeqFeature::AnnotationAdaptor	integrates SeqFeatureIs annotation	1.006000
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.	1.006000
Bio::SeqFeature::CollectionI	An interface for a collection of SeqFeatureI objects.	1.006000
Bio::SeqFeature::Computation	Computation SeqFeature	1.006000
Bio::SeqFeature::FeaturePair	hold pair feature information e.g. blast hits	1.006000
Bio::SeqFeature::Gene::Exon	a feature representing an exon	1.006000
Bio::SeqFeature::Gene::ExonI	Interface for a feature representing an exon	1.006000
Bio::SeqFeature::Gene::GeneStructure	A feature representing an arbitrarily complex structure of a gene	1.006000
Bio::SeqFeature::Gene::GeneStructureI	A feature representing an arbitrarily complex structure of a gene	1.006000
Bio::SeqFeature::Gene::Intron	An intron feature	1.006000
Bio::SeqFeature::Gene::NC_Feature	superclass for non-coding features	1.006000
Bio::SeqFeature::Gene::Poly_A_site	poly A feature	1.006000
Bio::SeqFeature::Gene::Promoter	Describes a promoter	1.006000
Bio::SeqFeature::Gene::Transcript	A feature representing a transcript	1.006000
Bio::SeqFeature::Gene::TranscriptI	Interface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site.	1.006000
Bio::SeqFeature::Gene::UTR	A feature representing an untranslated region that is part of a transcriptional unit	1.006000
Bio::SeqFeature::Generic	Generic SeqFeature	1.006000
Bio::SeqFeature::Lite	Lightweight Bio::SeqFeatureI class	1.006000
Bio::SeqFeature::PositionProxy	handle features when truncation/revcom sequences span a feature	1.006000
Bio::SeqFeature::Primer	Primer Generic SeqFeature	1.006000
Bio::SeqFeature::SiRNA::Oligo	Perl object for small inhibitory RNAs.	1.006000
Bio::SeqFeature::SiRNA::Pair	Perl object for small inhibitory RNA (SiRNA) oligo pairs	1.006000
Bio::SeqFeature::Similarity	A sequence feature based on similarity	1.006000
Bio::SeqFeature::SimilarityPair	Sequence feature based on the similarity of two sequences.	1.006000
Bio::SeqFeature::Tools::FeatureNamer	generates unique persistent names for features	1.006000
Bio::SeqFeature::Tools::IDHandler	maps $seq_feature->primary_tag	1.006000
Bio::SeqFeature::Tools::TypeMapper	maps $seq_feature->primary_tag	1.006000
Bio::SeqFeature::Tools::Unflattener	turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy	1.006000
Bio::SeqFeature::TypedSeqFeatureI	a strongly typed SeqFeature	1.006000
Bio::SeqFeatureI	Abstract interface of a Sequence Feature	1.006000
Bio::SeqI	[Developers] - Abstract Interface of Sequence (with features)	1.006000
Bio::SeqIO	Handler for SeqIO Formats	1.006000
Bio::SeqIO::FTHelper	Helper class for Embl/Genbank feature tables	1.006000
Bio::SeqIO::Handler::GenericRichSeqHandler	Bio::HandlerI-based data handler for GenBank/EMBL/UniProt (and other) sequence data	1.006000
Bio::SeqIO::MultiFile	Treating a set of files as a single input stream	1.006000
Bio::SeqIO::abi	abi trace sequence input/output stream	1.006000
Bio::SeqIO::ace	ace sequence input/output stream	1.006000
Bio::SeqIO::agave	AGAVE sequence output stream.	1.006000
Bio::SeqIO::alf	alf trace sequence input/output stream	1.006000
Bio::SeqIO::asciitree	asciitree sequence input/output stream	1.006000
Bio::SeqIO::bsml	BSML sequence input/output stream	1.006000
Bio::SeqIO::bsml_sax	BSML sequence input/output stream using SAX	1.006000
Bio::SeqIO::chadoxml	chadoxml sequence output stream	1.006000
Bio::SeqIO::chaos	chaos sequence input/output stream	1.006000
Bio::SeqIO::chaosxml	chaosxml sequence input/output stream	1.006000
Bio::SeqIO::ctf	ctf trace sequence input/output stream	1.006000
Bio::SeqIO::embl	EMBL sequence input/output stream	1.006000
Bio::SeqIO::embldriver	EMBL sequence input/output stream	1.006000
Bio::SeqIO::entrezgene	Entrez Gene ASN1 parser	1.006000
Bio::SeqIO::excel	sequence input/output stream from a MSExcel-formatted table	1.006000
Bio::SeqIO::exp	exp trace sequence input/output stream	1.006000
Bio::SeqIO::fasta	fasta sequence input/output stream	1.006000
Bio::SeqIO::fastq	fastq sequence input/output stream	1.006000
Bio::SeqIO::flybase_chadoxml	FlyBase variant of chadoxml with sequence output stream	1.006000
Bio::SeqIO::game	a class for parsing and writing game-XML	1.006000
Bio::SeqIO::game::featHandler	a class for handling feature elements	1.006000
Bio::SeqIO::game::gameHandler	PerlSAX handler for game-XML	1.006000
Bio::SeqIO::game::gameSubs	a base class for game-XML parsing	1.006000
Bio::SeqIO::game::gameWriter	a class for writing game-XML	1.006000
Bio::SeqIO::game::seqHandler	a class for handling game-XML sequences	1.006000
Bio::SeqIO::gbdriver	GenBank handler-based push parser	1.006000
Bio::SeqIO::gcg	GCG sequence input/output stream	1.006000
Bio::SeqIO::genbank	GenBank sequence input/output stream	1.006000
Bio::SeqIO::interpro	InterProScan XML input/output stream	1.006000
Bio::SeqIO::kegg	KEGG sequence input/output stream	1.006000
Bio::SeqIO::largefasta	method i/o on very large fasta sequence files	1.006000
Bio::SeqIO::lasergene	Lasergene sequence file input/output stream	1.006000
Bio::SeqIO::locuslink	LocusLink input/output stream	1.006000
Bio::SeqIO::metafasta	metafasta sequence input/output stream	1.006000
Bio::SeqIO::phd	.phd file input/output stream	1.006000
Bio::SeqIO::pir	PIR sequence input/output stream	1.006000
Bio::SeqIO::pln	pln trace sequence input/output stream	1.006000
Bio::SeqIO::qual	.qual file input/output stream	1.006000
Bio::SeqIO::raw	raw sequence file input/output stream	1.006000
Bio::SeqIO::scf	.scf file input/output stream	1.006000
Bio::SeqIO::strider	DNA strider sequence input/output stream	1.006000
Bio::SeqIO::swiss	Swissprot sequence input/output stream	1.006000
Bio::SeqIO::swissdriver	SwissProt/UniProt handler-based push parser	1.006000
Bio::SeqIO::tab	nearly raw sequence file input/output stream. Reads/writes id"\t"sequence"\n"	1.006000
Bio::SeqIO::table	sequence input/output stream from a delimited table	1.006000
Bio::SeqIO::tigr	TIGR XML sequence input/output stream	1.006000
Bio::SeqIO::tigrxml	Parse TIGR (new) XML	1.006000
Bio::SeqIO::tinyseq	reading/writing sequences in NCBI TinySeq format	1.006000
Bio::SeqIO::tinyseq::tinyseqHandler	XML event handlers to support NCBI TinySeq XML parsing	1.006000
Bio::SeqIO::ztr	ztr trace sequence input/output stream	1.006000
Bio::SeqUtils	Additional methods for PrimarySeq objects	1.006000
Bio::SimpleAlign	Multiple alignments held as a set of sequences	1.006000
Bio::SimpleAnalysisI	A simple interface to any (local or remote) analysis tool	1.006000
Bio::Species	Generic species object	1.006000
Bio::Structure::Atom	Bioperl structure Object, describes an Atom	1.006000
Bio::Structure::Chain	Bioperl structure Object, describes a chain	1.006000
Bio::Structure::Entry	Bioperl structure Object, describes the whole entry	1.006000
Bio::Structure::IO	Handler for Structure Formats	1.006000
Bio::Structure::IO::pdb	PDB input/output stream	1.006000
Bio::Structure::Model	Bioperl structure Object, describes a Model	1.006000
Bio::Structure::Residue	Bioperl structure Object, describes a Residue	1.006000
Bio::Structure::SecStr::DSSP::Res	Module for parsing/accessing dssp output	1.006000
Bio::Structure::SecStr::STRIDE::Res	Module for parsing/accessing stride output	1.006000
Bio::Structure::StructureI	Abstract Interface for a Structure objects	1.006000
Bio::Symbol::Alphabet	BSANE/BioCORBA compliant symbol list alphabet	1.006000
Bio::Symbol::AlphabetI	A Symbol Alphabet	1.006000
Bio::Symbol::DNAAlphabet	A ready made DNA alphabet	1.006000
Bio::Symbol::ProteinAlphabet	A ready made Protein alphabet	1.006000
Bio::Symbol::Symbol	A biological symbol	1.006000
Bio::Symbol::SymbolI	Interface for a Symbol	1.006000
Bio::Taxon	A node in a represented taxonomy	1.006000
Bio::Taxonomy	representing Taxonomy.	1.006000
Bio::Taxonomy::FactoryI	interface to define how to access NCBI Taxonoy	1.006000
Bio::Taxonomy::Node	A node in a represented taxonomy	1.006000
Bio::Taxonomy::Taxon	Generic Taxonomic Entity object	1.006000
Bio::Taxonomy::Tree	An Organism Level Implementation of TreeI interface.	1.006000
Bio::Tools::AlignFactory	Base object for alignment factories	1.006000
Bio::Tools::Alignment::Consed	A module to work with objects from consed .ace files	1.006000
Bio::Tools::Alignment::Trim	A kludge to do specialized trimming of sequence based on quality.	1.006000
Bio::Tools::Analysis::DNA::ESEfinder	a wrapper around ESEfinder server	1.006000
Bio::Tools::Analysis::Protein::Domcut	a wrapper around Domcut server	1.006000
Bio::Tools::Analysis::Protein::ELM	a wrapper around the ELM server which predicts short functional motifs on amino acid sequences	1.006000
Bio::Tools::Analysis::Protein::GOR4	a wrapper around GOR4 protein secondary structure prediction server	1.006000
Bio::Tools::Analysis::Protein::HNN	a wrapper around the HNN protein secondary structure prediction server	1.006000
Bio::Tools::Analysis::Protein::Mitoprot	a wrapper around Mitoprot server	1.006000
Bio::Tools::Analysis::Protein::NetPhos	a wrapper around NetPhos server	1.006000
Bio::Tools::Analysis::Protein::Scansite	a wrapper around the Scansite server	1.006000
Bio::Tools::Analysis::Protein::Sopma	a wrapper around the Sopma protein secondary structure prediction server	1.006000
Bio::Tools::Analysis::SimpleAnalysisBase	abstract superclass for SimpleAnalysis implementations	1.006000
Bio::Tools::AnalysisResult	Base class for analysis result objects and parsers	1.006000
Bio::Tools::Blat	parser for Blat program	1.006000
Bio::Tools::CodonTable	Codon table object	1.006000
Bio::Tools::Coil	parser for Coil output	1.006000
Bio::Tools::ECnumber	representation of EC numbers (Enzyme Classification)	1.006000
Bio::Tools::EMBOSS::Palindrome	parse EMBOSS palindrome output	1.006000
Bio::Tools::EPCR	Parse ePCR output and make features	1.006000
Bio::Tools::ERPIN	a parser for ERPIN output	1.006000
Bio::Tools::ESTScan	Results of one ESTScan run	1.006000
Bio::Tools::EUtilities	NCBI eutil XML parsers	1.006000
Bio::Tools::EUtilities::EUtilDataI	eutil data object interface	1.006000
Bio::Tools::EUtilities::EUtilParameters	Manipulation of NCBI eutil-based parameters for remote database requests.	1.006000
Bio::Tools::EUtilities::History	lightweight implementation of HistoryI interface (not bound to filehandles, extraneous methods, etc).	1.006000
Bio::Tools::EUtilities::HistoryI	simple extension of EUtilDataI interface class for classes which hold NCBI server history data	1.006000
Bio::Tools::EUtilities::Info	interface class for storing einfo data	1.006000
Bio::Tools::EUtilities::Info::FieldInfo	class for storing einfo field data	1.006000
Bio::Tools::EUtilities::Info::LinkInfo	class for storing einfo link data	1.006000
Bio::Tools::EUtilities::Link	general API for accessing data retrieved from elink queries	1.006000
Bio::Tools::EUtilities::Link::LinkSet		1.006000
Bio::Tools::EUtilities::Link::UrlLink		1.006000
Bio::Tools::EUtilities::Query	parse and collect esearch, epost, espell, egquery information	1.006000
Bio::Tools::EUtilities::Query::GlobalQuery		1.006000
Bio::Tools::EUtilities::Summary		1.006000
Bio::Tools::EUtilities::Summary::DocSum	data object for document summary data from esummary	1.006000
Bio::Tools::EUtilities::Summary::Item	simple layered object for DocSum item data	1.006000
Bio::Tools::Eponine	Results of one Eponine run	1.006000
Bio::Tools::Est2Genome	Parse est2genome output, makes simple Bio::SeqFeature::Generic objects	1.006000
Bio::Tools::Fgenesh	parse results of one Fgenesh run	1.006000
Bio::Tools::FootPrinter	write sequence features in FootPrinter format	1.006000
Bio::Tools::GFF	A Bio::SeqAnalysisParserI compliant GFF format parser	1.006000
Bio::Tools::Gel	Calculates relative electrophoretic migration distances	1.006000
Bio::Tools::Geneid	Results of one geneid run	1.006000
Bio::Tools::Genemark	Results of one Genemark run	1.006000
Bio::Tools::Genewise	Results of one Genewise run	1.006000
Bio::Tools::Genomewise	Results of one Genomewise run	1.006000
Bio::Tools::Genscan	Results of one Genscan run	1.006000
Bio::Tools::Glimmer	parser for Glimmer 2.X/3.X prokaryotic and GlimmerM/GlimmerHMM eukaryotic gene predictions	1.006000
Bio::Tools::Grail	Results of one Grail run	1.006000
Bio::Tools::GuessSeqFormat	Module for determining the sequence format of the contents of a file, a string, or through a filehandle.	1.006000
Bio::Tools::HMM	Perl extension to perform Hidden Markov Model calculations	1.006000
Bio::Tools::HMMER::Domain	One particular domain hit from HMMER	1.006000
Bio::Tools::HMMER::Results	Object representing HMMER output results	1.006000
Bio::Tools::HMMER::Set	Set of identical domains from HMMER matches	1.006000
Bio::Tools::Hmmpfam	Parser for Hmmpfam program	1.006000
Bio::Tools::IUPAC	Generates unique Seq objects from an ambiguous Seq object	1.006000
Bio::Tools::Infernal	A parser for Infernal output	1.006000
Bio::Tools::Lucy	Object for analyzing the output from Lucy, a vector and quality trimming program from TIGR	1.006000
Bio::Tools::MZEF	Results of one MZEF run	1.006000
Bio::Tools::Match	Parses output from Transfac's match(TM)	1.006000
Bio::Tools::OddCodes	Object holding alternative alphabet coding for one protein sequence	1.006000
Bio::Tools::Phylo::Gerp	Parses output from GERP	1.006000
Bio::Tools::Phylo::Gumby	Parses output from gumby	1.006000
Bio::Tools::Phylo::Molphy	parser for Molphy output	1.006000
Bio::Tools::Phylo::Molphy::Result	container for data parsed from a ProtML run	1.006000
Bio::Tools::Phylo::PAML	Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00	1.006000
Bio::Tools::Phylo::PAML::ModelResult	A container for NSSite Model Result from PAML	1.006000
Bio::Tools::Phylo::PAML::Result	A PAML result set object	1.006000
Bio::Tools::Phylo::Phylip::ProtDist	parser for ProtDist output	1.006000
Bio::Tools::Prediction::Exon	A predicted exon feature	1.006000
Bio::Tools::Prediction::Gene	a predicted gene structure feature	1.006000
Bio::Tools::Primer3	Create input for and work with the output from the program primer3	1.006000
Bio::Tools::Primer::Assessor::Base	base class for common assessor things	1.006000
Bio::Tools::Primer::AssessorI	interface for assessing primer pairs	1.006000
Bio::Tools::Primer::Feature	position of a single primer	1.006000
Bio::Tools::Primer::Pair	two primers on left and right side	1.006000
Bio::Tools::Prints	Parser for FingerPRINTScanII program	1.006000
Bio::Tools::Profile	parse Profile output	1.006000
Bio::Tools::Promoterwise	parser for Promoterwise tab format output	1.006000
Bio::Tools::PrositeScan	Parser for ps_scan result	1.006000
Bio::Tools::Protparam	submit to and parse output from protparam ;	1.006000
Bio::Tools::Pseudowise	Results of one Pseudowise run	1.006000
Bio::Tools::QRNA	A Parser for qrna output	1.006000
Bio::Tools::RNAMotif	A parser for RNAMotif output	1.006000
Bio::Tools::RandomDistFunctions	A set of routines useful for generating random data in different distributions	1.006000
Bio::Tools::RepeatMasker	a parser for RepeatMasker output	1.006000
Bio::Tools::Run::GenericParameters	An object for the parameters used to run programs	1.006000
Bio::Tools::Run::ParametersI	A Base object for the parameters used to run programs	1.006000
Bio::Tools::Run::RemoteBlast	Object for remote execution of the NCBI Blast via HTTP	1.006000
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.	1.006000
Bio::Tools::Run::StandAloneNCBIBlast	Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). With experimental support for NCBI rpsblast.	1.006000
Bio::Tools::Run::StandAloneWUBlast	Object for the local execution of WU-Blast.	1.006000
Bio::Tools::Run::WrapperBase	A Base object for wrappers around executables	1.006000
Bio::Tools::Seg	parse seg output	1.006000
Bio::Tools::SeqPattern	represent a sequence pattern or motif	1.006000
Bio::Tools::SeqStats	Object holding statistics for one particular sequence	1.006000
Bio::Tools::SeqWords	Object holding n-mer statistics for a sequence	1.006000
Bio::Tools::SiRNA	Perl object for designing small inhibitory RNAs.	1.006000
Bio::Tools::SiRNA::Ruleset::saigo	Perl object implementing the Saigo group's rules for designing small inhibitory RNAs	1.006000
Bio::Tools::SiRNA::Ruleset::tuschl	Perl object implementing the tuschl group's rules for designing small inhibitory RNAs	1.006000
Bio::Tools::Sigcleave	Bioperl object for sigcleave analysis	1.006000
Bio::Tools::Signalp	parser for Signalp output	1.006000
Bio::Tools::Signalp::ExtendedSignalp	enhanced parser for Signalp output	1.006000
Bio::Tools::Sim4::Exon	A single exon determined by an alignment	1.006000
Bio::Tools::Sim4::Results	Results of one Sim4 run	1.006000
Bio::Tools::Spidey::Exon	A single exon determined by an alignment	1.006000
Bio::Tools::Spidey::Results	Results of a Spidey run	1.006000
Bio::Tools::TandemRepeatsFinder	a parser for Tandem Repeats Finder output	1.006000
Bio::Tools::TargetP	Results of one TargetP run	1.006000
Bio::Tools::Tmhmm	parse TMHMM output (TransMembrane HMM)	1.006000
Bio::Tools::dpAlign	Perl extension to do pairwise dynamic programming sequence alignment	1.006000
Bio::Tools::ipcress	Parse ipcress output and make features	1.006000
Bio::Tools::isPcr	Parse isPcr output and make features	1.006000
Bio::Tools::pICalculator	calculate the isoelectric point of a protein	1.006000
Bio::Tools::pSW	pairwise Smith Waterman object	1.006000
Bio::Tools::tRNAscanSE	A parser for tRNAscan-SE output	1.006000
Bio::Tree::AlleleNode	A Node with Alleles attached	1.006000
Bio::Tree::AnnotatableNode	A Tree Node with support for annotation	1.006000
Bio::Tree::Compatible	Testing compatibility of phylogenetic trees with nested taxa.	1.006000
Bio::Tree::DistanceFactory	Construct a tree using distance based methods	1.006000
Bio::Tree::Draw::Cladogram	Drawing phylogenetic trees in Encapsulated PostScript (EPS) format.	1.006000
Bio::Tree::Node	A Simple Tree Node	1.006000
Bio::Tree::NodeI	Interface describing a Tree Node	1.006000
Bio::Tree::NodeNHX	A Simple Tree Node with support for NHX tags	1.006000
Bio::Tree::RandomFactory	TreeFactory for generating Random Trees	1.006000
Bio::Tree::Statistics	Calculate certain statistics for a Tree	1.006000
Bio::Tree::Tree	An Implementation of TreeI interface.	1.006000
Bio::Tree::TreeFunctionsI	Decorated Interface implementing basic Tree exploration methods	1.006000
Bio::Tree::TreeI	A Tree object suitable for lots of things, designed originally for Phylogenetic Trees.	1.006000
Bio::TreeIO	Parser for Tree files	1.006000
Bio::TreeIO::TreeEventBuilder	Build Bio::Tree::Tree's and Bio::Tree::Node's from Events	1.006000
Bio::TreeIO::cluster	A TreeIO driver module for parsing Algorithm::Cluster::treecluster() output	1.006000
Bio::TreeIO::lintree	Parser for lintree output trees	1.006000
Bio::TreeIO::newick	TreeIO implementation for parsing Newick/New Hampshire/PHYLIP format.	1.006000
Bio::TreeIO::nexus	A TreeIO driver module for parsing Nexus tree output from PAUP	1.006000
Bio::TreeIO::nhx	TreeIO implementation for parsing Newick/New Hampshire eXtendend (NHX) format.	1.006000
Bio::TreeIO::pag	Bio::TreeIO driver for Pagel format	1.006000
Bio::TreeIO::phyloxml	TreeIO implementation for parsing PhyloXML format.	1.006000
Bio::TreeIO::svggraph	A simple output format that converts a Tree object to an SVG output	1.006000
Bio::TreeIO::tabtree	A simple output format which displays a tree as an ASCII drawing	1.006000
Bio::UpdateableSeqI	Descendant of Bio::SeqI that allows updates	1.006000
Bio::Variation::AAChange	Sequence change class for polypeptides	1.006000
Bio::Variation::AAReverseMutate	point mutation and codon information from single amino acid changes	1.006000
Bio::Variation::Allele	Sequence object with allele-specific attributes	1.006000
Bio::Variation::DNAMutation	DNA level mutation class	1.006000
Bio::Variation::IO	Handler for sequence variation IO Formats	1.006000
Bio::Variation::IO::flat	flat file sequence variation input/output stream	1.006000
Bio::Variation::IO::xml	XML sequence variation input/output stream	1.006000
Bio::Variation::RNAChange	Sequence change class for RNA level	1.006000
Bio::Variation::SNP	submitted SNP	1.006000
Bio::Variation::SeqDiff	Container class for mutation/variant descriptions	1.006000
Bio::Variation::VariantI	Sequence Change SeqFeature abstract class	1.006000
Bio::WebAgent	A base class for Web (any protocol) access	1.006000
Deobfuscator	get BioPerl method and package information from a Berkeley DB	0.0.3
FeatureStore	Bio::DB::GFF database adaptor for in-memory databases	1.006000
HIVSchema	Routines and packages used by Bio::DB::HIV and Bio::DB::Query::HIVQuery	1.006000
TestInterface	A simple subclass of Interface
TestObject	An implementation of TestInterface

Bio::AnalysisI	An interface to any (local or remote) analysis tool
Bio::DB::Fasta	Fast indexed access to a directory of fasta files
Bio::DB::GFF	Storage and retrieval of sequence annotation data
Bio::DB::GFF::Adaptor::berkeleydb	Bio::DB::GFF database adaptor for in-memory databases
Bio::DB::GFF::Adaptor::dbi::caching_handle	Cache for database handles
Bio::DB::HIV::HIVQueryHelper	Routines and packages used by Bio::DB::HIV and Bio::DB::Query::HIVQuery
Bio::DB::Qual	Fast indexed access to a directory of quality files
Bio::DB::SeqFeature::Store::berkeleydb	Storage and retrieval of sequence annotation data in Berkeleydb files
Bio::Tools::EUtilities::Cookie	lightweight implementation of HistoryI interface (not bound to filehandles, extraneous methods, etc).
aacomp	amino acid composition of protein sequences
authors.pl	check modules and scripts for authors not in AUTHORS file
biblio-eutils-example.pl
biblio-soap-example.pl
biblio.PLS	bioperl client for accessing and querying a bibliographic repository.
biofetch_genbank_proxy.pl	Caching BioFetch-compatible web proxy for GenBank
bioflat_index.pl	index sequence files using Bio::DB::Flat
biogetseq	sequence retrieval using OBDA registry
bp_fast_load_gff.pl	Fast-load a Bio::DB::GFF database from GFF files.
bp_fetch.pl	fetches sequences from bioperl indexed databases
bp_genbank2gff.pl	Load a Bio::DB::GFF database from GENBANK files.
bp_index.pl	indexes files for use by bp_fetch.pl
bp_load_gff.pl	Load a Bio::DB::GFF database from GFF files.
bp_meta_gff.pl	Get/set Bio::DB::GFF meta-data
bp_mrtrans	implement a transformer of alignments from protein to mrna coordinates
bp_nrdb.PLS	a script to emulate Warren Gish's nrdb, make a unique sequence database from a set of input databases
bp_seqret	bioperl implementation of sequence fetch from local db (like EMBOSS seqret)
bpsreformat	convert sequence formats
bulk_load_gff.pl	Bulk-load a Bio::DB::GFF database from GFF files.
chaos_plot	a chaos plot from DNA and RNA sequences
check_NAMEs.pl	check NAME in module POD has fully qualified object name
check_URLs.pl	validate URLs located in module code and POD
classify_hits_kingdom	classify BLAST hits by taxonomic kingdom
composite_LD	i filename.prettybase.txt --sortbyld > outfile
cvs2cl_by_file.pl	convert cvs log messages to changelogs
dbfetch	generic CGI program to retrieve biological database entries in various formats and styles (using SRS)
dbsplit	script to split an input set of database(s) into smaller pieces
deob_detail.cgi	displays a web page of detailed information about a BioPerl method
deob_index.pl	extracts BioPerl documentation and indexes it in a database for easy retrieval
deob_interface.cgi	a WWW user interface to the BioPerl Deobfuscator
dependencies.pl	check modules and scripts for dependencies not in core
deprecated.pl	Check modules and scripts for use of deprecated modules and methods, indicates presence in a file to STDERR. Optionally accepts new modules and adds them to a newly formatted deprecation file.
extract_feature_seq	extract the corresponding sequence for a specified feature type
extract_genes.pl	extract genomic sequences from NCBI files using BioPerl
fastm9_to_table	turn FASTA -m 9 output into NCBI -m 9 tabular output
filter_search	filters searchio results, outputting a tab delimited summary
flanks	finding flanking sequences for a variant in a sequence position
gccalc	GC content of nucleotide sequences
genbank2gff3.pl	Genbank->gbrowse-friendly GFF3
generate_histogram.pl	Generate a histogram of Bio::DB::GFF features
gff2ps	you will want to change this script
heterogeneity_test	a test for distinguishing between selection and population expansion.
hmmer_to_table	turn HMMER output into tabular format
local_taxonomydb_query	query a local TaxonomyDB for species or taxonid
longorf	perl script to find the longest ORF of a sequence
maintenance/version.pl
make_mrna_protein	Convert an input mRNA/cDNA sequence into protein
mask_by_search	mask sequence(s) based on its alignment results
modules.pl	information about modules in BioPerl core
mutate.pl	randomly mutagenize a single protein or DNA sequence
nexus2nh	convert nexus format trees (from PAUP* and MrBayes) to new hampshire
oligo_count	oligo count and frequency
pairwise_kaks	script to calculate pairwise Ka,Ks for a set of sequences
parse_hmmsearch	parse single/multiple HMMSEARCH results file(s) with different output options
pod.pl	check the POD documentation syntax in modules and scripts
process_gadfly.pl	Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser
process_sgd.pl	Massage SGD annotation flat files into a version suitable for the Generic Genome Browser
process_wormbase.pl	Massage WormBase GFF files into a version suitable for the Generic Genome Browser
query_entrez_taxa	query Entrez taxonomy database and print out information
remote_blast.pl	script for submitting jobs to a remote blast server (ncbi blast queue at this time)
reverse-translate.pl
rnai_finder.cgi
run_primer3.pl	run primer3 and parse its output
scripts/utilities/download_query_genbank.PLS
search2alnblocks	Turn SearchIO parseable reports(s) into a set of aligned blocks
search2bsml	Turn SearchIO parseable reports(s) into a BSML report
search2gff	Turn SearchIO parseable reports(s) into a GFF report
search2table	turn SearchIO parseable reports into tab delimited format like NCBI's -m 9
search2tribe	Turn SearchIO parseable reports(s) into TRIBE matrix
seq_length.pl	lists the number of bases and number of sequences in specified sequence database files
seqconvert	generic BioPerl sequence format converter
seqretsplit	split a sequence (or stream) into a single file per sequence
split_seq	splits a sequence into equal sized chunks with an optional overlapping range
symlink_script.pl	install script to create symbolic links
taxid4species:	Simple script which returns the NCBI Taxanomic id for a requested species
taxonomy2tree	Building a taxonomic tree based on the full lineages of a set of species names
translate_seq	translates a sequence
tree2pag	convert Bio::TreeIO parseable format trees to pagel format
tree_from_seqsearch	builds a phylogenetic tree based on a sequence search (FastA,BLAST,HMMER)
unflatten_seq	unflatten a genbank or genbank-style feature file into a nested SeqFeature hierarchy
waba2gff3.pl	convert waba output into GFF3 suitable for Gbrowse

BioPerl

Modules

Documentation

Other Files