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Bio::Affymetrix::CDF	Bio::Affymetrix::CDF::Probe	Bio::Affymetrix::CDF::Probeset
Bio::Affymetrix::CEL	Bio::Affymetrix::CHP	Bio::AGP::LowLevel functions for dealing with AGP files
Bio::Align::AlignI An interface for describing sequence alignments.	Bio::Align::DNAStatistics Calculate some statistics for a DNA alignment	Bio::Align::Graphics Graphic Rendering of Bio::Align::AlignI Objects
Bio::Align::PairwiseStatistics Base statistic object for Pairwise Alignments	Bio::Align::ProteinStatistics Calculate Protein Alignment statistics (mostly distances)	Bio::Align::StatisticsI Calculate some statistics for an alignment
Bio::Align::Utilities A collection of utilities regarding converting	Bio::AlignIO Handler for AlignIO Formats	Bio::AlignIO::arp ARP MSA Sequence input/output stream
Bio::AlignIO::bl2seq bl2seq sequence input/output stream	Bio::AlignIO::clustalw clustalw sequence input/output stream	Bio::AlignIO::emboss Parse EMBOSS alignment output (from applications water and needle)
Bio::AlignIO::fasta fasta MSA Sequence input/output stream	Bio::AlignIO::Handler::GenericAlignHandler Bio::HandlerI-based	Bio::AlignIO::largemultifasta Largemultifasta MSA Sequence
Bio::AlignIO::maf Multiple Alignment Format sequence input stream	Bio::AlignIO::mase mase sequence input/output stream	Bio::AlignIO::mega Parse and Create MEGA format data files
Bio::AlignIO::meme meme sequence input/output stream	Bio::AlignIO::metafasta Metafasta MSA Sequence input/output stream	Bio::AlignIO::msf msf sequence input/output stream
Bio::AlignIO::nexml NeXML format sequence alignment input/output stream driver	Bio::AlignIO::nexus NEXUS format sequence input/output stream	Bio::AlignIO::pfam pfam sequence input/output stream
Bio::AlignIO::phylip PHYLIP format sequence input/output stream	Bio::AlignIO::po po MSA Sequence input/output stream	Bio::AlignIO::proda proda sequence input/output stream
Bio::AlignIO::prodom prodom sequence input/output stream	Bio::AlignIO::psi Read/Write PSI-BLAST profile alignment files	Bio::AlignIO::selex selex sequence input/output stream
Bio::AlignIO::stockholm stockholm sequence input/output stream	Bio::AlignIO::xmfa XMFA MSA Sequence input/output stream	Bio::AnalysisI An interface to any (local or remote) analysis tool
Bio::AnalysisParserI Generic analysis output parser interface	Bio::AnalysisResultI Interface for analysis result objects	Bio::AnnotatableI the base interface an annotatable object must implement
Bio::Annotation::AnnotationFactory Instantiates a new	Bio::Annotation::Collection Default Perl implementation of	Bio::Annotation::Comment A comment object, holding text
Bio::Annotation::DBLink untyped links between databases	Bio::Annotation::OntologyTerm An ontology term adapted to AnnotationI	Bio::Annotation::Reference Specialised DBLink object for Literature References
Bio::Annotation::Relation Relationship (pairwise) with other objects SeqI and NodeI;	Bio::Annotation::SimpleValue A simple scalar	Bio::Annotation::StructuredValue A scalar with embedded structured
Bio::Annotation::TagTree AnnotationI with tree-like hierarchal key-value	Bio::Annotation::Target Provides an object which represents a target (ie, a	Bio::Annotation::Tree Provide a tree as an annotation to a Bio::AnnotatableI
Bio::Annotation::TypeManager Manages types for annotation collections	Bio::AnnotationCollectionI Interface for annotation collections	Bio::AnnotationI Annotation interface
Bio::ASN1::EntrezGene Parser for NCBI Entrez Gene (ASN.1-format)	Bio::ASN1::EntrezGene::Indexer Indexes NCBI Entrez Gene files.	Bio::ASN1::Sequence Regular expression-based Perl Parser for ASN.1-formatted NCBI Sequences.
Bio::ASN1::Sequence::Indexer Indexes NCBI Sequence files.	Bio::Assembly::Contig Perl module to hold and manipulate	Bio::Assembly::ContigAnalysis
Bio::Assembly::IO Handler for Assembly::IO Formats	Bio::Assembly::IO::ace module to load ACE files from various assembly programs	Bio::Assembly::IO::bowtie An IO module for assemblies in Bowtie format BETA
Bio::Assembly::IO::maq Driver to read assembly files in maq format BETA	Bio::Assembly::IO::phrap driver to load phrap.out files.	Bio::Assembly::IO::sam An IO module for assemblies in Sam format BETA
Bio::Assembly::IO::tigr Driver to read and write assembly files in the TIGR	Bio::Assembly::Scaffold Perl module to hold and manipulate sequence assembly	Bio::Assembly::ScaffoldI Abstract Inteface of Sequence Assemblies
Bio::Assembly::Singlet Perl module to hold and manipulate	Bio::Assembly::Tools::ContigSpectrum create and manipulate contig spectra	Bio::Biblio A Bibliographic Query Service module
Bio::Biblio::Article Representation of a general article	Bio::Biblio::BiblioBase An abstract base for other biblio classes	Bio::Biblio::Book Representation of a book
Bio::Biblio::BookArticle Representation of a book article	Bio::Biblio::IO Handling the bibliographic references	Bio::Biblio::IO::medline2ref A converter of a raw hash to MEDLINE citations
Bio::Biblio::IO::medlinexml A converter of XML files with MEDLINE citations	Bio::Biblio::IO::pubmed2ref A converter of a raw hash to PUBMED citations	Bio::Biblio::IO::pubmedxml A converter of XML files with PUBMED citations
Bio::Biblio::Journal Representation of a journal	Bio::Biblio::JournalArticle Representation of a journal article	Bio::Biblio::MedlineArticle Representation of a MEDLINE article
Bio::Biblio::MedlineBook Representation of a MEDLINE book	Bio::Biblio::MedlineBookArticle Representation of a MEDLINE book article	Bio::Biblio::MedlineJournal Representation of a MEDLINE journal
Bio::Biblio::MedlineJournalArticle Representation of a MEDLINE journal article	Bio::Biblio::Organisation Representation of an organisation	Bio::Biblio::Patent Representation of a patent
Bio::Biblio::Person Representation of a person	Bio::Biblio::Proceeding Representation of a conference proceeding	Bio::Biblio::Provider Representation of a general provider
Bio::Biblio::PubmedArticle Representation of a PUBMED article	Bio::Biblio::PubmedBookArticle Representation of a PUBMED book article	Bio::Biblio::PubmedJournalArticle Representation of a PUBMED journal article
Bio::Biblio::Ref Representation of a bibliographic reference	Bio::Biblio::Service Representation of a provider of type service	Bio::Biblio::TechReport Representation of a technical report
Bio::Biblio::Thesis Representation of thesis	Bio::Biblio::WebResource Representation of a web resource	Bio::BLAST::Database work with formatted BLAST databases
Bio::BLAST::Database::Seq lazy-loading sequence from a BLAST database	Bio::BMI Body Mass Index calculate	Bio::Cellucidate Perl library for cellucidate.com
Bio::Cellucidate::Agent	Bio::Cellucidate::Base	Bio::Cellucidate::Book
Bio::Cellucidate::Bookshelf	Bio::Cellucidate::InitialCondition	Bio::Cellucidate::KappaImportJob
Bio::Cellucidate::Model	Bio::Cellucidate::ModelRule	Bio::Cellucidate::Plot
Bio::Cellucidate::Request	Bio::Cellucidate::Rule	Bio::Cellucidate::RuleObservable
Bio::Cellucidate::Series	Bio::Cellucidate::SimulationRun	Bio::Cellucidate::SolutionObservable
Bio::Chado::Schema standard DBIx::Class interface to GMOD Chado	Bio::Chado::Schema::Result::CellLine::CellLine	Bio::Chado::Schema::Result::CellLine::CellLineCvterm
Bio::Chado::Schema::Result::CellLine::CellLineCvtermprop	Bio::Chado::Schema::Result::CellLine::CellLineDbxref	Bio::Chado::Schema::Result::CellLine::CellLineFeature
Bio::Chado::Schema::Result::CellLine::CellLineLibrary	Bio::Chado::Schema::Result::CellLine::CellLineprop	Bio::Chado::Schema::Result::CellLine::CellLinepropPub
Bio::Chado::Schema::Result::CellLine::CellLinePub	Bio::Chado::Schema::Result::CellLine::CellLineRelationship	Bio::Chado::Schema::Result::CellLine::CellLineSynonym
Bio::Chado::Schema::Result::Companalysis::Analysis	Bio::Chado::Schema::Result::Companalysis::Analysisfeature	Bio::Chado::Schema::Result::Companalysis::Analysisfeatureprop
Bio::Chado::Schema::Result::Companalysis::Analysisprop	Bio::Chado::Schema::Result::Composite::AllFeatureNames	Bio::Chado::Schema::Result::Composite::Dfeatureloc
Bio::Chado::Schema::Result::Composite::FeatureContains	Bio::Chado::Schema::Result::Composite::FeatureDifference	Bio::Chado::Schema::Result::Composite::FeatureDisjoint featurelocs do not meet. symmetric
Bio::Chado::Schema::Result::Composite::FeatureDistance	Bio::Chado::Schema::Result::Composite::FeatureIntersection	Bio::Chado::Schema::Result::Composite::FeatureMeets
Bio::Chado::Schema::Result::Composite::FeatureMeetsOnSameStrand	Bio::Chado::Schema::Result::Composite::FeaturesetMeets	Bio::Chado::Schema::Result::Composite::FeatureUnion
Bio::Chado::Schema::Result::Composite::FLoc	Bio::Chado::Schema::Result::Composite::FnrType	Bio::Chado::Schema::Result::Composite::FpKey
Bio::Chado::Schema::Result::Composite::FType	Bio::Chado::Schema::Result::Composite::Gff3atts	Bio::Chado::Schema::Result::Composite::Gff3view
Bio::Chado::Schema::Result::Composite::Gffatts	Bio::Chado::Schema::Result::Contact::Contact Model persons, institutes, groups, organizations, etc.	Bio::Chado::Schema::Result::Contact::ContactRelationship Model relationships between contacts
Bio::Chado::Schema::Result::Cv::CommonAncestorCvterm	Bio::Chado::Schema::Result::Cv::CommonDescendantCvterm	Bio::Chado::Schema::Result::Cv::Cv
Bio::Chado::Schema::Result::Cv::CvCvtermCount per-cv terms counts (excludes obsoletes)	Bio::Chado::Schema::Result::Cv::CvCvtermCountWithObs per-cv terms counts (includes obsoletes)	Bio::Chado::Schema::Result::Cv::CvLeaf
Bio::Chado::Schema::Result::Cv::CvLinkCount	Bio::Chado::Schema::Result::Cv::CvPathCount	Bio::Chado::Schema::Result::Cv::Cvprop
Bio::Chado::Schema::Result::Cv::CvRoot	Bio::Chado::Schema::Result::Cv::Cvterm	Bio::Chado::Schema::Result::Cv::CvtermDbxref
Bio::Chado::Schema::Result::Cv::Cvtermpath	Bio::Chado::Schema::Result::Cv::Cvtermprop	Bio::Chado::Schema::Result::Cv::CvtermRelationship
Bio::Chado::Schema::Result::Cv::Cvtermsynonym	Bio::Chado::Schema::Result::Cv::Dbxrefprop	Bio::Chado::Schema::Result::Cv::StatsPathsToRoot
Bio::Chado::Schema::Result::Expression::Eimage	Bio::Chado::Schema::Result::Expression::Expression The expression table is essentially a bridge table.	Bio::Chado::Schema::Result::Expression::ExpressionCvterm
Bio::Chado::Schema::Result::Expression::ExpressionCvtermprop	Bio::Chado::Schema::Result::Expression::ExpressionImage	Bio::Chado::Schema::Result::Expression::Expressionprop
Bio::Chado::Schema::Result::Expression::ExpressionPub	Bio::Chado::Schema::Result::Expression::FeatureExpression	Bio::Chado::Schema::Result::Expression::FeatureExpressionprop
Bio::Chado::Schema::Result::General::Db	Bio::Chado::Schema::Result::General::DbDbxrefCount per-db dbxref counts	Bio::Chado::Schema::Result::General::Dbxref
Bio::Chado::Schema::Result::General::Tableinfo	Bio::Chado::Schema::Result::Genetic::Environment The environmental component of a phenotype description.	Bio::Chado::Schema::Result::Genetic::EnvironmentCvterm
Bio::Chado::Schema::Result::Genetic::FeatureGenotype	Bio::Chado::Schema::Result::Genetic::Genotype	Bio::Chado::Schema::Result::Genetic::Phendesc
Bio::Chado::Schema::Result::Genetic::PhenotypeComparison	Bio::Chado::Schema::Result::Genetic::PhenotypeComparisonCvterm	Bio::Chado::Schema::Result::Genetic::Phenstatement
Bio::Chado::Schema::Result::Library::Library	Bio::Chado::Schema::Result::Library::LibraryCvterm	Bio::Chado::Schema::Result::Library::LibraryDbxref
Bio::Chado::Schema::Result::Library::LibraryFeature	Bio::Chado::Schema::Result::Library::Libraryprop	Bio::Chado::Schema::Result::Library::LibrarypropPub
Bio::Chado::Schema::Result::Library::LibraryPub	Bio::Chado::Schema::Result::Library::LibrarySynonym	Bio::Chado::Schema::Result::Mage::Acquisition
Bio::Chado::Schema::Result::Mage::Acquisitionprop Parameters associated with image acquisition.	Bio::Chado::Schema::Result::Mage::AcquisitionRelationship	Bio::Chado::Schema::Result::Mage::Arraydesign
Bio::Chado::Schema::Result::Mage::Arraydesignprop	Bio::Chado::Schema::Result::Mage::Assay	Bio::Chado::Schema::Result::Mage::AssayBiomaterial
Bio::Chado::Schema::Result::Mage::AssayProject Link assays to projects.	Bio::Chado::Schema::Result::Mage::Assayprop Extra assay properties that are not accounted for in assay.	Bio::Chado::Schema::Result::Mage::Biomaterial
Bio::Chado::Schema::Result::Mage::BiomaterialDbxref	Bio::Chado::Schema::Result::Mage::Biomaterialprop	Bio::Chado::Schema::Result::Mage::BiomaterialRelationship
Bio::Chado::Schema::Result::Mage::BiomaterialTreatment	Bio::Chado::Schema::Result::Mage::Channel	Bio::Chado::Schema::Result::Mage::Control
Bio::Chado::Schema::Result::Mage::Element	Bio::Chado::Schema::Result::Mage::ElementRelationship	Bio::Chado::Schema::Result::Mage::Elementresult
Bio::Chado::Schema::Result::Mage::ElementresultRelationship	Bio::Chado::Schema::Result::Mage::Magedocumentation	Bio::Chado::Schema::Result::Mage::Mageml
Bio::Chado::Schema::Result::Mage::Protocol Procedural notes on how data was prepared and processed.	Bio::Chado::Schema::Result::Mage::Protocolparam	Bio::Chado::Schema::Result::Mage::Quantification
Bio::Chado::Schema::Result::Mage::Quantificationprop	Bio::Chado::Schema::Result::Mage::QuantificationRelationship	Bio::Chado::Schema::Result::Mage::Study
Bio::Chado::Schema::Result::Mage::StudyAssay	Bio::Chado::Schema::Result::Mage::Studydesign	Bio::Chado::Schema::Result::Mage::Studydesignprop
Bio::Chado::Schema::Result::Mage::Studyfactor	Bio::Chado::Schema::Result::Mage::Studyfactorvalue	Bio::Chado::Schema::Result::Mage::Studyprop
Bio::Chado::Schema::Result::Mage::StudypropFeature	Bio::Chado::Schema::Result::Mage::Treatment	Bio::Chado::Schema::Result::Map::Featuremap
Bio::Chado::Schema::Result::Map::FeaturemapPub	Bio::Chado::Schema::Result::Map::Featurepos	Bio::Chado::Schema::Result::Map::Featurerange
Bio::Chado::Schema::Result::NaturalDiversity::NdExperiment	Bio::Chado::Schema::Result::NaturalDiversity::NdExperimentContact	Bio::Chado::Schema::Result::NaturalDiversity::NdExperimentDbxref Cross-reference experiment to accessions, images, etc
Bio::Chado::Schema::Result::NaturalDiversity::NdExperimentGenotype	Bio::Chado::Schema::Result::NaturalDiversity::NdExperimentPhenotype	Bio::Chado::Schema::Result::NaturalDiversity::NdExperimentProject
Bio::Chado::Schema::Result::NaturalDiversity::NdExperimentprop	Bio::Chado::Schema::Result::NaturalDiversity::NdExperimentProtocol Linking table: experiments to the protocols they involve.	Bio::Chado::Schema::Result::NaturalDiversity::NdExperimentPub Linking nd_experiment(s) to publication(s)
Bio::Chado::Schema::Result::NaturalDiversity::NdExperimentStock	Bio::Chado::Schema::Result::NaturalDiversity::NdExperimentStockDbxref Cross-reference experiment_stock to accessions, images, etc	Bio::Chado::Schema::Result::NaturalDiversity::NdExperimentStockprop
Bio::Chado::Schema::Result::NaturalDiversity::NdGeolocation	Bio::Chado::Schema::Result::NaturalDiversity::NdGeolocationprop	Bio::Chado::Schema::Result::NaturalDiversity::NdProtocol
Bio::Chado::Schema::Result::NaturalDiversity::NdProtocolprop Property/value associations for protocol.	Bio::Chado::Schema::Result::NaturalDiversity::NdProtocolReagent	Bio::Chado::Schema::Result::NaturalDiversity::NdReagent
Bio::Chado::Schema::Result::NaturalDiversity::NdReagentprop	Bio::Chado::Schema::Result::NaturalDiversity::NdReagentRelationship	Bio::Chado::Schema::Result::Organism::Organism
Bio::Chado::Schema::Result::Organism::OrganismDbxref	Bio::Chado::Schema::Result::Organism::Organismprop Tag-value properties - follows standard chado model.	Bio::Chado::Schema::Result::Phenotype::FeaturePhenotype
Bio::Chado::Schema::Result::Phenotype::Phenotype	Bio::Chado::Schema::Result::Phenotype::PhenotypeCvterm	Bio::Chado::Schema::Result::Phylogeny::Phylonode
Bio::Chado::Schema::Result::Phylogeny::PhylonodeDbxref	Bio::Chado::Schema::Result::Phylogeny::PhylonodeOrganism	Bio::Chado::Schema::Result::Phylogeny::Phylonodeprop
Bio::Chado::Schema::Result::Phylogeny::PhylonodePub	Bio::Chado::Schema::Result::Phylogeny::PhylonodeRelationship	Bio::Chado::Schema::Result::Phylogeny::Phylotree Global anchor for phylogenetic tree.
Bio::Chado::Schema::Result::Phylogeny::PhylotreePub	Bio::Chado::Schema::Result::Project::Project	Bio::Chado::Schema::Result::Project::ProjectContact Linking project(s) to contact(s)
Bio::Chado::Schema::Result::Project::Projectprop	Bio::Chado::Schema::Result::Project::ProjectPub Linking project(s) to publication(s)	Bio::Chado::Schema::Result::Project::ProjectRelationship A project can be composed of several smaller scale projects
Bio::Chado::Schema::Result::Pub::Pub	Bio::Chado::Schema::Result::Pub::Pubauthor	Bio::Chado::Schema::Result::Pub::PubDbxref
Bio::Chado::Schema::Result::Pub::Pubprop	Bio::Chado::Schema::Result::Pub::PubRelationship	Bio::Chado::Schema::Result::Sequence::Cvtermsynonym
Bio::Chado::Schema::Result::Sequence::Feature	Bio::Chado::Schema::Result::Sequence::FeatureCvterm	Bio::Chado::Schema::Result::Sequence::FeatureCvtermDbxref
Bio::Chado::Schema::Result::Sequence::FeatureCvtermprop	Bio::Chado::Schema::Result::Sequence::FeatureCvtermPub	Bio::Chado::Schema::Result::Sequence::FeatureDbxref
Bio::Chado::Schema::Result::Sequence::Featureloc	Bio::Chado::Schema::Result::Sequence::FeaturelocPub	Bio::Chado::Schema::Result::Sequence::Featureprop
Bio::Chado::Schema::Result::Sequence::FeaturepropPub	Bio::Chado::Schema::Result::Sequence::FeaturePub	Bio::Chado::Schema::Result::Sequence::FeaturePubprop Property or attribute of a feature_pub link.
Bio::Chado::Schema::Result::Sequence::FeatureRelationship	Bio::Chado::Schema::Result::Sequence::FeatureRelationshipprop	Bio::Chado::Schema::Result::Sequence::FeatureRelationshippropPub Provenance for feature_relationshipprop.
Bio::Chado::Schema::Result::Sequence::FeatureRelationshipPub	Bio::Chado::Schema::Result::Sequence::FeatureSynonym Linking table between feature and synonym.	Bio::Chado::Schema::Result::Sequence::IntronCombinedView
Bio::Chado::Schema::Result::Sequence::IntronlocView	Bio::Chado::Schema::Result::Sequence::ProteinCodingGene	Bio::Chado::Schema::Result::Sequence::Synonym
Bio::Chado::Schema::Result::Sequence::TypeFeatureCount per-feature-type feature counts	Bio::Chado::Schema::Result::Stock::Stock	Bio::Chado::Schema::Result::Stock::Stockcollection
Bio::Chado::Schema::Result::Stock::Stockcollectionprop	Bio::Chado::Schema::Result::Stock::StockcollectionStock	Bio::Chado::Schema::Result::Stock::StockCvterm
Bio::Chado::Schema::Result::Stock::StockCvtermprop	Bio::Chado::Schema::Result::Stock::StockDbxref	Bio::Chado::Schema::Result::Stock::StockDbxrefprop
Bio::Chado::Schema::Result::Stock::StockGenotype	Bio::Chado::Schema::Result::Stock::Stockprop	Bio::Chado::Schema::Result::Stock::StockpropPub
Bio::Chado::Schema::Result::Stock::StockPub	Bio::Chado::Schema::Result::Stock::StockRelationship	Bio::Chado::Schema::Result::Stock::StockRelationshipCvterm
Bio::Chado::Schema::Result::Stock::StockRelationshipPub	Bio::Chado::Schema::Test Library to be used by Bio::Chado::Schema test scripts.	Bio::Chado::Schema::Util utility functions shared by Bio::Chado::Schema objects
Bio::Chaos utility class for handling Chaos-XML	Bio::Chaos::ChaosGraph object for representing a chaos-xml dataset	Bio::Chaos::DB::Chado I/O from a chado db
Bio::Chaos::FeatureUtil sequence and feature utilities	Bio::Chaos::Handler::base_handler	Bio::Chaos::Handler::gff3_to_chaos
Bio::Chaos::Parser::base_parser	Bio::Chaos::Parser::fasta fasta sequence input/output stream	Bio::Chaos::Parser::gff3
Bio::Chaos::Root root utility class for chaos objects	Bio::Chaos::XSLTHelper chains xslts	Bio::Cluster::ClusterFactory Instantiates a new Bio::ClusterI (or derived class) through a factory
Bio::Cluster::FamilyI Family Interface	Bio::Cluster::SequenceFamily Sequence Family object	Bio::Cluster::UniGene UniGene object
Bio::Cluster::UniGeneI abstract interface of UniGene object	Bio::ClusterI Cluster Interface	Bio::ClusterIO Handler for Cluster Formats
Bio::ClusterIO::dbsnp dbSNP input stream	Bio::ClusterIO::unigene UniGene input stream	Bio::CodonUsage::IO for reading and writing codon usage tables to file
Bio::CodonUsage::Table for access to the Codon usage Database	Bio::ConnectDots::Config	Bio::ConnectDots::ConnectDots Top level class for 'connect-the-dots'
Bio::ConnectDots::Connector one connection entry for 'connect-the-dots'	Bio::ConnectDots::ConnectorQuery	Bio::ConnectDots::ConnectorQuery::Alias
Bio::ConnectDots::ConnectorQuery::Constraint	Bio::ConnectDots::ConnectorQuery::Inner	Bio::ConnectDots::ConnectorQuery::Join
Bio::ConnectDots::ConnectorQuery::Operator::Constraint	Bio::ConnectDots::ConnectorQuery::Operator::CsConstraint	Bio::ConnectDots::ConnectorQuery::Operator::CsCsJoin
Bio::ConnectDots::ConnectorQuery::Operator::CsRootConstraint	Bio::ConnectDots::ConnectorQuery::Operator::CsSource	Bio::ConnectDots::ConnectorQuery::Operator::CtConstraint
Bio::ConnectDots::ConnectorQuery::Operator::CtCsJoin	Bio::ConnectDots::ConnectorQuery::Operator::CtCtJoin	Bio::ConnectDots::ConnectorQuery::Operator::CtSource
Bio::ConnectDots::ConnectorQuery::Operator::Join	Bio::ConnectDots::ConnectorQuery::Operator::Source	Bio::ConnectDots::ConnectorQuery::Outer
Bio::ConnectDots::ConnectorQuery::Term	Bio::ConnectDots::ConnectorSet 'connect-the-dots'	Bio::ConnectDots::ConnectorSet::DoTS
Bio::ConnectDots::ConnectorSet::ENZYME	Bio::ConnectDots::ConnectorSet::EPconDBhumanchip1	Bio::ConnectDots::ConnectorSet::EPconDBmousechip5
Bio::ConnectDots::ConnectorSet::GOA	Bio::ConnectDots::ConnectorSet::gse_platform	Bio::ConnectDots::ConnectorSet::gse_probe
Bio::ConnectDots::ConnectorSet::gse_sample	Bio::ConnectDots::ConnectorSet::gse_series	Bio::ConnectDots::ConnectorSet::HG_Focus_annot_csv
Bio::ConnectDots::ConnectorSet::HG_U133A_2_annot_csv	Bio::ConnectDots::ConnectorSet::HG_U133A_annot_csv	Bio::ConnectDots::ConnectorSet::HG_U133B_annot_csv
Bio::ConnectDots::ConnectorSet::HG_U133_Plus_2_annot_csv	Bio::ConnectDots::ConnectorSet::HG_U95Av2_annot_csv	Bio::ConnectDots::ConnectorSet::homologene
Bio::ConnectDots::ConnectorSet::homologene_xml	Bio::ConnectDots::ConnectorSet::IPI	Bio::ConnectDots::ConnectorSet::kegg_title
Bio::ConnectDots::ConnectorSet::loc2cit	Bio::ConnectDots::ConnectorSet::loc2go	Bio::ConnectDots::ConnectorSet::LocusLink
Bio::ConnectDots::ConnectorSet::MG_U74Av2_annot_csv	Bio::ConnectDots::ConnectorSet::MG_U74Bv2_annot_csv	Bio::ConnectDots::ConnectorSet::MG_U74Cv2_annot_csv
Bio::ConnectDots::ConnectorSet::Mouse430A_2_annot_csv	Bio::ConnectDots::ConnectorSet::Mouse430_2_annot_csv	Bio::ConnectDots::ConnectorSet::Mu11KsubA_annot_csv
Bio::ConnectDots::ConnectorSet::Mu11KsubB_annot_csv	Bio::ConnectDots::ConnectorSet::OMIM	Bio::ConnectDots::ConnectorSet::RefGene
Bio::ConnectDots::ConnectorSet::rgd	Bio::ConnectDots::ConnectorSet::RG_U34A_annot_csv	Bio::ConnectDots::ConnectorSet::RG_U34B_annot_csv
Bio::ConnectDots::ConnectorSet::RG_U34C_annot_csv	Bio::ConnectDots::ConnectorSet::Unigene	Bio::ConnectDots::ConnectorSet::Uniprot
Bio::ConnectDots::ConnectorTable	Bio::ConnectDots::DB Database adapter for 'connect-the-dots'	Bio::ConnectDots::DB::ConnectDots
Bio::ConnectDots::DB::ConnectorSet	Bio::ConnectDots::DB::ConnectorTable	Bio::ConnectDots::DB::DotSet
Bio::ConnectDots::DB::DotTable	Bio::ConnectDots::Dot one dot entry for 'connect-the-dots'	Bio::ConnectDots::DotQuery
Bio::ConnectDots::DotQuery::Constraint	Bio::ConnectDots::DotQuery::CsMixin	Bio::ConnectDots::DotQuery::CtMixin
Bio::ConnectDots::DotQuery::InnerCs	Bio::ConnectDots::DotQuery::InnerCt	Bio::ConnectDots::DotQuery::OuterCs
Bio::ConnectDots::DotQuery::OuterCt	Bio::ConnectDots::DotQuery::Output	Bio::ConnectDots::DotQuery::Term
Bio::ConnectDots::DotSet	Bio::ConnectDots::DotTable	Bio::ConnectDots::Parser
Bio::ConnectDots::QueryGraph	Bio::ConnectDots::SimpleGraph	Bio::ConnectDots::SimpleGraph::ShortestPaths
Bio::ConnectDots::SimpleGraph::Traversal	Bio::ConnectDots::Util	Bio::Coordinate::Chain Mapping locations through a chain of coordinate mappers
Bio::Coordinate::Collection Noncontinuous match between two coordinate sets	Bio::Coordinate::ExtrapolatingPair Continuous match between two coordinate sets	Bio::Coordinate::GeneMapper transformations between gene related coordinate systems
Bio::Coordinate::Graph Finds shortest path between nodes in a graph	Bio::Coordinate::MapperI Interface describing coordinate mappers	Bio::Coordinate::Pair Continuous match between two coordinate sets
Bio::Coordinate::Result Results from coordinate transformation	Bio::Coordinate::Result::Gap Another name for Bio::Location::Simple	Bio::Coordinate::Result::Match Another name for Bio::Location::Simple
Bio::Coordinate::ResultI Interface to identify coordinate mapper results	Bio::Coordinate::Utils Additional methods to create Bio::Coordinate objects	Bio::Das Interface to Distributed Annotation System
Bio::Das::AGPServer::Config	Bio::Das::AGPServer::Daemon	Bio::Das::AGPServer::Parser
Bio::Das::AGPServer::SQLStorage	Bio::Das::AGPServer::SQLStorage::CSV::DB	Bio::Das::AGPServer::SQLStorage::MySQL::DB
Bio::Das::DSN Object encapsulation of a DAS data source	Bio::Das::Feature	Bio::Das::FeatureIterator Iterate over a set of Bio::Das::Features
Bio::Das::FeatureTypeI Simple interface to Sequence Ontology feature types	Bio::Das::HTTP::Fetch Manage the HTTP protocol for DAS transactions	Bio::Das::Lite A client for the DAS protocol
Bio::Das::Map Resolve map coordinates	Bio::Das::ProServer A modular server for the DAS protocol	Bio::Das::ProServer::Authenticator authenticates DAS requests
Bio::Das::ProServer::Authenticator::http authenticates DAS requests by issuing	Bio::Das::ProServer::Authenticator::ip authenticates DAS requests by IP address	Bio::Das::ProServer::SourceAdaptor::all_in_group
Bio::Das::ProServer::SourceAdaptor::bed12	Bio::Das::ProServer::SourceAdaptor::edgeexpress	Bio::Das::ProServer::SourceAdaptor::grouped_db
Bio::Das::ProServer::SourceAdaptor::proxy	Bio::Das::ProServer::SourceAdaptor::sif	Bio::Das::ProServer::SourceAdaptor::simpledb Builds simple DAS features from a database
Bio::Das::ProServer::SourceAdaptor::simple_interaction	Bio::Das::ProServer::SourceAdaptor::simple_volmap	Bio::Das::ProServer::SourceAdaptor::styletest
Bio::Das::ProServer::SourceAdaptor::Transport::bed12 DBI-like access to a BED file	Bio::Das::ProServer::SourceAdaptor::Transport::csv Comma-separated-values transport layer	Bio::Das::ProServer::SourceAdaptor::Transport::edgeexpress
Bio::Das::ProServer::SourceAdaptor::Transport::ensembl	Bio::Das::ProServer::SourceAdaptor::Transport::sif	Bio::Das::ProServer::SourceHydra A runtime factory for B::D::P::SourceAdaptors
Bio::Das::ProServer::SourceHydra::dbi A database-backed implementation of B::D::P::SourceHydra	Bio::Das::ProServer::SourceHydra::sql A database-backed implementation of B::D::P::SourceHydra	Bio::Das::Request Base class for a request on a DAS server
Bio::Das::Request::Dnas The DAS "dna" request	Bio::Das::Request::Dsn The DAS "dsn" request	Bio::Das::Request::Entry_points The DAS "entry_points" request
Bio::Das::Request::Feature2Segments Translate feature names into segments	Bio::Das::Request::Features	Bio::Das::Request::Sequences The DAS "sequence" request
Bio::Das::Request::Stylesheet The DAS "stylesheet" request	Bio::Das::Request::Types The DAS "types" request	Bio::Das::Segment Serial access to Bio::Das sequence "segments"
Bio::Das::SegmentI DAS-style access to a feature database	Bio::Das::Stylesheet Access to DAS stylesheets	Bio::Das::Type A sequence annotation type
Bio::Das::TypeHandler Utilities for handling types	Bio::Das::Util Das Utilities	Bio::DasI DAS-style access to a feature database
Bio::Data::Plasmid::CloningVector Provides plasmid cloning vector data	Bio::DB::Ace Database object interface to ACeDB servers	Bio::DB::Bam::Alignment The SAM/BAM alignment object
Bio::DB::Bam::AlignWrapper Add high-level methods to Bio::DB::Bam::Alignment	Bio::DB::Bam::FetchIterator	Bio::DB::Bam::Pileup Object passed to pileup() callback
Bio::DB::Bam::PileupWrapper Add high-level methods to Bio::DB::Bam::Pileup	Bio::DB::Bam::Query Object representing the query portion of a BAM/SAM alignment	Bio::DB::Bam::ReadIterator
Bio::DB::Bam::Target Object representing the query portion of a BAM/SAM alignment in NATIVE alignment	Bio::DB::Biblio::biofetch A BioFetch-based access to a bibliographic	Bio::DB::Biblio::eutils Access to PubMed's bibliographic query service
Bio::DB::Biblio::soap A SOAP-based access to a bibliographic query service	Bio::DB::BiblioI An interface to a Bibliographic Query Service	Bio::DB::BigBed
Bio::DB::BigFile Low-level interface to BigWig & BigBed files	Bio::DB::BigFile::Constants	Bio::DB::BigFile::Iterators
Bio::DB::BigWig	Bio::DB::BigWigSet	Bio::DB::BioFetch Database object interface to BioFetch retrieval
Bio::DB::CUTG for access to the Codon usage Database	Bio::DB::Das::BioSQL DAS-style access to a BioSQL database	Bio::DB::Das::Chado DAS-style access to a chado database
Bio::DB::DBFetch Database object for retrieving using the dbfetch script	Bio::DB::EMBL Database object interface for EMBL entry retrieval	Bio::DB::EntrezGene Database object interface to Entrez Gene
Bio::DB::ESoap Client for the NCBI Entrez EUtilities SOAP server	Bio::DB::ESoap::WSDL WSDL parsing for Entrez SOAP EUtilities	Bio::DB::EUtilities webagent which interacts with and retrieves data from
Bio::DB::Expression DESCRIPTION of Object	Bio::DB::Expression::geo *** DESCRIPTION of Class	Bio::DB::Failover A Bio::DB::RandomAccessI compliant class which
Bio::DB::Fasta Fast indexed access to a directory of fasta files	Bio::DB::FileCache In file cache for BioSeq objects	Bio::DB::Flat Interface for indexed flat files
Bio::DB::Flat::BDB Interface for BioHackathon standard BDB-indexed flat file	Bio::DB::Flat::BDB::embl embl adaptor for Open-bio standard BDB-indexed flat file	Bio::DB::Flat::BDB::fasta fasta adaptor for Open-bio standard BDB-indexed flat file
Bio::DB::Flat::BDB::genbank genbank adaptor for Open-bio standard BDB-indexed flat file	Bio::DB::Flat::BDB::swiss swissprot adaptor for Open-bio standard BDB-indexed flat file	Bio::DB::Flat::BinarySearch BinarySearch search indexing system for sequence files
Bio::DB::GenBank Database object interface to GenBank	Bio::DB::GenericWebAgent helper base class for parameter-based remote server	Bio::DB::GenPept Database object interface to GenPept
Bio::DB::GFF Storage and retrieval of sequence annotation data	Bio::DB::GFF::Adaptor::ace ace interface (for multiple inheritance)	Bio::DB::GFF::Adaptor::berkeleydb Bio::DB::GFF database adaptor for in-memory databases
Bio::DB::GFF::Adaptor::berkeleydb::iterator iterator for Bio::DB::GFF::Adaptor::berkeleydb	Bio::DB::GFF::Adaptor::biofetch Cache BioFetch objects in a Bio::DB::GFF database	Bio::DB::GFF::Adaptor::biofetch_oracle Cache BioFetch objects in a Bio::DB::GFF database
Bio::DB::GFF::Adaptor::dbi Database adaptor for DBI (SQL) databases	Bio::DB::GFF::Adaptor::dbi::caching_handle Cache for database handles	Bio::DB::GFF::Adaptor::dbi::iterator iterator for Bio::DB::GFF::Adaptor::dbi
Bio::DB::GFF::Adaptor::dbi::mysql Database adaptor for a specific mysql schema	Bio::DB::GFF::Adaptor::dbi::mysqlace Unholy union between mysql GFF database and acedb database	Bio::DB::GFF::Adaptor::dbi::mysqlcmap Database adaptor for an integraded
Bio::DB::GFF::Adaptor::dbi::mysqlopt Deprecated database adaptor	Bio::DB::GFF::Adaptor::dbi::oracle Database adaptor for a specific oracle schema	Bio::DB::GFF::Adaptor::dbi::oracleace Unholy union between oracle GFF database and acedb database
Bio::DB::GFF::Adaptor::dbi::pg Database adaptor for a specific postgres schema	Bio::DB::GFF::Adaptor::dbi::pg_fts Database adaptor for a specific postgres schema with a TSearch2 implementation	Bio::DB::GFF::Adaptor::memory Bio::DB::GFF database adaptor for in-memory databases
Bio::DB::GFF::Adaptor::memory::feature_serializer utility methods for serializing and deserializing GFF features	Bio::DB::GFF::Adaptor::memory::iterator iterator for Bio::DB::GFF::Adaptor::memory	Bio::DB::GFF::Aggregator Aggregate GFF groups into composite features
Bio::DB::GFF::Aggregator::alignment Alignment aggregator	Bio::DB::GFF::Aggregator::clone Clone aggregator	Bio::DB::GFF::Aggregator::coding The Coding Region Aggregator
Bio::DB::GFF::Aggregator::gene Sequence Ontology Geene	Bio::DB::GFF::Aggregator::match Match aggregator	Bio::DB::GFF::Aggregator::match_gap GFF3 match aggregator
Bio::DB::GFF::Aggregator::none No aggregation	Bio::DB::GFF::Aggregator::orf An aggregator for orf regions	Bio::DB::GFF::Aggregator::processed_transcript Sequence Ontology Transcript
Bio::DB::GFF::Aggregator::reftranscript	Bio::DB::GFF::Aggregator::so_transcript Sequence Ontology Transcript	Bio::DB::GFF::Aggregator::transcript Transcript aggregator
Bio::DB::GFF::Aggregator::ucsc_acembly UCSC acembly aggregator	Bio::DB::GFF::Aggregator::ucsc_ensgene UCSC ensGene aggregator	Bio::DB::GFF::Aggregator::ucsc_genscan UCSC genscan aggregator
Bio::DB::GFF::Aggregator::ucsc_refgene UCSC refGene aggregator	Bio::DB::GFF::Aggregator::ucsc_sanger22 UCSC sanger22 aggregator	Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo UCSC sanger22pseudo aggregator
Bio::DB::GFF::Aggregator::ucsc_softberry UCSC softberry aggregator	Bio::DB::GFF::Aggregator::ucsc_twinscan UCSC twinscan aggregator	Bio::DB::GFF::Aggregator::ucsc_unigene UCSC UniGene aggregator
Bio::DB::GFF::Aggregator::waba_alignment A WABA alignment	Bio::DB::GFF::Aggregator::wormbase_gene Wormbase gene aggregator	Bio::DB::GFF::Featname The name of a feature
Bio::DB::GFF::Feature A relative segment identified by a feature type	Bio::DB::GFF::Homol A segment of DNA that is homologous to another	Bio::DB::GFF::RelSegment Sequence segment with relative coordinate support
Bio::DB::GFF::Segment Simple DNA segment object	Bio::DB::GFF::Typename The name of a feature type	Bio::DB::GFF::Util::Binning binning utility for Bio::DB::GFF index
Bio::DB::GFF::Util::Rearrange rearrange utility	Bio::DB::HIV Database object interface to the Los Alamos HIV Sequence Database	Bio::DB::HIV::HIVAnnotProcessor
Bio::DB::HIV::HIVQueryHelper Routines and packages used by Bio::DB::HIV and	Bio::DB::InMemoryCache Abstract interface for a sequence database	Bio::DB::LocationI A RandomAccessI-like abstract interface for
Bio::DB::MeSH Term retrieval from a Web MeSH database	Bio::DB::NCBIHelper A collection of routines useful for queries to	Bio::DB::Qual Fast indexed access to a directory of quality files
Bio::DB::Query::GenBank Build a GenBank Entrez Query	Bio::DB::Query::HIVQuery Query interface to the Los Alamos HIV Sequence Database	Bio::DB::Query::WebQuery Helper class for web-based sequence queryies
Bio::DB::QueryI Object Interface to queryable sequence databases	Bio::DB::RandomAccessI Abstract interface for a sequence database	Bio::DB::ReferenceI A RandomAccessI-like abstract interface for
Bio::DB::RefSeq Database object interface for RefSeq retrieval	Bio::DB::Registry Access to the Open Bio Database Access registry scheme	Bio::DB::Sam Read SAM/BAM database files
Bio::DB::Sam::Constants Constants for use with SAM/BAM	Bio::DB::Sam::SamToGBrowse	Bio::DB::Sam::Segment
Bio::DB::SeqFeature Normalized feature for use with Bio::DB::SeqFeature::Store	Bio::DB::SeqFeature::NormalizedFeature Normalized feature for use with Bio::DB::SeqFeature::Store	Bio::DB::SeqFeature::NormalizedFeatureI Interface for normalized features
Bio::DB::SeqFeature::NormalizedTableFeatureI Interface for normalized features whose hierarchy is stored in a table	Bio::DB::SeqFeature::Segment Location-based access to genome annotation data	Bio::DB::SeqFeature::Store Storage and retrieval of sequence annotation data
Bio::DB::SeqFeature::Store::bdb fetch and store objects from a BerkeleyDB	Bio::DB::SeqFeature::Store::BedLoader	Bio::DB::SeqFeature::Store::berkeleydb Storage and retrieval of sequence annotation data in Berkeleydb files
Bio::DB::SeqFeature::Store::berkeleydb3 Storage and retrieval of sequence	Bio::DB::SeqFeature::Store::DBI::Iterator utility methods for creating and iterating over SeqFeature records	Bio::DB::SeqFeature::Store::DBI::mysql Mysql implementation of Bio::DB::SeqFeature::Store
Bio::DB::SeqFeature::Store::DBI::Pg PostgreSQL implementation of Bio::DB::SeqFeature::Store	Bio::DB::SeqFeature::Store::DBI::SQLite SQLite implementation of Bio::DB::SeqFeature::Store	Bio::DB::SeqFeature::Store::FeatureFileLoader feature file loader for Bio::DB::SeqFeature::Store
Bio::DB::SeqFeature::Store::GFF2Loader GFF2 file loader for Bio::DB::SeqFeature::Store	Bio::DB::SeqFeature::Store::GFF3Loader GFF3 file loader for Bio::DB::SeqFeature::Store	Bio::DB::SeqFeature::Store::Loader Loader
Bio::DB::SeqFeature::Store::LoadHelper Internal utility for Bio::DB::SeqFeature::Store	Bio::DB::SeqFeature::Store::memory In-memory implementation of Bio::DB::SeqFeature::Store	Bio::DB::SeqHound Database object interface to SeqHound
Bio::DB::SeqI Abstract Interface for Sequence databases	Bio::DB::SeqVersion front end to querying databases for identifier	Bio::DB::SeqVersion::gi interface to NCBI Sequence Revision History page
Bio::DB::SoapEUtilities Interface to the NCBI Entrez web service BETA	Bio::DB::SoapEUtilities::DocSumAdaptor Handle for Entrez SOAP DocSums	Bio::DB::SoapEUtilities::FetchAdaptor Conversion of Entrez SOAP messages to BioPerl objects
Bio::DB::SoapEUtilities::FetchAdaptor::seq Fetch adaptor for 'seq'	Bio::DB::SoapEUtilities::FetchAdaptor::species Fetch adaptor for	Bio::DB::SoapEUtilities::GQueryAdaptor Handle for Entrez SOAP GlobalQuery items
Bio::DB::SoapEUtilities::LinkAdaptor Handle for Entrez SOAP LinkSets	Bio::DB::SoapEUtilities::Result Accessor object for SoapEUtilities results	Bio::DB::SwissProt Database object interface to SwissProt retrieval
Bio::DB::Tagger Simple object tagging system	Bio::DB::Tagger::mysql	Bio::DB::Tagger::Tag Authored tags
Bio::DB::Taxonomy Access to a taxonomy database	Bio::DB::Taxonomy::entrez Taxonomy Entrez driver	Bio::DB::Taxonomy::flatfile An implementation of Bio::DB::Taxonomy
Bio::DB::Taxonomy::list An implementation of Bio::DB::Taxonomy	Bio::DB::TFBS Access to a Transcription Factor Binding Site database	Bio::DB::TFBS::transfac_pro An implementation of Bio::DB::TFBS
Bio::DB::Universal Artificial database that delegates to specific databases	Bio::DB::UpdateableSeqI An interface for writing to a database of sequences.	Bio::DB::WebDBSeqI Object Interface to generalize Web Databases
Bio::DBLinkContainerI Abstract interface for any object wanting to use	Bio::DescribableI interface for objects with human readable names and descriptions	Bio::DOOP::Cluster DoOP cluster object
Bio::DOOP::ClusterSubset One subset of a cluster	Bio::DOOP::DBSQL MySQL control object	Bio::DOOP::DOOP DOOP API main module
Bio::DOOP::Graphics::Feature Graphical representation of the features	Bio::DOOP::Motif DOOP database motif object	Bio::DOOP::Sequence Sequence (promoter region) object
Bio::DOOP::SequenceFeature Object for the sequence features	Bio::DOOP::Util::Filt Filter a cluster list	Bio::DOOP::Util::Run::Fuzznuc Fuzznuc module
Bio::DOOP::Util::Run::GeneMerge GeneMerge based GO analyzer	Bio::DOOP::Util::Run::Mofext Mofext module	Bio::DOOP::Util::Search Useful methods for easy search
Bio::DOOP::Util::Sort Sort an array of arrays	Bio::Draw::Pictogram generate SVG output of Pictogram display for consensus motifs	Bio::ECell Perl interface for E-Cell Simulator.
Bio::Emboss Write EMBOSS programs in Perl	Bio::Emboss::Methods	Bio::Event::EventGeneratorI This interface describes the basic event
Bio::Event::EventHandlerI An Event Handler Interface	Bio::Factory::AnalysisI An interface to analysis tool factory	Bio::Factory::ApplicationFactoryI Interface class for Application Factories
Bio::Factory::DriverFactory Base class for factory classes loading drivers	Bio::Factory::FTLocationFactory A FeatureTable Location Parser	Bio::Factory::LocationFactoryI A factory interface for generating locations from a string
Bio::Factory::MapFactoryI A Factory for getting markers	Bio::Factory::ObjectBuilderI Interface for an object builder	Bio::Factory::ObjectFactory Instantiates a new Bio::Root::RootI (or derived class) through a factory
Bio::Factory::ObjectFactoryI A General object creator factory	Bio::Factory::SeqAnalysisParserFactory class capable of creating	Bio::Factory::SeqAnalysisParserFactoryI interface describing objects capable
Bio::Factory::SequenceFactoryI This interface allows for generic building of sequences in factories which create sequences (like SeqIO)	Bio::Factory::SequenceProcessorI Interface for chained sequence	Bio::Factory::SequenceStreamI Interface describing the basics of a Sequence Stream.
Bio::Factory::TreeFactoryI Factory Interface for getting and writing trees	Bio::FASTASequence Perl extension for Bioinformatics. Parsing sequence informations.	Bio::FASTASequence::File Perl extension for Bio::FASTASequence
Bio::FdrFet Perl extension for False Discovery Rate and Fisher Exact Test applied to pathway analysis.	Bio::FeatureHolderI the base interface an object with features must implement	Bio::FeatureIO Handler for FeatureIO
Bio::FeatureIO::bed read/write features from UCSC BED format	Bio::FeatureIO::gff read/write GFF feature files	Bio::FeatureIO::gtf read write features in GTF format
Bio::FeatureIO::interpro read features from InterPro XML	Bio::FeatureIO::ptt read/write features in PTT format	Bio::FeatureIO::vecscreen_simple read/write features from NCBI vecscreen -f 3
Bio::GenBankParser Parse::RecDescent parser for a GenBank record	Bio::Genex::AL_Spots Methods for processing data from the GeneX DB	Bio::Genex::AM_FactorValues Methods for processing data from the GeneX DB
Bio::Genex::AM_Spots Methods for processing data from the GeneX DB	Bio::Genex::AM_SuspectSpots Methods for processing data from the GeneX DB	Bio::Genex::ArrayLayout Methods for processing data from the GeneX DB
Bio::Genex::ArrayMeasurement Methods for processing data from the GeneX DB	Bio::Genex::BlastHits Methods for processing data from the GeneX DB	Bio::Genex::Chromosome Methods for processing data from the GeneX DB
Bio::Genex::Citation Methods for processing data from the GeneX DB	Bio::Genex::Contact Methods for processing data from the GeneX DB	Bio::Genex::ControlledVocab Methods for processing data from the GeneX DB
Bio::Genex::ExperimentFactors Methods for processing data from the GeneX DB	Bio::Genex::ExperimentSet Methods for processing data from the GeneX DB	Bio::Genex::ExternalDatabase Methods for processing data from the GeneX DB
Bio::Genex::Fkey Perl extension for representing Database Foreign Keys	Bio::Genex::GenexAdmin Methods for processing data from the GeneX DB	Bio::Genex::GroupLink Methods for processing data from the GeneX DB
Bio::Genex::GroupSec Methods for processing data from the GeneX DB	Bio::Genex::HotSpots Methods for processing data from the GeneX DB	Bio::Genex::Protocol Methods for processing data from the GeneX DB
Bio::Genex::Sample Methods for processing data from the GeneX DB	Bio::Genex::SampleProtocols Methods for processing data from the GeneX DB	Bio::Genex::Scanner Methods for processing data from the GeneX DB
Bio::Genex::Software Methods for processing data from the GeneX DB	Bio::Genex::Species Methods for processing data from the GeneX DB	Bio::Genex::SpotLink Methods for processing data from the GeneX DB
Bio::Genex::Spotter Methods for processing data from the GeneX DB	Bio::Genex::TL_FactorValues Methods for processing data from the GeneX DB	Bio::Genex::TreatmentLevel Methods for processing data from the GeneX DB
Bio::Genex::Treatment_AMs Methods for processing data from the GeneX DB	Bio::Genex::UserSec Methods for processing data from the GeneX DB	Bio::Genex::UserSequenceFeature Methods for processing data from the GeneX DB
Bio::Genex::USF_ExternalDBLink Methods for processing data from the GeneX DB	Bio::GFF3::LowLevel fast, low-level functions for parsing and formatting GFF3	Bio::GFF3::Transform::FromFasta make gff3 for the sequences in a fasta file
Bio::GFF3::Transform::SyncDirectives insert sync (###) directives into an existing GFF3 file.	Bio::Glite Web service wrapper for G-language System.	Bio::GMOD Unified Generic Model Organism Database API
Bio::GMOD::Adaptor Generic factory for Bio::GMOD::Adaptor::* objects	Bio::GMOD::Adaptor::FlyBase Defaults for programmatically interacting with Wormbase	Bio::GMOD::Adaptor::generic A generic adaptor for working with multiple MODs simultaneously
Bio::GMOD::Adaptor::SGD Defaults for programmatically interacting with SGD	Bio::GMOD::Admin::Archive	Bio::GMOD::Admin::Monitor Monitor the status of an installed MOD
Bio::GMOD::Admin::Monitor::acedb Monitor acedb/sgifaceserver	Bio::GMOD::Admin::Monitor::blat Monitor a BLAT server	Bio::GMOD::Admin::Monitor::httpd Monitor httpd
Bio::GMOD::Admin::Monitor::mysqld Monitor mysqld	Bio::GMOD::Admin::Monitor::WormBase WormBase monitoring utils	Bio::GMOD::Admin::Update Generics methods for updating a Bio::GMOD installation
Bio::GMOD::Admin::Update::WormBase Methods for updating a WormBase installation	Bio::GMOD::Blast::Graph display a graphical summary of a BLAST report	Bio::GMOD::Blast::Graph::BaseObj
Bio::GMOD::Blast::Graph::Bucket	Bio::GMOD::Blast::Graph::BucketSet	Bio::GMOD::Blast::Graph::HitWrapper
Bio::GMOD::Blast::Graph::IntSpan Manages sets of integers	Bio::GMOD::Blast::Graph::List	Bio::GMOD::Blast::Graph::ListEnumerator
Bio::GMOD::Blast::Graph::ListSet	Bio::GMOD::Blast::Graph::ListSetEnumerator	Bio::GMOD::Blast::Graph::MapDefs
Bio::GMOD::Blast::Graph::MapSpace	Bio::GMOD::Blast::Graph::MapUtils	Bio::GMOD::Blast::Graph::MyDebug
Bio::GMOD::Blast::Graph::MyMath	Bio::GMOD::Blast::Graph::MyUtils	Bio::GMOD::Blast::Graph::ScientificNotation
Bio::GMOD::Blast::Graph::WrapList	Bio::GMOD::Blast::Graph::WrapPartitionsFixed	Bio::GMOD::GenericGenePage Generic GMOD gene page base class
Bio::GMOD::GenericGenePage::Chado	Bio::GMOD::Query Execute generic queries for different MODs	Bio::GMOD::Query::FlyBase
Bio::GMOD::Query::WormBase Defaults for programmatically interacting with Wormbase	Bio::GMOD::StandardURLs Discover and fetch Standard URLs from MODs	Bio::GMOD::Util::CheckVersions Find current versions of GMOD installations
Bio::GMOD::Util::CheckVersions::WormBase Versioning code for WormBase	Bio::GMOD::Util::Mirror File and directory mirroring	Bio::GMOD::Util::Rearrange Named parameter processing
Bio::GMOD::Util::Status Message processing for Bio::GMOD	Bio::Graphics Generate GD images of Bio::Seq objects	Bio::Graphics::Browser2
Bio::Graphics::Browser2::Action	Bio::Graphics::Browser2::AuthorizedFeatureFile Add HTTP authorization features to FeatureFile	Bio::Graphics::Browser2::CachedTrack
Bio::Graphics::Browser2::CAlign Compiled helper for Bio::Graphics::Browser::Realign	Bio::Graphics::Browser2::DataBase A simple cache for database handles	Bio::Graphics::Browser2::DataLoader
Bio::Graphics::Browser2::DataLoader::bam	Bio::Graphics::Browser2::DataLoader::bed	Bio::Graphics::Browser2::DataLoader::bigwig
Bio::Graphics::Browser2::DataLoader::featurefile	Bio::Graphics::Browser2::DataLoader::generic	Bio::Graphics::Browser2::DataLoader::gff
Bio::Graphics::Browser2::DataLoader::gff3	Bio::Graphics::Browser2::DataLoader::sam	Bio::Graphics::Browser2::DataLoader::wiggle
Bio::Graphics::Browser2::DataSource	Bio::Graphics::Browser2::ExternalData	Bio::Graphics::Browser2::GFFhelper Helps gbrowse plugins handle GFF
Bio::Graphics::Browser2::I18n	Bio::Graphics::Browser2::Markup Markup routines for sequences in text form	Bio::Graphics::Browser2::OptionPick Pick options
Bio::Graphics::Browser2::PadAlignment Insert pads into a multiple alignment	Bio::Graphics::Browser2::Plugin Base class for gbrowse plugins.	Bio::Graphics::Browser2::Plugin::AuthPlugin Base class for authentication plugins
Bio::Graphics::Browser2::PluginSet A set of plugins	Bio::Graphics::Browser2::Realign Perl extension for Smith-Waterman alignments	Bio::Graphics::Browser2::Region
Bio::Graphics::Browser2::RegionSearch Search through multiple databases for feature matches.	Bio::Graphics::Browser2::RemoteSet	Bio::Graphics::Browser2::Render
Bio::Graphics::Browser2::Render::HTML	Bio::Graphics::Browser2::Render::Login	Bio::Graphics::Browser2::Render::Slave
Bio::Graphics::Browser2::Render::Slave::Status	Bio::Graphics::Browser2::Render::TrackConfig	Bio::Graphics::Browser2::RenderPanels
Bio::Graphics::Browser2::Session	Bio::Graphics::Browser2::Shellwords	Bio::Graphics::Browser2::SubtrackTable
Bio::Graphics::Browser2::TrackDumper	Bio::Graphics::Browser2::UserDB	Bio::Graphics::Browser2::UserTracks
Bio::Graphics::Browser2::UserTracks::Database	Bio::Graphics::Browser2::UserTracks::Filesystem	Bio::Graphics::Browser2::Util Exported utilities
Bio::Graphics::ConfiguratorI A sectioned map of configuration	Bio::Graphics::DrawTransmembrane draw a cartoon of an Alpha-helical transmembrane protein.	Bio::Graphics::Feature A simple feature object for use with Bio::Graphics::Panel
Bio::Graphics::FeatureBase Compatibility module	Bio::Graphics::FeatureDir A directory of feature files and conf files	Bio::Graphics::FeatureFile A set of Bio::Graphics features, stored in a file
Bio::Graphics::FeatureFile::Iterator Iterator across a Bio::Graphics::FeatureFile	Bio::Graphics::GBrowseFeature	Bio::Graphics::Glyph Base class for Bio::Graphics::Glyph objects
Bio::Graphics::Glyph::alignment The "alignment" glyph	Bio::Graphics::Glyph::allele_tower The "allele_tower" glyph	Bio::Graphics::Glyph::anchored_arrow The "anchored_arrow" glyph
Bio::Graphics::Glyph::arrow the "arrow" glyph	Bio::Graphics::Glyph::box The "box" glyph	Bio::Graphics::Glyph::broken_line The "broken line" glyph
Bio::Graphics::Glyph::cds The "cds" glyph	Bio::Graphics::Glyph::christmas_arrow The "christmas arrow" glyph	Bio::Graphics::Glyph::cross
Bio::Graphics::Glyph::crossbox The "crossbox" glyph	Bio::Graphics::Glyph::dashed_line The "dashed line" glyph	Bio::Graphics::Glyph::diamond The "diamond" glyph
Bio::Graphics::Glyph::dna The "dna" glyph	Bio::Graphics::Glyph::dot The "dot" glyph	Bio::Graphics::Glyph::dumbbell A glyph that draws a "dumbbell" with the same shapes on both ends.
Bio::Graphics::Glyph::ellipse The "ellipse" glyph	Bio::Graphics::Glyph::ex the "ex", or "crossed box" glyph	Bio::Graphics::Glyph::extending_arrow The "extending arrow" glyph
Bio::Graphics::Glyph::Factory Factory for Bio::Graphics::Glyph objects	Bio::Graphics::Glyph::fixedwidth A base class fixed width glyphs	Bio::Graphics::Glyph::flag the "flag" glyph
Bio::Graphics::Glyph::gene A GFF3-compatible gene glyph	Bio::Graphics::Glyph::generic The "generic" glyph	Bio::Graphics::Glyph::graded_segments The "graded_segments" glyph
Bio::Graphics::Glyph::group The "group" glyph	Bio::Graphics::Glyph::hat The "hat" glyph	Bio::Graphics::Glyph::heat_map The "heat_map" glyph
Bio::Graphics::Glyph::heat_map_ideogram The "heat_map_ideogram" glyph	Bio::Graphics::Glyph::heterogeneous_segments The "heterogeneous_segments" glyph	Bio::Graphics::Glyph::hidden The "hidden" glyph
Bio::Graphics::Glyph::hybrid_plot An xyplot plot drawing dual graph using data from two wiggle files per track	Bio::Graphics::Glyph::ideogram The "ideogram" glyph	Bio::Graphics::Glyph::image A glyph that draws photographs & other images
Bio::Graphics::Glyph::lightning The "lightning" glyph	Bio::Graphics::Glyph::line The "line" glyph	Bio::Graphics::Glyph::merged_alignment The "merged_alignment" glyph
Bio::Graphics::Glyph::merge_parts a base class which suppors semantic zooming of scored alignment features	Bio::Graphics::Glyph::minmax The minmax glyph	Bio::Graphics::Glyph::operon The "polycistronic operon" glyph
Bio::Graphics::Glyph::oval The "oval" glyph	Bio::Graphics::Glyph::pairplot The "pairwise plot" glyph	Bio::Graphics::Glyph::pentagram The "pentagram" glyph
Bio::Graphics::Glyph::phylo_align The "phylogenetic alignment" glyph	Bio::Graphics::Glyph::pinsertion The "Drosophila P-element Insertion" glyph	Bio::Graphics::Glyph::primers The "STS primers" glyph
Bio::Graphics::Glyph::processed_transcript The sequence ontology transcript glyph	Bio::Graphics::Glyph::protein The "protein" glyph	Bio::Graphics::Glyph::ragged_ends The "ragged ends" glyph
Bio::Graphics::Glyph::rainbow_gene	Bio::Graphics::Glyph::read_pair	Bio::Graphics::Glyph::redgreen_box The "redgreen_box" glyph
Bio::Graphics::Glyph::redgreen_segment The "redgreen_segments" glyph	Bio::Graphics::Glyph::repeating_shape A glyph that draws the same shape repeatedly.	Bio::Graphics::Glyph::rndrect The "round rect" glyph
Bio::Graphics::Glyph::ruler_arrow glyph for drawing an arrow as ruler (5' and 3' are marked as label)	Bio::Graphics::Glyph::saw_teeth The "saw teeth" glyph	Bio::Graphics::Glyph::segmented_keyglyph The "segmented_keyglyph" glyph
Bio::Graphics::Glyph::segments The "segments" glyph	Bio::Graphics::Glyph::smoothing	Bio::Graphics::Glyph::so_transcript The sequence ontology transcript glyph
Bio::Graphics::Glyph::span The "span" glyph	Bio::Graphics::Glyph::spectrogram The "spectrogram" glyph	Bio::Graphics::Glyph::splice_site The "splice_site" glyph
Bio::Graphics::Glyph::stackedplot The stackedplot glyph	Bio::Graphics::Glyph::ternary_plot Draw ternary plot data	Bio::Graphics::Glyph::text_in_box The "text in box" glyph
Bio::Graphics::Glyph::three_letters DAS-compatible package to use for drawing a line of groups of three letters	Bio::Graphics::Glyph::tic_tac_toe The "tic-tac-toe" glyph	Bio::Graphics::Glyph::toomany The "too many to show" glyph
Bio::Graphics::Glyph::trace A glyph that visualizes a trace file	Bio::Graphics::Glyph::track The "track" glyph	Bio::Graphics::Glyph::transcript The "transcript" glyph
Bio::Graphics::Glyph::transcript2 The "transcript2" glyph	Bio::Graphics::Glyph::translation The "6-frame translation" glyph	Bio::Graphics::Glyph::triangle The "triangle" glyph
Bio::Graphics::Glyph::two_bolts The "two bolts" glyph	Bio::Graphics::Glyph::vista_plot The "vista_plot" glyph	Bio::Graphics::Glyph::wave The "wave" glyph
Bio::Graphics::Glyph::weighted_arrow The "weighted arrow" glyph	Bio::Graphics::Glyph::whiskerplot The whiskerplot glyph	Bio::Graphics::Glyph::wiggle_box A generic box glyph compatible with dense "wig"data
Bio::Graphics::Glyph::wiggle_density A density plot compatible with dense "wig"data	Bio::Graphics::Glyph::wiggle_minmax	Bio::Graphics::Glyph::wiggle_whiskers
Bio::Graphics::Glyph::wiggle_xyplot An xyplot plot compatible with dense "wig"data	Bio::Graphics::Glyph::xyplot The xyplot glyph	Bio::Graphics::Karyotype
Bio::Graphics::Layout	Bio::Graphics::Panel Generate GD images of Bio::Seq objects	Bio::Graphics::Pictogram generate SVG output of Pictogram display for consensus motifs
Bio::Graphics::RendererI A renderer for the Bio::Graphics class that	Bio::Graphics::Util non-object-oriented utilities used in Bio::Graphics modules	Bio::Graphics::Wiggle Binary storage for dense genomic features
Bio::Graphics::Wiggle::Loader	Bio::Grep Perl extension for searching in DNA and Protein sequences	Bio::Grep::Backend::Agrep Agrep back-end
Bio::Grep::Backend::BackendI Superclass for all back-ends	Bio::Grep::Backend::GUUGle GUUGle back-end	Bio::Grep::Backend::RE Perl Regular Expression back-end
Bio::Grep::Backend::Vmatch Vmatch back-end	Bio::Grep::Filter::FilterI Superclass for all filter modules	Bio::Grep::Filter::FilterRemoveDuplicates Example Filter
Bio::Grep::Root Superclass for all Bio::Grep* packages	Bio::Grep::SearchResult Data structure for a back-end search hit	Bio::Grep::SearchSettings Data structure for all search settings
Bio::HandlerBaseI Interface class for handler methods which interact with any	Bio::Homology::InterologWalk Retrieve putative PPIs through Interologs	Bio::IdCollectionI interface for objects with multiple identifiers
Bio::IdentifiableI interface for objects with identifiers	Bio::Index::Abstract Abstract interface for indexing a flat file	Bio::Index::AbstractSeq base class for AbstractSeq
Bio::Index::Blast Indexes Blast reports and supports retrieval	Bio::Index::BlastTable Indexes tabular Blast reports (-m 8 or -m 9 format) and	Bio::Index::EMBL Interface for indexing (multiple) EMBL/Swissprot
Bio::Index::Fasta Interface for indexing (multiple) fasta files	Bio::Index::Fastq Interface for indexing (multiple) fastq files	Bio::Index::GenBank Interface for indexing one or more GenBank
Bio::Index::Hmmer indexes HMMER reports and supports retreival based on query	Bio::Index::Qual Interface for indexing (multiple) fasta qual files	Bio::Index::Stockholm Indexes Stockholm format alignments (such as those from
Bio::Index::SwissPfam Interface for indexing swisspfam files	Bio::Index::Swissprot Interface for indexing one or more	Bio::KEGG Perl module to fetch details parsed by Bio::KEGGI.
Bio::KEGG::genome Perl module to fetch details of KEGG file 'genome'.	Bio::KEGG::ko	Bio::KEGG::pathway
Bio::KEGGI Perl module to parse KEGG genome, ko and pathway files.	Bio::KEGGI::genome Parse KEGG genome entry file.	Bio::KEGGI::ko
Bio::KEGGI::pathway	Bio::LITE::Taxonomy Lightweight and efficient taxonomic tree manager	Bio::LITE::Taxonomy::NCBI Lightweight and efficient NCBI taxonomic manager
Bio::LITE::Taxonomy::NCBI::Gi2taxid Mappings of NCBI GIs to Taxids fast and with very low memory footprint.	Bio::LITE::Taxonomy::RDP Lightweight and efficient RDP taxonomic manager	Bio::LiveSeq::AARange AARange abstract class for LiveSeq
Bio::LiveSeq::Chain DoubleChain DataStructure for Perl	Bio::LiveSeq::ChainI Double linked chain data structure	Bio::LiveSeq::DNA DNA object for LiveSeq
Bio::LiveSeq::Exon Range abstract class for LiveSeq	Bio::LiveSeq::Gene Range abstract class for LiveSeq	Bio::LiveSeq::Intron Range abstract class for LiveSeq
Bio::LiveSeq::IO::BioPerl Loader for LiveSeq from EMBL entries with BioPerl	Bio::LiveSeq::IO::Loader Parent Loader for LiveSeq	Bio::LiveSeq::Mutation Mutation event descriptor class
Bio::LiveSeq::Mutator Package mutating LiveSequences	Bio::LiveSeq::Prim_Transcript Prim_Transcript class for LiveSeq	Bio::LiveSeq::Range Range abstract class for LiveSeq
Bio::LiveSeq::Repeat_Region Repeat_Region class for LiveSeq	Bio::LiveSeq::Repeat_Unit Repeat_Unit class for LiveSeq	Bio::LiveSeq::SeqI Abstract sequence interface class for LiveSeq
Bio::LiveSeq::Transcript Transcript class for LiveSeq	Bio::LiveSeq::Translation Translation class for LiveSeq	Bio::Location::Atomic Implementation of a Atomic Location on a Sequence
Bio::Location::AvWithinCoordPolicy class implementing	Bio::Location::CoordinatePolicyI Abstract interface for objects implementing	Bio::Location::Fuzzy Implementation of a Location on a Sequence
Bio::Location::FuzzyLocationI Abstract interface of a Location on a Sequence	Bio::Location::NarrowestCoordPolicy class implementing	Bio::Location::Simple Implementation of a Simple Location on a Sequence
Bio::Location::Split Implementation of a Location on a Sequence	Bio::Location::SplitLocationI Abstract interface of a Location on a Sequence	Bio::Location::WidestCoordPolicy class implementing
Bio::LocationI Abstract interface of a Location on a Sequence	Bio::MAGE microarray gene expression (MAGE) API	Bio::MAGE::Association
Bio::MAGE::Base generic base class	Bio::MAGE::Tools::MGEDOntologyClassEntry	Bio::MAGE::Tools::MGEDOntologyEntry
Bio::MAGE::Tools::MGEDOntologyHelper	Bio::MAGE::Tools::MGEDOntologyPropertyEntry	Bio::MAGE::XML::Handler
Bio::MAGE::XML::Handler::ContentHandler	Bio::MAGE::XML::Handler::DocumentHandler	Bio::MAGE::XML::Handler::ObjectHandler::SQL DESCRIPTION of Object
Bio::MAGE::XML::Handler::ObjectHandlerI Abstract class for processing	Bio::MAGE::XML::Reader a module for exporting MAGE-ML	Bio::MAGE::XML::Writer a module for exporting MAGE-ML
Bio::MAGE::XMLUtils	Bio::MAGETAB Reading and writing MAGE-TAB documents	Bio::MAGETAB::ArrayDesign MAGE-TAB array design class
Bio::MAGETAB::Assay MAGE-TAB assay class	Bio::MAGETAB::BaseClass Abstract base class for all MAGE-TAB classes.	Bio::MAGETAB::Comment MAGE-TAB user-defined comment class
Bio::MAGETAB::CompositeElement MAGE-TAB composite element class	Bio::MAGETAB::Contact MAGE-TAB contact class	Bio::MAGETAB::ControlledTerm MAGE-TAB controlled term class
Bio::MAGETAB::Data Abstract data class	Bio::MAGETAB::DataAcquisition MAGE-TAB data acquisition class	Bio::MAGETAB::DatabaseEntry MAGE-TAB database entry class
Bio::MAGETAB::DataFile MAGE-TAB data file class	Bio::MAGETAB::DataMatrix MAGE-TAB data matrix class	Bio::MAGETAB::DesignElement Abstract design element class
Bio::MAGETAB::Edge MAGE-TAB edge class	Bio::MAGETAB::Event Abstract event class	Bio::MAGETAB::Extract MAGE-TAB extract class
Bio::MAGETAB::Factor MAGE-TAB experimental factor class	Bio::MAGETAB::FactorValue MAGE-TAB experimental factor class	Bio::MAGETAB::Feature MAGE-TAB feature class
Bio::MAGETAB::Investigation MAGE-TAB investigation class	Bio::MAGETAB::LabeledExtract MAGE-TAB labeled extract class	Bio::MAGETAB::Material Abstract material class
Bio::MAGETAB::MatrixColumn MAGE-TAB matrix column class	Bio::MAGETAB::MatrixRow MAGE-TAB matrix row class	Bio::MAGETAB::Measurement MAGE-TAB measurement class
Bio::MAGETAB::Node Abstract node class	Bio::MAGETAB::Normalization MAGE-TAB data acquisition class	Bio::MAGETAB::ParameterValue MAGE-TAB parameter value class
Bio::MAGETAB::Protocol MAGE-TAB protocol class	Bio::MAGETAB::ProtocolApplication MAGE-TAB protocol application class	Bio::MAGETAB::ProtocolParameter MAGE-TAB protocol parameter class
Bio::MAGETAB::Publication MAGE-TAB publication class	Bio::MAGETAB::Reporter MAGE-TAB reporter class	Bio::MAGETAB::Sample MAGE-TAB sample class
Bio::MAGETAB::SDRF MAGE-TAB SDRF class	Bio::MAGETAB::SDRFRow MAGE-TAB SDRF row class	Bio::MAGETAB::Source MAGE-TAB source class
Bio::MAGETAB::TermSource MAGE-TAB term source class	Bio::MAGETAB::Types custom data types for Bio::MAGETAB	Bio::MAGETAB::Util::Builder A storage class used to track
Bio::MAGETAB::Util::DBLoader A persistent storage class used to	Bio::MAGETAB::Util::Persistence A Tangram-based object persistence	Bio::MAGETAB::Util::Reader A parser/validator for MAGE-TAB documents.
Bio::MAGETAB::Util::Reader::ADF ADF parser class.	Bio::MAGETAB::Util::Reader::DataMatrix Data matrix parser class.	Bio::MAGETAB::Util::Reader::IDF IDF parser class.
Bio::MAGETAB::Util::Reader::SDRF SDRF parser class.	Bio::MAGETAB::Util::Reader::Tabfile An abstract class providing methods for	Bio::MAGETAB::Util::Reader::TagValueFile An abstract class providing methods for
Bio::MAGETAB::Util::RewriteAE A utility class providing methods to	Bio::MAGETAB::Util::Writer Export of MAGE-TAB objects.	Bio::MAGETAB::Util::Writer::ADF Export of MAGE-TAB ArrayDesign
Bio::MAGETAB::Util::Writer::GraphViz Visualization of MAGE-TAB objects.	Bio::MAGETAB::Util::Writer::IDF Export of MAGE-TAB Investigation	Bio::MAGETAB::Util::Writer::SDRF Export of MAGE-TAB SDRF
Bio::MAGETAB::Util::Writer::Tabfile Abstract MAGE-TAB exporter class.	Bio::Map::Clone An central map object representing a clone	Bio::Map::Contig A MapI implementation handling the contigs of a
Bio::Map::CytoMap A Bio::MapI compliant map implementation handling cytogenic bands	Bio::Map::CytoMarker An object representing a marker.	Bio::Map::CytoPosition Marker class with cytogenetic band storing attributes
Bio::Map::EntityI An Entity Interface	Bio::Map::FPCMarker An central map object representing a marker	Bio::Map::Gene An gene modelled as a mappable element.
Bio::Map::GeneMap A MapI implementation to represent the area around a gene	Bio::Map::GenePosition A typed position, suitable for modelling the various	Bio::Map::GeneRelative Represents being relative to named sub-regions of a
Bio::Map::LinkageMap A representation of a genetic linkage map.	Bio::Map::LinkagePosition Create a Position for a Marker that will be placed	Bio::Map::MapI Interface for describing Map objects in bioperl
Bio::Map::Mappable An object representing a generic map element	Bio::Map::MappableI An object that can be placed in a map	Bio::Map::Marker An central map object representing a generic marker
Bio::Map::MarkerI Interface for basic marker functionality	Bio::Map::Microsatellite An object representing a Microsatellite marker.	Bio::Map::OrderedPosition Abstracts the notion of a member
Bio::Map::OrderedPositionWithDistance Abstracts the notion of a member	Bio::Map::Physical A class for handling a Physical Map (such as FPC)	Bio::Map::Position A single position of a Marker, or the range over which
Bio::Map::PositionHandler A Position Handler Implementation	Bio::Map::PositionHandlerI A Position Handler Interface	Bio::Map::PositionI Abstracts the notion of a position having a value in the context of a marker and a Map
Bio::Map::PositionWithSequence A position with a sequence.	Bio::Map::Prediction An object representing the predictions of something	Bio::Map::Relative Represents what a Position's coordiantes are relative to.
Bio::Map::RelativeI Interface for describing what a Position's coordiantes are	Bio::Map::SimpleMap A MapI implementation handling the basics of a Map	Bio::Map::TranscriptionFactor A transcription factor modelled as a mappable
Bio::MapIO A Map Factory object	Bio::MapIO::fpc A FPC Map reader	Bio::MapIO::mapmaker A Mapmaker Map reader
Bio::Matrix::Generic A generic matrix implementation	Bio::Matrix::IO A factory for Matrix parsing	Bio::Matrix::IO::mlagan A parser for the mlagan substitution matrix
Bio::Matrix::IO::phylip A parser for PHYLIP distance matricies	Bio::Matrix::IO::scoring A parser for PAM/BLOSUM matricies	Bio::Matrix::MatrixI An interface for describing a Matrix
Bio::Matrix::Mlagan A generic matrix with mlagan fields	Bio::Matrix::PhylipDist A Phylip Distance Matrix object	Bio::Matrix::PSM::InstanceSite A PSM site occurance
Bio::Matrix::PSM::InstanceSiteI InstanceSite interface, holds an instance of a PSM	Bio::Matrix::PSM::IO PSM parser	Bio::Matrix::PSM::IO::mast PSM mast parser implementation
Bio::Matrix::PSM::IO::masta motif fasta format parser	Bio::Matrix::PSM::IO::meme PSM meme parser implementation	Bio::Matrix::PSM::IO::psiblast PSM psiblast parser
Bio::Matrix::PSM::IO::transfac PSM transfac parser	Bio::Matrix::PSM::ProtMatrix SiteMatrixI implementation, holds a	Bio::Matrix::PSM::ProtPsm handle combination of site matricies
Bio::Matrix::PSM::Psm handle combination of site matricies	Bio::Matrix::PSM::PsmHeader PSM mast parser implementation	Bio::Matrix::PSM::PsmHeaderI handles the header data from a PSM file
Bio::Matrix::PSM::PsmI abstract interface to handler of site matricies	Bio::Matrix::PSM::SiteMatrix SiteMatrixI implementation, holds a	Bio::Matrix::PSM::SiteMatrixI SiteMatrixI implementation, holds a
Bio::Matrix::Scoring Object which can hold scoring matrix information	Bio::Maxd Perl extension for storing and retrieving data from maxd	Bio::MCPrimers Design molecular cloning PCR primers
Bio::MedChunker NP chunker for MEDLINE texts	Bio::Medpost Part of speech tagger for MEDLINE text	Bio::Medpost::Var
Bio::Metabolic Perl extension for representing and simulating metabolic networks	Bio::Metabolic::Dynamics Dynamical features for biochemical reaction networks	Bio::Metabolic::Dynamics::Network
Bio::Metabolic::Dynamics::Reaction	Bio::Metabolic::Dynamics::Substrate	Bio::Metabolic::Network Perl extension for biochemical reaction networks
Bio::Metabolic::Reaction Perl extension for biochemical reactions	Bio::Metabolic::Substrate Perl extension for the description of biochemical substrates	Bio::Metabolic::Substrate::Cluster Perl extension for lists of
Bio::mGen Preparsed Genbank for DNA extraction	Bio::MolEvol::CodonModel Codon Evolution Models	Bio::Nexml::Factory A factory module for creating BioPerl and Bio::Phylo objects from/to nexml documents
Bio::NexmlIO stream handler for NeXML documents	Bio::NEXUS An object-oriented Perl Applications Programming Interface (API) for the NEXUS file format	Bio::NEXUS::AssumptionsBlock Represents ASSUMPTIONS block of a NEXUS file
Bio::NEXUS::Block Provides useful functions for blocks in NEXUS file (parent class).	Bio::NEXUS::CharactersBlock Represents a CHARACTERS Block (Data or Characters) of a NEXUS file	Bio::NEXUS::CodonsBlock Represents CODONS block in NEXUS file
Bio::NEXUS::DataBlock Represents the deprecated DATA Block in NEXUS file.	Bio::NEXUS::DistancesBlock Represents DISTANCES block in NEXUS file	Bio::NEXUS::Functions Provides private utiliy functions for the module
Bio::NEXUS::HistoryBlock Represents a HISTORY block of a NEXUS file	Bio::NEXUS::Import Extends Bio::NEXUS with parsers for file formats of	Bio::NEXUS::Matrix Provides functions for handling blocks that have matrices
Bio::NEXUS::NHXCmd Provides functions for manipulating nodes in trees	Bio::NEXUS::Node Provides functions for manipulating nodes in trees	Bio::NEXUS::NotesBlock Represents a NOTES block in a NEXUS file.
Bio::NEXUS::SetsBlock Represents SETS block of a NEXUS file	Bio::NEXUS::SpanBlock Represent SPAN block in a NEXUS file (contains meta data).	Bio::NEXUS::TaxaBlock Represents TAXA block of a NEXUS file
Bio::NEXUS::TaxUnit Represents a taxon unit in a NEXUS file	Bio::NEXUS::TaxUnitSet Represents a sets of OTUS (Bio::NEXUS::TaxUnits objects) in a NEXUS file	Bio::NEXUS::Tools::GraphicsParams
Bio::NEXUS::Tools::NexModifier	Bio::NEXUS::Tools::NexPlotter	Bio::NEXUS::Tree Provides functions for manipulating trees
Bio::NEXUS::TreesBlock Represents TREES block of a NEXUS file	Bio::NEXUS::UnalignedBlock Represents an UNALIGNED block of a NEXUS file	Bio::NEXUS::UnknownBlock Represents a simple object for storing information unrecognized blocks by the Bio::NEXUS module.
Bio::NEXUS::Util::Exceptions Exception classes for Bio::NEXUS.	Bio::NEXUS::Util::Logger Logging for Bio::NEXUS.	Bio::NEXUS::WeightSet Represents column weights in alignment ( for each character)
Bio::Ontology::DocumentRegistry Keep track of where to find ontologies.	Bio::Ontology::GOterm representation of GO terms	Bio::Ontology::InterProTerm Implementation of InterProI term interface
Bio::Ontology::OBOEngine An Ontology Engine for OBO style flat file	Bio::Ontology::OBOterm representation of OBO terms	Bio::Ontology::Ontology standard implementation of an Ontology
Bio::Ontology::OntologyEngineI Interface a minimal Ontology implementation should satisfy	Bio::Ontology::OntologyI Interface for an ontology implementation	Bio::Ontology::OntologyStore A repository of ontologies
Bio::Ontology::Path a path for an ontology term graph	Bio::Ontology::PathI Interface for a path between ontology terms	Bio::Ontology::Relationship a relationship for an ontology
Bio::Ontology::RelationshipFactory Instantiates a new	Bio::Ontology::RelationshipI Interface for a relationship between ontology terms	Bio::Ontology::RelationshipType a relationship type for an ontology
Bio::Ontology::SimpleGOEngine::GraphAdaptor Graph adaptor for	Bio::Ontology::SimpleGOEngine::GraphAdaptor02 Graph adaptor (v02.x) for	Bio::Ontology::SimpleOntologyEngine Implementation of OntologyEngineI interface
Bio::Ontology::Term implementation of the interface for ontology terms	Bio::Ontology::TermFactory Instantiates a new	Bio::Ontology::TermI interface for ontology terms
Bio::OntologyIO Parser factory for Ontology formats	Bio::OntologyIO::dagflat a base class parser for GO flat-file type formats	Bio::OntologyIO::goflat a parser for the Gene Ontology flat-file format
Bio::OntologyIO::Handlers::BaseSAXHandler	Bio::OntologyIO::Handlers::InterProHandler XML handler class for InterProParser	Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler parse an InterPro XML file and persist the resulting terms to a Biosql database
Bio::OntologyIO::InterProParser Parser for InterPro xml files.	Bio::OntologyIO::obo a parser for OBO flat-file format from Gene Ontology Consortium	Bio::OntologyIO::simplehierarchy a base class parser for simple hierarchy-by-indentation
Bio::OntologyIO::soflat a parser for the Sequence Ontology flat-file format	Bio::ORA Olfactory Receptor family Assigner (bioperl module)	Bio::Oxbench::Util
Bio::ParameterBaseI Simple interface class for any parameter-related data such	Bio::Perl Functional access to BioPerl for people who don't know objects	Bio::Phenotype::Correlate Representation of a correlating phenotype in a given species
Bio::Phenotype::Measure Representation of context/value(-range)/unit triplets	Bio::Phenotype::MeSH::Term A MeSH term	Bio::Phenotype::MeSH::Twig Context for a MeSH term
Bio::Phenotype::OMIM::MiniMIMentry Representation of a Mini MIM entry	Bio::Phenotype::OMIM::OMIMentry represents OMIM (Online Mendelian	Bio::Phenotype::OMIM::OMIMentryAllelicVariant Representation of a allelic
Bio::Phenotype::OMIM::OMIMparser parser for the OMIM database	Bio::Phenotype::Phenotype A class for modeling phenotypes	Bio::Phenotype::PhenotypeI An interface for classes modeling phenotypes
Bio::Phylo Analysis and manipulation of phylogenies.	Bio::Phylo::EvolutionaryModels Evolutionary models for phylogenetic trees and methods to sample these	Bio::Phylo::Factory Creator of objects, reduces hardcoded class names in code
Bio::Phylo::Forest Container for tree objects	Bio::Phylo::Forest::DrawNode Tree node with extra methods for tree drawing	Bio::Phylo::Forest::DrawTree Tree with extra methods for tree drawing
Bio::Phylo::Forest::Node Node in a phylogenetic tree	Bio::Phylo::Forest::Tree Phylogenetic tree	Bio::Phylo::Generator Generator of tree topologies
Bio::Phylo::Identifiable Objects with unique identifiers	Bio::Phylo::IO Front end for parsers and serializers	Bio::Phylo::Listable List of things, super class for many objects
Bio::Phylo::Matrices Container of matrix objects	Bio::Phylo::Matrices::Character A character (column) in a matrix	Bio::Phylo::Matrices::Characters Container of character objects
Bio::Phylo::Matrices::Datatype Validator of character state data	Bio::Phylo::Matrices::Datatype::Continuous Validator subclass,	Bio::Phylo::Matrices::Datatype::Custom Validator subclass,
Bio::Phylo::Matrices::Datatype::Dna Validator subclass,	Bio::Phylo::Matrices::Datatype::Mixed Validator subclass,	Bio::Phylo::Matrices::Datatype::Protein Validator subclass,
Bio::Phylo::Matrices::Datatype::Restriction Validator subclass,	Bio::Phylo::Matrices::Datatype::Rna Validator subclass,	Bio::Phylo::Matrices::Datatype::Standard Validator subclass,
Bio::Phylo::Matrices::Datum Character state sequence	Bio::Phylo::Matrices::Matrix Character state matrix	Bio::Phylo::Matrices::TypeSafeData Superclass for objects that contain
Bio::Phylo::Mediators::TaxaMediator Mediator for links between taxa and other objects	Bio::Phylo::NeXML::DOM XML DOM support for Bio::Phylo	Bio::Phylo::NeXML::DOM::Document XML DOM Abstract class for
Bio::Phylo::NeXML::DOM::Document::Libxml XML DOM document mappings to the	Bio::Phylo::NeXML::DOM::Document::Twig XML DOM document mappings to the	Bio::Phylo::NeXML::DOM::Element XML DOM Abstract class for
Bio::Phylo::NeXML::DOM::Element::Libxml XML DOM element mappings to the	Bio::Phylo::NeXML::DOM::Element::Twig XML DOM mappings to the	Bio::Phylo::NeXML::Meta Single predicate/object annotation, attached to an
Bio::Phylo::NeXML::Meta::XMLLiteral Annotation value adaptor, no direct usage	Bio::Phylo::NeXML::Writable Superclass for objects that serialize to NeXML	Bio::Phylo::Parsers::Abstract Superclass for parsers used by Bio::Phylo::IO
Bio::Phylo::Parsers::Fasta Parser used by Bio::Phylo::IO, no serviceable parts inside	Bio::Phylo::Parsers::Json Parser used by Bio::Phylo::IO, no serviceable parts inside	Bio::Phylo::Parsers::Newick Parser used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Parsers::Nexml Parser used by Bio::Phylo::IO, no serviceable parts inside	Bio::Phylo::Parsers::Nexus Parser used by Bio::Phylo::IO, no serviceable parts inside	Bio::Phylo::Parsers::Phylip Parser used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Parsers::Phyloxml Parser used by Bio::Phylo::IO, no serviceable parts inside	Bio::Phylo::Parsers::Table Parser used by Bio::Phylo::IO, no serviceable parts inside	Bio::Phylo::Parsers::Taxlist Parser used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Parsers::Tolweb Parser used by Bio::Phylo::IO, no serviceable parts inside	Bio::Phylo::Project Container for related data	Bio::Phylo::Set Subset of the parts inside a container
Bio::Phylo::Taxa Container of taxon objects	Bio::Phylo::Taxa::TaxaLinker Superclass for objects that link to taxa objects	Bio::Phylo::Taxa::Taxon Operational taxonomic unit
Bio::Phylo::Taxa::TaxonLinker Superclass for objects that link to taxon objects	Bio::Phylo::Treedrawer Visualizer of tree shapes	Bio::Phylo::Treedrawer::Abstract Abstract graphics writer used by treedrawer, no
Bio::Phylo::Treedrawer::Canvas Graphics format writer used by treedrawer, no	Bio::Phylo::Treedrawer::Gif Graphics format writer used by treedrawer, no	Bio::Phylo::Treedrawer::Jpeg Graphics format writer used by treedrawer, no
Bio::Phylo::Treedrawer::Pdf Graphics format writer used by treedrawer, no	Bio::Phylo::Treedrawer::Png Graphics format writer used by treedrawer, no	Bio::Phylo::Treedrawer::Processing Graphics format writer used by treedrawer,
Bio::Phylo::Treedrawer::Svg Graphics format writer used by treedrawer, no	Bio::Phylo::Treedrawer::Swf Graphics format writer used by treedrawer, no	Bio::Phylo::Unparsers::Abstract Superclass for unparsers used by Bio::Phylo::IO
Bio::Phylo::Unparsers::Fasta Serializer used by Bio::Phylo::IO, no serviceable parts inside	Bio::Phylo::Unparsers::Json Serializer used by Bio::Phylo::IO, no serviceable	Bio::Phylo::Unparsers::Mrp Serializer used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Unparsers::Newick Serializer used by Bio::Phylo::IO, no serviceable parts inside	Bio::Phylo::Unparsers::Nexml Serializer used by Bio::Phylo::IO, no serviceable parts inside	Bio::Phylo::Unparsers::Nexus Serializer used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Unparsers::Pagel Serializer used by Bio::Phylo::IO, no serviceable parts inside	Bio::Phylo::Unparsers::Phylip Serializer used by Bio::Phylo::IO, no serviceable parts inside	Bio::Phylo::Unparsers::Phyloxml Serializer used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Util::CONSTANT Global constants and utility functions	Bio::Phylo::Util::Dependency Utility class for importing external	Bio::Phylo::Util::Exceptions Errors ($@) that are objects
Bio::Phylo::Util::IDPool Utility class for generating object IDs. No serviceable parts inside.	Bio::Phylo::Util::Logger Logger of internal messages of several severity	Bio::Phylo::Util::OptionalInterface Utility class for managing optional
Bio::Phylo::Util::StackTrace Stack traces for exceptions	Bio::PhyloNetwork Module to compute with Phylogenetic Networks	Bio::PhyloNetwork::Factory Module to sequentially generate
Bio::PhyloNetwork::FactoryX Module to sequentially generate	Bio::PhyloNetwork::GraphViz Interface between PhyloNetwork and GraphViz	Bio::PhyloNetwork::muVector Module to compute with vectors of arbitrary
Bio::PhyloNetwork::RandomFactory Module to generate random	Bio::PhyloNetwork::TreeFactory Module to sequentially generate	Bio::PhyloNetwork::TreeFactoryMulti Module to sequentially generate
Bio::PhyloNetwork::TreeFactoryX Module to sequentially generate	Bio::Polloc Molecular Biology/Polymorphic Loci analysis	Bio::Polloc::Genome A group of sequences from the same organism
Bio::Polloc::GroupCriteria Rules to group loci	Bio::Polloc::GroupCriteria::operator An acillary object for Bio::Polloc::GroupCriteria	Bio::Polloc::GroupCriteria::operator::bool A boolean operator
Bio::Polloc::GroupCriteria::operator::cons A constant	Bio::Polloc::GroupCriteria::operator::num A numeric operator	Bio::Polloc::GroupCriteria::operator::seq A sequence operator
Bio::Polloc::LociGroup A group of loci	Bio::Polloc::Locus::amplicon An amplification product	Bio::Polloc::Locus::composition A composition feature
Bio::Polloc::Locus::crispr A CRISPR locus	Bio::Polloc::Locus::extend A feature based on another one	Bio::Polloc::Locus::generic An unknown feature
Bio::Polloc::Locus::pattern A loci matching a pattern.	Bio::Polloc::Locus::repeat A repetitive locus	Bio::Polloc::LocusI Interface of C<Bio::Polloc::Locus::*> objects
Bio::Polloc::LocusIO I/O interface of C<Bio::Polloc::Locus::*> objects	Bio::Polloc::LocusIO::gff3 A LocusIO for Gff3	Bio::Polloc::Polloc::Config Handles .cfg files
Bio::Polloc::Polloc::Error Errors handler for the Bio::Polloc::* packages	Bio::Polloc::Polloc::IO I/O interface for the Bio::Polloc::* packages	Bio::Polloc::Polloc::Root
Bio::Polloc::Polloc::Version Provides central package-wide version	Bio::Polloc::Rule::boolean A rule of type boolean operator	Bio::Polloc::Rule::composition A rule of type composition
Bio::Polloc::Rule::crispr A rule of type CRISPR	Bio::Polloc::Rule::pattern A rule determined by a pattern	Bio::Polloc::Rule::profile A rule of type profile
Bio::Polloc::Rule::repeat A rule of type repeat	Bio::Polloc::Rule::tandemrepeat A rule of type tandemrepeat	Bio::Polloc::RuleI Generic rules interface
Bio::Polloc::RuleIO I/O interface for the sets of rules (L<Bio::Polloc::RuleI>)	Bio::Polloc::RuleSet::cfg Implementation of Bio::Polloc::RuleIO for .cfg files	Bio::Polloc::Typing::bandingPattern banding-pattern-based methods
Bio::Polloc::Typing::bandingPattern::amplification banding-pattern-based	Bio::Polloc::TypingI Generic typing interface	Bio::Polloc::TypingIO I/O interface for genotyping methods (L<Bio::Polloc::TypingI>)
Bio::Polloc::TypingIO::cfg Implementation of Bio::Polloc::TypingIO for .cfg files	Bio::PopGen::Genotype An implementation of GenotypeI which is just an allele container	Bio::PopGen::GenotypeI A marker and alleles for a specific individual
Bio::PopGen::HtSNP	Bio::PopGen::Individual An implementation of an Individual who has	Bio::PopGen::IndividualI An individual who has Genotype or Sequence Results
Bio::PopGen::IO Input individual,marker,allele information	Bio::PopGen::IO::csv	Bio::PopGen::IO::hapmap A parser for HapMap output data
Bio::PopGen::IO::phase A parser for Phase format data	Bio::PopGen::IO::prettybase Extract individual allele data from PrettyBase format	Bio::PopGen::Marker A genetic marker which one uses to generate genotypes
Bio::PopGen::MarkerI A Population Genetic conceptual marker	Bio::PopGen::PopStats A collection of methods for calculating	Bio::PopGen::Population A population of individuals
Bio::PopGen::PopulationI Interface for Populations	Bio::PopGen::Simulation::Coalescent A Coalescent simulation factory	Bio::PopGen::Simulation::GeneticDrift A simple genetic drift simulation
Bio::PopGen::Statistics Population Genetics statistical tests	Bio::PopGen::TagHaplotype Haplotype tag object.	Bio::PopGen::Utilities Utilities for working with PopGen data and objects
Bio::PrimarySeq Bioperl lightweight Sequence Object	Bio::PrimarySeq::Fasta	Bio::PrimarySeqI Interface definition for a Bio::PrimarySeq
Bio::PrimerDesigner Design PCR Primers using primer3 and epcr	Bio::Prospect::Align Package for overlaying multiple Prospect alignments	Bio::Prospect::Client base class for Bio::Prospect::LocalClient and
Bio::Prospect::File interface to Prospect Files	Bio::Prospect::Init initialization parameters for Bio::Prospect::	Bio::Prospect::LocalClient execute Prospect locally
Bio::Prospect::Options Package for representing options	Bio::Prospect::SoapClient execute Prospect remotely	Bio::Prospect::SoapServer execute Prospect locally
Bio::Prospect::Thread Representation of a Prospect thread.	Bio::Prospect::ThreadSummary Distilled version of a Bio::Prospect::Thread	Bio::Prospect::utilities miscellaneous utilities for Prospect
Bio::Protease Digest your protein substrates with customizable specificity	Bio::Protease::Role::Specificity::Regex A role that implements a regex-based specificity	Bio::Protease::Role::WithCache A role that adds optional memoization of ProteaseI methods
Bio::Protease::Types Specific types for Bio::Protease	Bio::ProteaseI A role to build your customized Protease	Bio::PullParserI A base module for fast 'pull' parsing
Bio::Range Pure perl RangeI implementation	Bio::RangeI Range interface	Bio::Restriction::Analysis cutting sequences with restriction
Bio::Restriction::Enzyme A single restriction endonuclease	Bio::Restriction::Enzyme::MultiCut A single restriction endonuclease	Bio::Restriction::Enzyme::MultiSite A single restriction endonuclease
Bio::Restriction::EnzymeCollection Set of restriction endonucleases	Bio::Restriction::EnzymeI Interface class for restriction endonuclease	Bio::Restriction::IO Handler for sequence variation IO Formats
Bio::Restriction::IO::bairoch bairoch enzyme set	Bio::Restriction::IO::base base enzyme set	Bio::Restriction::IO::itype2 itype2 enzyme set
Bio::Restriction::IO::prototype prototype enzyme set	Bio::Restriction::IO::withrefm withrefm enzyme set	Bio::Root::Build A common Module::Build subclass base for BioPerl distributions
Bio::Root::Exception Generic exception objects for Bioperl	Bio::Root::HTTPget module for fallback HTTP get operations when	Bio::Root::IO module providing several methods often needed when dealing with file IO
Bio::Root::Root Hash-based implementation of Bio::Root::RootI	Bio::Root::RootI Abstract interface to root object code	Bio::Root::Storable object serialisation methods
Bio::Root::Test A common base for all Bioperl test scripts.	Bio::Root::Test::Warn Perl extension to test Bioperl methods for warnings	Bio::Root::Utilities General-purpose utility module
Bio::Root::Version provide global, distribution-level versioning	Bio::SABio::NCBI	Bio::SAGE::Comparison Compares data from serial analysis of gene expression (SAGE) libraries.
Bio::SAGE::DataProcessing Processes raw serial analysis of gene expression (SAGE) data.	Bio::SAGE::DataProcessing::AveragePhredFilter A filter that validates sequences based on average Phred score.	Bio::SAGE::DataProcessing::Filter An abstract filter for determining whether a [di]tag is worth keeping.
Bio::SAGE::DataProcessing::MinimumPhredFilter A filter that validates sequences based on minimum Phred score.	Bio::SCF Perl extension for reading and writting SCF sequence files	Bio::SCF::Arrays
Bio::SDRS Perl extension for Sigmoidal Dose Response Search, a tool	Bio::Search::BlastStatistics An object for Blast statistics	Bio::Search::BlastUtils Utility functions for Bio::Search:: BLAST objects
Bio::Search::DatabaseI Interface for a database used in a sequence search	Bio::Search::GenericDatabase Generic implementation of Bio::Search::DatabaseI	Bio::Search::GenericStatistics An object for statistics
Bio::Search::Hit::BlastHit Blast-specific subclass of Bio::Search::Hit::GenericHit	Bio::Search::Hit::BlastPullHit A parser and hit object for BLASTN hits	Bio::Search::Hit::Fasta Hit object specific for Fasta-generated hits
Bio::Search::Hit::GenericHit A generic implementation of the Bio::Search::Hit::HitI interface	Bio::Search::Hit::HitFactory A factory to create Bio::Search::Hit::HitI objects	Bio::Search::Hit::HitI Interface for a hit in a similarity search result
Bio::Search::Hit::hmmer3Hit DESCRIPTION of Object	Bio::Search::Hit::HMMERHit A Hit module for HMMER hits	Bio::Search::Hit::HmmpfamHit A parser and hit object for hmmpfam hits
Bio::Search::Hit::ModelHit A model-based implementation of the Bio::Search::Hit::HitI interface	Bio::Search::Hit::PsiBlastHit Bioperl BLAST Hit object	Bio::Search::Hit::PullHitI Bio::Search::Hit::HitI interface for pull parsers.
Bio::Search::HSP::BlastHSP Bioperl BLAST High-Scoring Pair object	Bio::Search::HSP::BlastPullHSP A parser and HSP object for BlastN hsps	Bio::Search::HSP::FastaHSP HSP object for FASTA specific data
Bio::Search::HSP::GenericHSP A "Generic" implementation of a High Scoring Pair	Bio::Search::HSP::hmmer3HSP DESCRIPTION of Object	Bio::Search::HSP::HMMERHSP A HSP object for HMMER results
Bio::Search::HSP::HmmpfamHSP A parser and HSP object for hmmpfam hsps	Bio::Search::HSP::HSPFactory A factory to create Bio::Search::HSP::HSPI objects	Bio::Search::HSP::ModelHSP A HSP object for model-based searches
Bio::Search::HSP::PsiBlastHSP Bioperl BLAST High-Scoring Pair object	Bio::Search::HSP::PSLHSP A HSP for PSL output	Bio::Search::HSP::PullHSPI Bio::Search::HSP::HSPI interface for pull parsers.
Bio::Search::HSP::WABAHSP HSP object suitable for describing WABA alignments	Bio::Search::Iteration::GenericIteration A generic implementation of the Bio::Search::Iteration::IterationI interface.	Bio::Search::Iteration::IterationI Abstract interface to an
Bio::Search::Processor DESCRIPTION of Object	Bio::Search::Result::BlastPullResult A parser and result object for BLASTN	Bio::Search::Result::BlastResult Blast-specific subclass of Bio::Search::Result::GenericResult
Bio::Search::Result::CrossMatchResult CrossMatch-specific subclass of Bio::Search::Result::GenericResult	Bio::Search::Result::GenericResult Generic Implementation of	Bio::Search::Result::hmmer3Result DESCRIPTION of Object
Bio::Search::Result::HMMERResult A Result object for HMMER results	Bio::Search::Result::HmmpfamResult A parser and result object for hmmpfam	Bio::Search::Result::PullResultI Bio::Search::Result::ResultI interface for
Bio::Search::Result::ResultFactory A factory to create Bio::Search::Result::ResultI objects	Bio::Search::Result::ResultI Abstract interface to Search Result objects	Bio::Search::Result::WABAResult Result object for WABA alignment output
Bio::Search::SearchUtils Utility functions for Bio::Search:: objects	Bio::Search::StatisticsI A Base object for statistics	Bio::Search::Tiling::MapTileUtils utilities for manipulating closed intervals for an HSP tiling algorithm
Bio::Search::Tiling::MapTiling An implementation of an HSP tiling	Bio::Search::Tiling::TilingI Abstract interface for an HSP tiling module	Bio::SearchDist A perl wrapper around Sean Eddy's histogram object
Bio::SearchIO Driver for parsing Sequence Database Searches	Bio::SearchIO::axt a parser for axt format reports	Bio::SearchIO::blast Event generator for event based parsing of
Bio::SearchIO::blasttable Driver module for SearchIO for parsing NCBI -m 8/9 format	Bio::SearchIO::blastxml A SearchIO implementation of NCBI Blast XML parsing.	Bio::SearchIO::blast_pull A parser for BLAST output
Bio::SearchIO::cross_match CrossMatch-specific subclass of Bio::SearchIO	Bio::SearchIO::erpin SearchIO-based ERPIN parser	Bio::SearchIO::EventHandlerI An abstract Event Handler for Search Result parsing
Bio::SearchIO::exonerate parser for Exonerate	Bio::SearchIO::fasta A SearchIO parser for FASTA results	Bio::SearchIO::FastHitEventBuilder Event Handler for SearchIO events.
Bio::SearchIO::gmap_f9 Event generator for parsing gmap reports (Z format)	Bio::SearchIO::hmmer A parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam)	Bio::SearchIO::hmmer2 A parser for HMMER output (hmmpfam, hmmsearch)
Bio::SearchIO::hmmer3 DESCRIPTION of Object	Bio::SearchIO::hmmer_pull A parser for HMMER output	Bio::SearchIO::infernal SearchIO-based Infernal parser
Bio::SearchIO::IteratedSearchResultEventBuilder Event Handler for	Bio::SearchIO::megablast a driver module for Bio::SearchIO to parse	Bio::SearchIO::psl A parser for PSL output (UCSC)
Bio::SearchIO::rnamotif SearchIO-based RNAMotif parser	Bio::SearchIO::SearchResultEventBuilder Event Handler for SearchIO events.	Bio::SearchIO::SearchWriterI Interface for outputting parsed Search results
Bio::SearchIO::sim4 parser for Sim4 alignments	Bio::SearchIO::waba SearchIO parser for Jim Kent WABA program	Bio::SearchIO::wise Parsing of wise output as alignments
Bio::SearchIO::Writer::BSMLResultWriter BSML output writer	Bio::SearchIO::Writer::GbrowseGFF Interface for outputting parsed search results in Gbrowse GFF format	Bio::SearchIO::Writer::HitTableWriter Tab-delimited data for Bio::Search::Hit::HitI objects
Bio::SearchIO::Writer::HSPTableWriter Tab-delimited data for Bio::Search::HSP::HSPI objects	Bio::SearchIO::Writer::HTMLResultWriter write a Bio::Search::ResultI in HTML	Bio::SearchIO::Writer::ResultTableWriter Outputs tab-delimited data for each Bio::Search::Result::ResultI object.
Bio::SearchIO::Writer::TextResultWriter Object to implement writing	Bio::SearchIO::XML::BlastHandler XML Handler for NCBI Blast XML parsing.	Bio::SearchIO::XML::PsiBlastHandler XML Handler for NCBI Blast PSIBLAST XML parsing.
Bio::Seq Sequence object, with features	Bio::Seq::BaseSeqProcessor Base implementation for a SequenceProcessor	Bio::Seq::EncodedSeq subtype of L<Bio::LocatableSeq\|Bio::LocatableSeq> to store DNA that encodes a protein
Bio::Seq::LargeLocatableSeq LocatableSeq object that stores sequence as	Bio::Seq::LargePrimarySeq PrimarySeq object that stores sequence as	Bio::Seq::LargeSeq SeqI compliant object that stores sequence as
Bio::Seq::LargeSeqI Interface class for sequences that cache their	Bio::Seq::Meta Generic superclass for sequence objects with	Bio::Seq::Meta::Array array-based generic implementation of a
Bio::Seq::MetaI Interface for sequence objects with residue-based	Bio::Seq::PrimaryQual Bioperl lightweight Quality Object	Bio::Seq::PrimaryQual::Qual
Bio::Seq::PrimedSeq A representation of a sequence and two primers	Bio::Seq::QualI Interface definition for a Bio::Seq::Qual	Bio::Seq::Quality Implementation of sequence with residue quality
Bio::Seq::RichSeq Module implementing a sequence created from a rich	Bio::Seq::RichSeqI interface for sequences from rich data sources, mostly databases	Bio::Seq::SeqBuilder Configurable object builder for sequence stream parsers
Bio::Seq::SeqFactory Instantiates a new Bio::PrimarySeqI (or derived class) through a factory	Bio::Seq::SeqFastaSpeedFactory Instantiates a new Bio::PrimarySeqI (or derived class) through a factory	Bio::Seq::SequenceTrace Bioperl object packaging a sequence with its trace
Bio::Seq::SeqWithQuality Bioperl object packaging a sequence with its quality.	Bio::Seq::TraceI Interface definition for a Bio::Seq::Trace	Bio::SeqAnalysisParserI Sequence analysis output parser interface
Bio::SeqEvolution::DNAPoint evolve a sequence by point mutations	Bio::SeqEvolution::EvolutionI the interface for evolving sequences	Bio::SeqEvolution::Factory Factory object to instantiate sequence evolving classes
Bio::SeqFeature::Annotated PLEASE PUT SOMETHING HERE	Bio::SeqFeature::AnnotationAdaptor integrates SeqFeatureIs annotation	Bio::SeqFeature::Collection A container class for SeqFeatures
Bio::SeqFeature::CollectionI An interface for a collection of SeqFeatureI objects.	Bio::SeqFeature::Computation Computation SeqFeature	Bio::SeqFeature::FeaturePair hold pair feature information e.g. blast hits
Bio::SeqFeature::Gene::Exon a feature representing an exon	Bio::SeqFeature::Gene::ExonI Interface for a feature representing an exon	Bio::SeqFeature::Gene::GeneStructure A feature representing an arbitrarily complex structure of a gene
Bio::SeqFeature::Gene::GeneStructureI A feature representing an arbitrarily	Bio::SeqFeature::Gene::Intron An intron feature	Bio::SeqFeature::Gene::NC_Feature superclass for non-coding features
Bio::SeqFeature::Gene::Poly_A_site poly A feature	Bio::SeqFeature::Gene::Promoter Describes a promoter	Bio::SeqFeature::Gene::Transcript A feature representing a transcript
Bio::SeqFeature::Gene::TranscriptI Interface for a feature representing a	Bio::SeqFeature::Gene::UTR A feature representing an untranslated region	Bio::SeqFeature::Generic Generic SeqFeature
Bio::SeqFeature::Lite Lightweight Bio::SeqFeatureI class	Bio::SeqFeature::PositionProxy handle features when truncation/revcom sequences span a feature	Bio::SeqFeature::Primer Primer Generic SeqFeature
Bio::SeqFeature::Similarity A sequence feature based on similarity	Bio::SeqFeature::SimilarityPair Sequence feature based on the similarity	Bio::SeqFeature::SiRNA::Oligo Perl object for small inhibitory RNAs.
Bio::SeqFeature::SiRNA::Pair Perl object for small inhibitory RNA	Bio::SeqFeature::Tools::FeatureNamer generates unique persistent names for features	Bio::SeqFeature::Tools::IDHandler maps $seq_feature-E<gt>primary_tag
Bio::SeqFeature::Tools::TypeMapper maps $seq_feature-E<gt>primary_tag	Bio::SeqFeature::Tools::Unflattener turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy	Bio::SeqFeature::TypedSeqFeatureI a strongly typed SeqFeature
Bio::SeqFeatureI Abstract interface of a Sequence Feature	Bio::SeqI [Developers] Abstract Interface of Sequence (with features)	Bio::SeqIO Handler for SeqIO Formats
Bio::SeqIO::abi abi trace sequence input/output stream	Bio::SeqIO::ace ace sequence input/output stream	Bio::SeqIO::agave AGAVE sequence output stream.
Bio::SeqIO::alf alf trace sequence input/output stream	Bio::SeqIO::asciitree asciitree sequence input/output stream	Bio::SeqIO::bsml BSML sequence input/output stream
Bio::SeqIO::bsml_sax BSML sequence input/output stream using SAX	Bio::SeqIO::chadoxml chadoxml sequence output stream	Bio::SeqIO::chaos chaos sequence input/output stream
Bio::SeqIO::chaosxml chaosxml sequence input/output stream	Bio::SeqIO::ctf ctf trace sequence input/output stream	Bio::SeqIO::embl EMBL sequence input/output stream
Bio::SeqIO::embldriver EMBL sequence input/output stream	Bio::SeqIO::entrezgene Entrez Gene ASN1 parser	Bio::SeqIO::excel sequence input/output stream from a
Bio::SeqIO::exp exp trace sequence input/output stream	Bio::SeqIO::fasta fasta sequence input/output stream	Bio::SeqIO::fastq fastq sequence input/output stream
Bio::SeqIO::flybase_chadoxml FlyBase variant of chadoxml with sequence output stream	Bio::SeqIO::FTHelper Helper class for Embl/Genbank feature tables	Bio::SeqIO::game a class for parsing and writing game-XML
Bio::SeqIO::game::featHandler a class for handling feature elements	Bio::SeqIO::game::gameHandler PerlSAX handler for game-XML	Bio::SeqIO::game::gameSubs a base class for game-XML parsing
Bio::SeqIO::game::gameWriter a class for writing game-XML	Bio::SeqIO::game::seqHandler a class for handling game-XML sequences	Bio::SeqIO::gbdriver GenBank handler-based push parser
Bio::SeqIO::gbxml GenBank sequence input/output stream using SAX	Bio::SeqIO::gcg GCG sequence input/output stream	Bio::SeqIO::genbank GenBank sequence input/output stream
Bio::SeqIO::Handler::GenericRichSeqHandler Bio::HandlerI-based	Bio::SeqIO::interpro InterProScan XML input/output stream	Bio::SeqIO::kegg KEGG sequence input/output stream
Bio::SeqIO::largefasta method i/o on very large fasta sequence files	Bio::SeqIO::lasergene Lasergene sequence file input/output stream	Bio::SeqIO::locuslink LocusLink input/output stream
Bio::SeqIO::mbsout input stream for output by Teshima et al.'s mbs.	Bio::SeqIO::metafasta metafasta sequence input/output stream	Bio::SeqIO::msout input stream for output by Hudson's ms
Bio::SeqIO::MultiFile Treating a set of files as a single input stream	Bio::SeqIO::nexml NeXML sequence input/output stream	Bio::SeqIO::phd phd file input/output stream
Bio::SeqIO::pir PIR sequence input/output stream	Bio::SeqIO::pln pln trace sequence input/output stream	Bio::SeqIO::qual .qual file input/output stream
Bio::SeqIO::raw raw sequence file input/output stream	Bio::SeqIO::scf .scf file input/output stream	Bio::SeqIO::seqxml SeqXML sequence input/output stream
Bio::SeqIO::strider DNA strider sequence input/output stream	Bio::SeqIO::swiss Swissprot sequence input/output stream	Bio::SeqIO::swissdriver SwissProt/UniProt handler-based push parser
Bio::SeqIO::tab nearly raw sequence file input/output	Bio::SeqIO::table sequence input/output stream from a delimited table	Bio::SeqIO::tigr TIGR XML sequence input/output stream
Bio::SeqIO::tigrxml Parse TIGR (new) XML	Bio::SeqIO::tinyseq reading/writing sequences in NCBI TinySeq format	Bio::SeqIO::tinyseq::tinyseqHandler XML event handlers to support NCBI TinySeq XML parsing
Bio::SeqIO::ztr ztr trace sequence input/output stream	Bio::SeqUtils Additional methods for PrimarySeq objects	Bio::SimpleAlign Multiple alignments held as a set of sequences
Bio::SimpleAnalysisI A simple interface to any (local or remote) analysis tool	Bio::Species Generic species object.	Bio::Structure::Atom Bioperl structure Object, describes an Atom
Bio::Structure::Chain Bioperl structure Object, describes a chain	Bio::Structure::Entry Bioperl structure Object, describes the whole entry	Bio::Structure::IO Handler for Structure Formats
Bio::Structure::IO::pdb PDB input/output stream	Bio::Structure::Model Bioperl structure Object, describes a Model	Bio::Structure::Residue Bioperl structure Object, describes a Residue
Bio::Structure::SecStr::DSSP::Res Module for parsing/accessing dssp output	Bio::Structure::SecStr::STRIDE::Res Module for parsing/accessing stride output	Bio::Structure::StructureI Abstract Interface for a Structure objects
Bio::Symbol::Alphabet BSANE/BioCORBA compliant symbol list alphabet	Bio::Symbol::AlphabetI A Symbol Alphabet	Bio::Symbol::DNAAlphabet A ready made DNA alphabet
Bio::Symbol::ProteinAlphabet A ready made Protein alphabet	Bio::Symbol::Symbol A biological symbol	Bio::Symbol::SymbolI Interface for a Symbol
Bio::Taxon A node in a represented taxonomy	Bio::Taxonomy representing Taxonomy.	Bio::Taxonomy::FactoryI interface to define how to access NCBI Taxonoy
Bio::Taxonomy::Node A node in a represented taxonomy	Bio::Taxonomy::Taxon Generic Taxonomic Entity object	Bio::Taxonomy::Tree An Organism Level Implementation of TreeI interface.
Bio::Tools::AlignFactory Base object for alignment factories	Bio::Tools::Alignment::Consed A module to work with objects from consed .ace files	Bio::Tools::Alignment::Trim A kludge to do specialized trimming of
Bio::Tools::Analysis::DNA::ESEfinder a wrapper around ESEfinder	Bio::Tools::Analysis::Protein::Domcut a wrapper around Domcut server	Bio::Tools::Analysis::Protein::ELM a wrapper around the ELM server which predicts short functional motifs on amino acid sequences
Bio::Tools::Analysis::Protein::GOR4 a wrapper around GOR4 protein	Bio::Tools::Analysis::Protein::HNN a wrapper around the HNN protein	Bio::Tools::Analysis::Protein::Mitoprot a wrapper around Mitoprot
Bio::Tools::Analysis::Protein::NetPhos a wrapper around NetPhos server	Bio::Tools::Analysis::Protein::Scansite a wrapper around the Scansite server	Bio::Tools::Analysis::Protein::Sopma a wrapper around the
Bio::Tools::Analysis::SimpleAnalysisBase abstract superclass for	Bio::Tools::AnalysisResult Base class for analysis result objects and parsers	Bio::Tools::Blat parser for Blat program
Bio::Tools::CodonOptTable A more elaborative way to check the codons usage!	Bio::Tools::CodonTable Codon table object	Bio::Tools::Coil parser for Coil output
Bio::Tools::DNAGen Generating a pool of DNA sequences	Bio::Tools::dpAlign Perl extension to do pairwise dynamic programming sequence alignment	Bio::Tools::ECnumber representation of EC numbers (Enzyme Classification)
Bio::Tools::EMBOSS::Palindrome parse EMBOSS palindrome output	Bio::Tools::EPCR Parse ePCR output and make features	Bio::Tools::Eponine Results of one Eponine run
Bio::Tools::ERPIN a parser for ERPIN output	Bio::Tools::Est2Genome Parse est2genome output, makes simple Bio::SeqFeature::Generic objects	Bio::Tools::ESTScan Results of one ESTScan run
Bio::Tools::EUtilities NCBI eutil XML parsers	Bio::Tools::EUtilities::EUtilDataI eutil data object interface	Bio::Tools::EUtilities::EUtilParameters Manipulation of NCBI eutil-based
Bio::Tools::EUtilities::History lightweight implementation of HistoryI	Bio::Tools::EUtilities::HistoryI simple extension of EUtilDataI interface	Bio::Tools::EUtilities::Info interface class for storing einfo data
Bio::Tools::EUtilities::Info::FieldInfo class for storing einfo field data	Bio::Tools::EUtilities::Info::LinkInfo class for storing einfo link data	Bio::Tools::EUtilities::Link general API for accessing data retrieved from elink queries
Bio::Tools::EUtilities::Link::LinkSet class for EUtils LinkSets	Bio::Tools::EUtilities::Link::UrlLink class for EUtils UrlLinks	Bio::Tools::EUtilities::Query parse and collect esearch, epost, espell,
Bio::Tools::EUtilities::Query::GlobalQuery container class for egquery data	Bio::Tools::EUtilities::Summary class for handling data output (XML) from	Bio::Tools::EUtilities::Summary::DocSum data object for document summary data
Bio::Tools::EUtilities::Summary::Item simple layered object for DocSum item data	Bio::Tools::EUtilities::Summary::ItemContainerI abtract interface methods	Bio::Tools::Fgenesh parse results of one Fgenesh run
Bio::Tools::FootPrinter write sequence features in FootPrinter format	Bio::Tools::Gel Calculates relative electrophoretic migration distances	Bio::Tools::Geneid Results of one geneid run
Bio::Tools::Genemark Results of one Genemark run	Bio::Tools::Genewise Results of one Genewise run	Bio::Tools::Genomewise Results of one Genomewise run
Bio::Tools::Genscan Results of one Genscan run	Bio::Tools::GFF A Bio::SeqAnalysisParserI compliant GFF format parser	Bio::Tools::Glimmer parser for Glimmer 2.X/3.X prokaryotic and
Bio::Tools::Grail Results of one Grail run	Bio::Tools::GuessSeqFormat Module for determining the sequence	Bio::Tools::HMMER::Domain One particular domain hit from HMMER
Bio::Tools::HMMER::Results Object representing HMMER output results	Bio::Tools::HMMER::Set Set of identical domains from HMMER matches	Bio::Tools::Hmmpfam Parser for Hmmpfam program
Bio::Tools::Infernal A parser for Infernal output	Bio::Tools::ipcress Parse ipcress output and make features	Bio::Tools::isPcr Parse isPcr output and make features
Bio::Tools::IUPAC Generates unique Seq objects from an ambiguous Seq object	Bio::Tools::Lucy Object for analyzing the output from Lucy,	Bio::Tools::Match Parses output from Transfac's match(TM)
Bio::Tools::MZEF Results of one MZEF run	Bio::Tools::OddCodes Object holding alternative alphabet coding for	Bio::Tools::Phylo::Gerp Parses output from GERP
Bio::Tools::Phylo::Gumby Parses output from gumby	Bio::Tools::Phylo::Molphy parser for Molphy output	Bio::Tools::Phylo::Molphy::Result container for data parsed from a ProtML run
Bio::Tools::Phylo::PAML Parses output from the PAML programs codeml,	Bio::Tools::Phylo::PAML::Codeml Parses output from the PAML program codeml.	Bio::Tools::Phylo::PAML::ModelResult A container for NSSite Model Result from PAML
Bio::Tools::Phylo::PAML::Result A PAML result set object	Bio::Tools::Phylo::Phylip::ProtDist parser for ProtDist output	Bio::Tools::pICalculator calculate the isoelectric point of a protein
Bio::Tools::Prediction::Exon A predicted exon feature	Bio::Tools::Prediction::Gene a predicted gene structure feature	Bio::Tools::Prepeat Finding repeats in protein sequences
Bio::Tools::Primer3 Create input for and work with the output from	Bio::Tools::Primer3Redux BioPerl-based tools for Primer3 (redone)	Bio::Tools::Primer3Redux::Primer Simple Decorator of a
Bio::Tools::Primer3Redux::PrimerPair Simple Decorator of a	Bio::Tools::Primer3Redux::Result Result class for Primer3 data	Bio::Tools::Primer::Assessor::Base base class for common assessor things
Bio::Tools::Primer::AssessorI interface for assessing primer pairs	Bio::Tools::Primer::Feature position of a single primer	Bio::Tools::Primer::Pair two primers on left and right side
Bio::Tools::Prints Parser for FingerPRINTScanII program	Bio::Tools::Profile parse Profile output	Bio::Tools::Promoterwise parser for Promoterwise tab format output
Bio::Tools::PrositeScan Parser for ps_scan result	Bio::Tools::Protparam submit to and parse output from protparam ;	Bio::Tools::Pseudowise Results of one Pseudowise run
Bio::Tools::pSW pairwise Smith Waterman object	Bio::Tools::QRNA A Parser for qrna output	Bio::Tools::RandomDistFunctions A set of routines useful for
Bio::Tools::RepeatMasker a parser for RepeatMasker output	Bio::Tools::RNAMotif A parser for RNAMotif output	Bio::Tools::Run::Alignment::Gmap Wrapper for running gmap.
Bio::Tools::Run::AssemblerBase base class for wrapping external assemblers	Bio::Tools::Run::BEDTools Run wrapper for the BEDTools suite of programs BETA	Bio::Tools::Run::BEDTools::Config Configuration data for bowtie commands
Bio::Tools::Run::BlastPlus A wrapper for NCBI's blast+ suite	Bio::Tools::Run::BlastPlus::Config	Bio::Tools::Run::Bowtie Run wrapper for the Bowtie short-read assembler BETA
Bio::Tools::Run::Bowtie::Config Configuration data for bowtie commands	Bio::Tools::Run::BWA Run wrapper for the BWA short-read assembler BETA	Bio::Tools::Run::BWA::Config Configuration data for BWA commands
Bio::Tools::Run::GenericParameters An object for the parameters used to run programs	Bio::Tools::Run::Maq Run wrapper for the Maq short-read assembler BETA	Bio::Tools::Run::Maq::Config Configuration data for maq commands
Bio::Tools::Run::Minimo Wrapper for local execution of the Minimo assembler	Bio::Tools::Run::Newbler Wrapper for local execution of Newbler	Bio::Tools::Run::ParametersI A Base object for the parameters used to run programs
Bio::Tools::Run::Primer3Redux Create input for and work with the output	Bio::Tools::Run::RemoteBlast Object for remote execution of the NCBI Blast	Bio::Tools::Run::Samtools a run wrapper for the samtools suite BETA
Bio::Tools::Run::Samtools::Config configurator for Bio::Tools::Run::Samtools	Bio::Tools::Run::StandAloneBlast Object for the local execution	Bio::Tools::Run::StandAloneBlastPlus Compute with NCBI's blast+ suite ALPHA
Bio::Tools::Run::StandAloneNCBIBlast Object for the local execution	Bio::Tools::Run::StandAloneWUBlast Object for the local execution	Bio::Tools::Run::WrapperBase A Base object for wrappers around executables
Bio::Tools::Seg parse C<seg> output	Bio::Tools::SeqPattern represent a sequence pattern or motif	Bio::Tools::SeqPattern::Backtranslate
Bio::Tools::SeqStats Object holding statistics for one	Bio::Tools::SeqWords Object holding n-mer statistics for a sequence	Bio::Tools::Sigcleave Bioperl object for sigcleave analysis
Bio::Tools::Signalp parser for Signalp output	Bio::Tools::Signalp::ExtendedSignalp enhanced parser for Signalp output	Bio::Tools::Sim4::Exon A single exon determined by an alignment
Bio::Tools::Sim4::Results Results of one Sim4 run	Bio::Tools::SiRNA	Bio::Tools::SiRNA::Ruleset::saigo Perl object implementing the Saigo
Bio::Tools::SiRNA::Ruleset::tuschl Perl object implementing the	Bio::Tools::Spidey::Exon A single exon determined by an alignment	Bio::Tools::Spidey::Results Results of a Spidey run
Bio::Tools::TandemRepeatsFinder a parser for Tandem Repeats Finder output	Bio::Tools::TargetP Results of one TargetP run	Bio::Tools::Tmhmm parse TMHMM output (TransMembrane HMM)
Bio::Tools::tRNAscanSE A parser for tRNAscan-SE output	Bio::Trace::ABIF Read and parse ABIF file format	Bio::Translator Translate DNA sequences
Bio::Translator::Table translation table	Bio::Translator::Utils Utilities that requrie a translation table	Bio::Translator::Validations validation methods and objects
Bio::Tree::AlleleNode A Node with Alleles attached	Bio::Tree::AnnotatableNode A Tree Node with support for annotation	Bio::Tree::Compatible Testing compatibility of phylogenetic trees
Bio::Tree::DistanceFactory Construct a tree using distance based methods	Bio::Tree::Draw::Cladogram Drawing phylogenetic trees in	Bio::Tree::Node A Simple Tree Node
Bio::Tree::NodeI Interface describing a Tree Node	Bio::Tree::NodeNHX A Simple Tree Node with support for NHX tags	Bio::Tree::RandomFactory TreeFactory for generating Random Trees
Bio::Tree::Statistics Calculate certain statistics for a Tree	Bio::Tree::Tree An Implementation of TreeI interface.	Bio::Tree::TreeFunctionsI Decorated Interface implementing basic Tree exploration methods
Bio::Tree::TreeI A Tree object suitable for lots of things, designed	Bio::TreeIO Parser for Tree files	Bio::TreeIO::cluster A TreeIO driver module for parsing Algorithm::Cluster::treecluster() output
Bio::TreeIO::lintree Parser for lintree output trees	Bio::TreeIO::newick TreeIO implementation for parsing	Bio::TreeIO::NewickParser
Bio::TreeIO::nexml A TreeIO driver module for parsing NeXML tree files	Bio::TreeIO::nexus A TreeIO driver module for parsing Nexus tree output from PAUP	Bio::TreeIO::nhx TreeIO implementation for parsing
Bio::TreeIO::pag Bio::TreeIO driver for Pagel format	Bio::TreeIO::phyloxml TreeIO implementation for parsing PhyloXML format.	Bio::TreeIO::svggraph A simple output format that converts a Tree object to an SVG output
Bio::TreeIO::tabtree A simple output format which displays a tree as an ASCII drawing	Bio::TreeIO::TreeEventBuilder Build Bio::Tree::Tree's and	Bio::UpdateableSeqI Descendant of Bio::SeqI that allows updates
Bio::Util::AA Basic Amino Acid utilities	Bio::Util::DNA Basic DNA utilities	Bio::Variation::AAChange Sequence change class for polypeptides
Bio::Variation::AAReverseMutate point mutation and codon	Bio::Variation::Allele Sequence object with allele-specific attributes	Bio::Variation::DNAMutation DNA level mutation class
Bio::Variation::IO Handler for sequence variation IO Formats	Bio::Variation::IO::flat flat file sequence variation input/output stream	Bio::Variation::IO::xml XML sequence variation input/output stream
Bio::Variation::RNAChange Sequence change class for RNA level	Bio::Variation::SeqDiff Container class for mutation/variant descriptions	Bio::Variation::SNP submitted SNP
Bio::Variation::VariantI Sequence Change SeqFeature abstract class	Bio::WebAgent A base class for Web (any protocol) access

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