BioPerl documentation

• BioPerl - README
• BioPerl - Changes
• BioPerl - INSTALL
• BioPerl - META.yml
• BioPerl Build.PL
• Bio::Align::AlignI - An interface for describing sequence alignments.  [view source]
• Bio::Align::DNAStatistics - Calculate some statistics for a DNA alignment  [view source]
• Bio::Align::Graphics - Graphic Rendering of Bio::Align::AlignI Objects  [view source]
• Bio::Align::PairwiseStatistics - Base statistic object for Pairwise Alignments  [view source]
• Bio::Align::ProteinStatistics - Calculate Protein Alignment statistics (mostly distances)  [view source]
• Bio::Align::StatisticsI - Calculate some statistics for an alignment  [view source]
• Bio::Align::Utilities - A collection of utilities regarding converting  [view source]
• Bio::AlignIO - Handler for AlignIO Formats  [view source]
• Bio::AlignIO::arp - ARP MSA Sequence input/output stream  [view source]
• Bio::AlignIO::bl2seq - bl2seq sequence input/output stream  [view source]
• Bio::AlignIO::clustalw - clustalw sequence input/output stream  [view source]
• Bio::AlignIO::emboss - Parse EMBOSS alignment output (from applications water and needle)  [view source]
• Bio::AlignIO::fasta - fasta MSA Sequence input/output stream  [view source]
• Bio::AlignIO::Handler::GenericAlignHandler - Bio::HandlerI-based  [view source]
• Bio::AlignIO::largemultifasta - Largemultifasta MSA Sequence  [view source]
• Bio::AlignIO::maf - Multiple Alignment Format sequence input stream  [view source]
• Bio::AlignIO::mase - mase sequence input/output stream  [view source]
• Bio::AlignIO::mega - Parse and Create MEGA format data files  [view source]
• Bio::AlignIO::meme - meme sequence input/output stream  [view source]
• Bio::AlignIO::metafasta - Metafasta MSA Sequence input/output stream  [view source]
• Bio::AlignIO::msf - msf sequence input/output stream  [view source]
• Bio::AlignIO::nexml - NeXML format sequence alignment input/output stream driver  [view source]
• Bio::AlignIO::nexus - NEXUS format sequence input/output stream  [view source]
• Bio::AlignIO::pfam - pfam sequence input/output stream  [view source]
• Bio::AlignIO::phylip - PHYLIP format sequence input/output stream  [view source]
• Bio::AlignIO::po - po MSA Sequence input/output stream  [view source]
• Bio::AlignIO::proda - proda sequence input/output stream  [view source]
• Bio::AlignIO::prodom - prodom sequence input/output stream  [view source]
• Bio::AlignIO::psi - Read/Write PSI-BLAST profile alignment files  [view source]
• Bio::AlignIO::selex - selex sequence input/output stream  [view source]
• Bio::AlignIO::stockholm - stockholm sequence input/output stream  [view source]
• Bio::AlignIO::xmfa - XMFA MSA Sequence input/output stream  [view source]
• Bio::AnalysisI - An interface to any (local or remote) analysis tool  [view source]
• Bio::AnalysisParserI - Generic analysis output parser interface  [view source]
• Bio::AnalysisResultI - Interface for analysis result objects  [view source]
• Bio::AnnotatableI - the base interface an annotatable object must implement  [view source]
• Bio::Annotation::AnnotationFactory - Instantiates a new  [view source]
• Bio::Annotation::Collection - Default Perl implementation of  [view source]
• Bio::Annotation::Comment - A comment object, holding text  [view source]
• Bio::Annotation::DBLink - untyped links between databases  [view source]
• Bio::Annotation::OntologyTerm - An ontology term adapted to AnnotationI  [view source]
• Bio::Annotation::Reference - Specialised DBLink object for Literature References  [view source]
• Bio::Annotation::Relation - Relationship (pairwise) with other objects SeqI and NodeI;  [view source]
• Bio::Annotation::SimpleValue - A simple scalar  [view source]
• Bio::Annotation::StructuredValue - A scalar with embedded structured  [view source]
• Bio::Annotation::TagTree - AnnotationI with tree-like hierarchal key-value  [view source]
• Bio::Annotation::Target - Provides an object which represents a target (ie, a  [view source]
• Bio::Annotation::Tree - Provide a tree as an annotation to a Bio::AnnotatableI  [view source]
• Bio::Annotation::TypeManager - Manages types for annotation collections  [view source]
• Bio::AnnotationCollectionI - Interface for annotation collections  [view source]
• Bio::AnnotationI - Annotation interface  [view source]
• Bio::Assembly::Contig - Perl module to hold and manipulate  [view source]
• Bio::Assembly::ContigAnalysis - Bio::Assembly::ContigAnalysis documentation  [view source]
• Bio::Assembly::IO - Handler for Assembly::IO Formats  [view source]
• Bio::Assembly::IO::ace - module to load ACE files from various assembly programs  [view source]
• Bio::Assembly::IO::bowtie - An IO module for assemblies in Bowtie format *BETA*  [view source]
• Bio::Assembly::IO::maq - Driver to read assembly files in maq format *BETA*  [view source]
• Bio::Assembly::IO::phrap - driver to load phrap.out files.  [view source]
• Bio::Assembly::IO::sam - An IO module for assemblies in Sam format *BETA*  [view source]
• Bio::Assembly::IO::tigr - Driver to read and write assembly files in the TIGR  [view source]
• Bio::Assembly::Scaffold - Perl module to hold and manipulate sequence assembly  [view source]
• Bio::Assembly::ScaffoldI - Abstract Inteface of Sequence Assemblies  [view source]
• Bio::Assembly::Singlet - Perl module to hold and manipulate  [view source]
• Bio::Assembly::Tools::ContigSpectrum - create and manipulate contig spectra  [view source]
• Bio::Biblio - A Bibliographic Query Service module  [view source]
• Bio::Biblio::Article - Representation of a general article  [view source]
• Bio::Biblio::BiblioBase - An abstract base for other biblio classes  [view source]
• Bio::Biblio::Book - Representation of a book  [view source]
• Bio::Biblio::BookArticle - Representation of a book article  [view source]
• Bio::Biblio::IO - Handling the bibliographic references  [view source]
• Bio::Biblio::IO::medline2ref - A converter of a raw hash to MEDLINE citations  [view source]
• Bio::Biblio::IO::medlinexml - A converter of XML files with MEDLINE citations  [view source]
• Bio::Biblio::IO::pubmed2ref - A converter of a raw hash to PUBMED citations  [view source]
• Bio::Biblio::IO::pubmedxml - A converter of XML files with PUBMED citations  [view source]
• Bio::Biblio::Journal - Representation of a journal  [view source]
• Bio::Biblio::JournalArticle - Representation of a journal article  [view source]
• Bio::Biblio::MedlineArticle - Representation of a MEDLINE article  [view source]
• Bio::Biblio::MedlineBook - Representation of a MEDLINE book  [view source]
• Bio::Biblio::MedlineBookArticle - Representation of a MEDLINE book article  [view source]
• Bio::Biblio::MedlineJournal - Representation of a MEDLINE journal  [view source]
• Bio::Biblio::MedlineJournalArticle - Representation of a MEDLINE journal article  [view source]
• Bio::Biblio::Organisation - Representation of an organisation  [view source]
• Bio::Biblio::Patent - Representation of a patent  [view source]
• Bio::Biblio::Person - Representation of a person  [view source]
• Bio::Biblio::Proceeding - Representation of a conference proceeding  [view source]
• Bio::Biblio::Provider - Representation of a general provider  [view source]
• Bio::Biblio::PubmedArticle - Representation of a PUBMED article  [view source]
• Bio::Biblio::PubmedBookArticle - Representation of a PUBMED book article  [view source]
• Bio::Biblio::PubmedJournalArticle - Representation of a PUBMED journal article  [view source]
• Bio::Biblio::Ref - Representation of a bibliographic reference  [view source]
• Bio::Biblio::Service - Representation of a provider of type service  [view source]
• Bio::Biblio::TechReport - Representation of a technical report  [view source]
• Bio::Biblio::Thesis - Representation of thesis  [view source]
• Bio::Biblio::WebResource - Representation of a web resource  [view source]
• Bio::Cluster::ClusterFactory - Instantiates a new Bio::ClusterI (or derived class) through a factory  [view source]
• Bio::Cluster::FamilyI - Family Interface  [view source]
• Bio::Cluster::SequenceFamily - Sequence Family object  [view source]
• Bio::Cluster::UniGene - UniGene object  [view source]
• Bio::Cluster::UniGeneI - abstract interface of UniGene object  [view source]
• Bio::ClusterI - Cluster Interface  [view source]
• Bio::ClusterIO - Handler for Cluster Formats  [view source]
• Bio::ClusterIO::dbsnp - dbSNP input stream  [view source]
• Bio::ClusterIO::unigene - UniGene input stream  [view source]
• Bio::CodonUsage::IO - for reading and writing codon usage tables to file  [view source]
• Bio::CodonUsage::Table - for access to the Codon usage Database  [view source]
• Bio::Coordinate::Chain - Mapping locations through a chain of coordinate mappers  [view source]
• Bio::Coordinate::Collection - Noncontinuous match between two coordinate sets  [view source]
• Bio::Coordinate::ExtrapolatingPair - Continuous match between two coordinate sets  [view source]
• Bio::Coordinate::GeneMapper - transformations between gene related coordinate systems  [view source]
• Bio::Coordinate::Graph - Finds shortest path between nodes in a graph  [view source]
• Bio::Coordinate::MapperI - Interface describing coordinate mappers  [view source]
• Bio::Coordinate::Pair - Continuous match between two coordinate sets  [view source]
• Bio::Coordinate::Result - Results from coordinate transformation  [view source]
• Bio::Coordinate::Result::Gap - Another name for Bio::Location::Simple  [view source]
• Bio::Coordinate::Result::Match - Another name for Bio::Location::Simple  [view source]
• Bio::Coordinate::ResultI - Interface to identify coordinate mapper results  [view source]
• Bio::Coordinate::Utils - Additional methods to create Bio::Coordinate objects  [view source]
• Bio::Das::FeatureTypeI - Simple interface to Sequence Ontology feature types  [view source]
• Bio::Das::SegmentI - DAS-style access to a feature database  [view source]
• Bio::DasI - DAS-style access to a feature database  [view source]
• Bio::DB::Ace - Database object interface to ACeDB servers  [view source]
• Bio::DB::Biblio::biofetch - A BioFetch-based access to a bibliographic  [view source]
• Bio::DB::Biblio::eutils - Access to PubMed's bibliographic query service  [view source]
• Bio::DB::Biblio::soap - A SOAP-based access to a bibliographic query service  [view source]
• Bio::DB::BiblioI - An interface to a Bibliographic Query Service  [view source]
• Bio::DB::BioFetch - Database object interface to BioFetch retrieval  [view source]
• Bio::DB::CUTG - for access to the Codon usage Database  [view source]
• Bio::DB::DBFetch - Database object for retrieving using the dbfetch script  [view source]
• Bio::DB::EMBL - Database object interface for EMBL entry retrieval  [view source]
• Bio::DB::EntrezGene - Database object interface to Entrez Gene  [view source]
• Bio::DB::EUtilities - webagent which interacts with and retrieves data from  [view source]
• Bio::DB::Expression - DESCRIPTION of Object  [view source]
• Bio::DB::Expression::geo - *** DESCRIPTION of Class  [view source]
• Bio::DB::Failover - A Bio::DB::RandomAccessI compliant class which  [view source]
• Bio::DB::Fasta - Fast indexed access to a directory of fasta files  [view source]
• Bio::DB::FileCache - In file cache for BioSeq objects  [view source]
• Bio::DB::Flat - Interface for indexed flat files  [view source]
• Bio::DB::Flat::BDB - Interface for BioHackathon standard BDB-indexed flat file  [view source]
• Bio::DB::Flat::BDB::embl - embl adaptor for Open-bio standard BDB-indexed flat file  [view source]
• Bio::DB::Flat::BDB::fasta - fasta adaptor for Open-bio standard BDB-indexed flat file  [view source]
• Bio::DB::Flat::BDB::genbank - genbank adaptor for Open-bio standard BDB-indexed flat file  [view source]
• Bio::DB::Flat::BDB::swiss - swissprot adaptor for Open-bio standard BDB-indexed flat file  [view source]
• Bio::DB::Flat::BinarySearch - BinarySearch search indexing system for sequence files  [view source]
• Bio::DB::GenBank - Database object interface to GenBank  [view source]
• Bio::DB::GenericWebAgent - helper base class for parameter-based remote server  [view source]
• Bio::DB::GenPept - Database object interface to GenPept  [view source]
• Bio::DB::GFF - Storage and retrieval of sequence annotation data  [view source]
• Bio::DB::GFF::Adaptor::ace - ace interface (for multiple inheritance)  [view source]
• Bio::DB::GFF::Adaptor::berkeleydb - Bio::DB::GFF database adaptor for in-memory databases  [view source]
• Bio::DB::GFF::Adaptor::berkeleydb::iterator - iterator for Bio::DB::GFF::Adaptor::berkeleydb  [view source]
• Bio::DB::GFF::Adaptor::biofetch - Cache BioFetch objects in a Bio::DB::GFF database  [view source]
• Bio::DB::GFF::Adaptor::biofetch_oracle - Cache BioFetch objects in a Bio::DB::GFF database  [view source]
• Bio::DB::GFF::Adaptor::dbi - Database adaptor for DBI (SQL) databases  [view source]
• Bio::DB::GFF::Adaptor::dbi::caching_handle - Cache for database handles  [view source]
• Bio::DB::GFF::Adaptor::dbi::iterator - iterator for Bio::DB::GFF::Adaptor::dbi  [view source]
• Bio::DB::GFF::Adaptor::dbi::mysql - Database adaptor for a specific mysql schema  [view source]
• Bio::DB::GFF::Adaptor::dbi::mysqlace - Unholy union between mysql GFF database and acedb database  [view source]
• Bio::DB::GFF::Adaptor::dbi::mysqlcmap - Database adaptor for an integraded  [view source]
• Bio::DB::GFF::Adaptor::dbi::mysqlopt - Deprecated database adaptor  [view source]
• Bio::DB::GFF::Adaptor::dbi::oracle - Database adaptor for a specific oracle schema  [view source]
• Bio::DB::GFF::Adaptor::dbi::oracleace - Unholy union between oracle GFF database and acedb database  [view source]
• Bio::DB::GFF::Adaptor::dbi::pg - Database adaptor for a specific postgres schema  [view source]
• Bio::DB::GFF::Adaptor::dbi::pg_fts - Database adaptor for a specific postgres schema with a TSearch2 implementation  [view source]
• Bio::DB::GFF::Adaptor::memory - Bio::DB::GFF database adaptor for in-memory databases  [view source]
• Bio::DB::GFF::Adaptor::memory::feature_serializer - utility methods for serializing and deserializing GFF features  [view source]
• Bio::DB::GFF::Adaptor::memory::iterator - iterator for Bio::DB::GFF::Adaptor::memory  [view source]
• Bio::DB::GFF::Aggregator - Aggregate GFF groups into composite features  [view source]
• Bio::DB::GFF::Aggregator::alignment - Alignment aggregator  [view source]
• Bio::DB::GFF::Aggregator::clone - Clone aggregator  [view source]
• Bio::DB::GFF::Aggregator::coding - The Coding Region Aggregator  [view source]
• Bio::DB::GFF::Aggregator::gene - Sequence Ontology Geene  [view source]
• Bio::DB::GFF::Aggregator::match - Match aggregator  [view source]
• Bio::DB::GFF::Aggregator::none - No aggregation  [view source]
• Bio::DB::GFF::Aggregator::orf - An aggregator for orf regions  [view source]
• Bio::DB::GFF::Aggregator::processed_transcript - Sequence Ontology Transcript  [view source]
• Bio::DB::GFF::Aggregator::so_transcript - Sequence Ontology Transcript  [view source]
• Bio::DB::GFF::Aggregator::transcript - Transcript aggregator  [view source]
• Bio::DB::GFF::Aggregator::ucsc_acembly - UCSC acembly aggregator  [view source]
• Bio::DB::GFF::Aggregator::ucsc_ensgene - UCSC ensGene aggregator  [view source]
• Bio::DB::GFF::Aggregator::ucsc_genscan - UCSC genscan aggregator  [view source]
• Bio::DB::GFF::Aggregator::ucsc_refgene - UCSC refGene aggregator  [view source]
• Bio::DB::GFF::Aggregator::ucsc_sanger22 - UCSC sanger22 aggregator  [view source]
• Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo - UCSC sanger22pseudo aggregator  [view source]
• Bio::DB::GFF::Aggregator::ucsc_softberry - UCSC softberry aggregator  [view source]
• Bio::DB::GFF::Aggregator::ucsc_twinscan - UCSC twinscan aggregator  [view source]
• Bio::DB::GFF::Aggregator::ucsc_unigene - UCSC UniGene aggregator  [view source]
• Bio::DB::GFF::Featname - The name of a feature  [view source]
• Bio::DB::GFF::Feature - A relative segment identified by a feature type  [view source]
• Bio::DB::GFF::Homol - A segment of DNA that is homologous to another  [view source]
• Bio::DB::GFF::RelSegment - Sequence segment with relative coordinate support  [view source]
• Bio::DB::GFF::Segment - Simple DNA segment object  [view source]
• Bio::DB::GFF::Typename - The name of a feature type  [view source]
• Bio::DB::GFF::Util::Binning - binning utility for Bio::DB::GFF index  [view source]
• Bio::DB::GFF::Util::Rearrange - rearrange utility  [view source]
• Bio::DB::HIV - Database object interface to the Los Alamos HIV Sequence Database  [view source]
• Bio::DB::HIV::HIVQueryHelper - Routines and packages used by Bio::DB::HIV and  [view source]
• Bio::DB::InMemoryCache - Abstract interface for a sequence database  [view source]
• Bio::DB::LocationI - A RandomAccessI-like abstract interface for  [view source]
• Bio::DB::MeSH - Term retrieval from a Web MeSH database  [view source]
• Bio::DB::NCBIHelper - A collection of routines useful for queries to  [view source]
• Bio::DB::Qual - Fast indexed access to a directory of quality files  [view source]
• Bio::DB::Query::GenBank - Build a GenBank Entrez Query  [view source]
• Bio::DB::Query::HIVQuery - Query interface to the Los Alamos HIV Sequence Database  [view source]
• Bio::DB::Query::WebQuery - Helper class for web-based sequence queryies  [view source]
• Bio::DB::QueryI - Object Interface to queryable sequence databases  [view source]
• Bio::DB::RandomAccessI - Abstract interface for a sequence database  [view source]
• Bio::DB::ReferenceI - A RandomAccessI-like abstract interface for  [view source]
• Bio::DB::RefSeq - Database object interface for RefSeq retrieval  [view source]
• Bio::DB::Registry - Access to the Open Bio Database Access registry scheme  [view source]
• Bio::DB::SeqFeature - Normalized feature for use with Bio::DB::SeqFeature::Store  [view source]
• Bio::DB::SeqFeature::NormalizedFeature - Normalized feature for use with Bio::DB::SeqFeature::Store  [view source]
• Bio::DB::SeqFeature::NormalizedFeatureI - Interface for normalized features  [view source]
• Bio::DB::SeqFeature::NormalizedTableFeatureI - Interface for normalized features whose hierarchy is stored in a table  [view source]
• Bio::DB::SeqFeature::Segment - Location-based access to genome annotation data  [view source]
• Bio::DB::SeqFeature::Store - Storage and retrieval of sequence annotation data  [view source]
• Bio::DB::SeqFeature::Store::bdb - fetch and store objects from a BerkeleyDB  [view source]
• Bio::DB::SeqFeature::Store::berkeleydb - Storage and retrieval of sequence annotation data in Berkeleydb files  [view source]
• Bio::DB::SeqFeature::Store::berkeleydb3 - Storage and retrieval of sequence  [view source]
• Bio::DB::SeqFeature::Store::DBI::Iterator - utility methods for creating and iterating over SeqFeature records  [view source]
• Bio::DB::SeqFeature::Store::DBI::mysql - Mysql implementation of Bio::DB::SeqFeature::Store  [view source]
• Bio::DB::SeqFeature::Store::DBI::Pg - PostgreSQL implementation of Bio::DB::SeqFeature::Store  [view source]
• Bio::DB::SeqFeature::Store::DBI::SQLite - SQLite implementation of Bio::DB::SeqFeature::Store  [view source]
• Bio::DB::SeqFeature::Store::FeatureFileLoader - feature file loader for Bio::DB::SeqFeature::Store  [view source]
• Bio::DB::SeqFeature::Store::GFF2Loader - GFF2 file loader for Bio::DB::SeqFeature::Store  [view source]
• Bio::DB::SeqFeature::Store::GFF3Loader - GFF3 file loader for Bio::DB::SeqFeature::Store  [view source]
• Bio::DB::SeqFeature::Store::Loader - Loader  [view source]
• Bio::DB::SeqFeature::Store::LoadHelper - Internal utility for Bio::DB::SeqFeature::Store  [view source]
• Bio::DB::SeqFeature::Store::memory - In-memory implementation of Bio::DB::SeqFeature::Store  [view source]
• Bio::DB::SeqHound - Database object interface to SeqHound  [view source]
• Bio::DB::SeqI - Abstract Interface for Sequence databases  [view source]
• Bio::DB::SeqVersion - front end to querying databases for identifier  [view source]
• Bio::DB::SeqVersion::gi - interface to NCBI Sequence Revision History page  [view source]
• Bio::DB::SwissProt - Database object interface to SwissProt retrieval  [view source]
• Bio::DB::Taxonomy - Access to a taxonomy database  [view source]
• Bio::DB::Taxonomy::entrez - Taxonomy Entrez driver  [view source]
• Bio::DB::Taxonomy::flatfile - An implementation of Bio::DB::Taxonomy  [view source]
• Bio::DB::Taxonomy::list - An implementation of Bio::DB::Taxonomy  [view source]
• Bio::DB::TFBS - Access to a Transcription Factor Binding Site database  [view source]
• Bio::DB::TFBS::transfac_pro - An implementation of Bio::DB::TFBS  [view source]
• Bio::DB::Universal - Artificial database that delegates to specific databases  [view source]
• Bio::DB::UpdateableSeqI - An interface for writing to a database of sequences.  [view source]
• Bio::DB::WebDBSeqI - Object Interface to generalize Web Databases  [view source]
• Bio::DBLinkContainerI - Abstract interface for any object wanting to use  [view source]
• Bio::DescribableI - interface for objects with human readable names and descriptions  [view source]
• Bio::Draw::Pictogram - generate SVG output of Pictogram display for consensus motifs  [view source]
• Bio::Event::EventGeneratorI - This interface describes the basic event  [view source]
• Bio::Event::EventHandlerI - An Event Handler Interface  [view source]
• Bio::Factory::AnalysisI - An interface to analysis tool factory  [view source]
• Bio::Factory::ApplicationFactoryI - Interface class for Application Factories  [view source]
• Bio::Factory::DriverFactory - Base class for factory classes loading drivers  [view source]
• Bio::Factory::FTLocationFactory - A FeatureTable Location Parser  [view source]
• Bio::Factory::LocationFactoryI - A factory interface for generating locations from a string  [view source]
• Bio::Factory::MapFactoryI - A Factory for getting markers  [view source]
• Bio::Factory::ObjectBuilderI - Interface for an object builder  [view source]
• Bio::Factory::ObjectFactory - Instantiates a new Bio::Root::RootI (or derived class) through a factory  [view source]
• Bio::Factory::ObjectFactoryI - A General object creator factory  [view source]
• Bio::Factory::SeqAnalysisParserFactory - class capable of creating  [view source]
• Bio::Factory::SeqAnalysisParserFactoryI - interface describing objects capable  [view source]
• Bio::Factory::SequenceFactoryI - This interface allows for generic building of sequences in factories which create sequences (like SeqIO)  [view source]
• Bio::Factory::SequenceProcessorI - Interface for chained sequence  [view source]
• Bio::Factory::SequenceStreamI - Interface describing the basics of a Sequence Stream.  [view source]
• Bio::Factory::TreeFactoryI - Factory Interface for getting and writing trees  [view source]
• Bio::FeatureHolderI - the base interface an object with features must implement  [view source]
• Bio::FeatureIO - Handler for FeatureIO  [view source]
• Bio::FeatureIO::bed - read/write features from UCSC BED format  [view source]
• Bio::FeatureIO::gff - read/write GFF feature files  [view source]
• Bio::FeatureIO::gtf - read write features in GTF format  [view source]
• Bio::FeatureIO::interpro - read features from InterPro XML  [view source]
• Bio::FeatureIO::ptt - read/write features in PTT format  [view source]
• Bio::FeatureIO::vecscreen_simple - read/write features from NCBI vecscreen -f 3  [view source]
• Bio::HandlerBaseI - Interface class for handler methods which interact with any  [view source]
• Bio::IdCollectionI - interface for objects with multiple identifiers  [view source]
• Bio::IdentifiableI - interface for objects with identifiers  [view source]
• Bio::Index::Abstract - Abstract interface for indexing a flat file  [view source]
• Bio::Index::AbstractSeq - base class for AbstractSeq  [view source]
• Bio::Index::Blast - Indexes Blast reports and supports retrieval  [view source]
• Bio::Index::BlastTable - Indexes tabular Blast reports (-m 8 or -m 9 format) and  [view source]
• Bio::Index::EMBL - Interface for indexing (multiple) EMBL/Swissprot  [view source]
• Bio::Index::Fasta - Interface for indexing (multiple) fasta files  [view source]
• Bio::Index::Fastq - Interface for indexing (multiple) fastq files  [view source]
• Bio::Index::GenBank - Interface for indexing one or more GenBank  [view source]
• Bio::Index::Hmmer - indexes HMMER reports and supports retreival based on query  [view source]
• Bio::Index::Qual - Interface for indexing (multiple) fasta qual files  [view source]
• Bio::Index::Stockholm - Indexes Stockholm format alignments (such as those from  [view source]
• Bio::Index::SwissPfam - Interface for indexing swisspfam files  [view source]
• Bio::Index::Swissprot - Interface for indexing one or more  [view source]
• Bio::LiveSeq::AARange - AARange abstract class for LiveSeq  [view source]
• Bio::LiveSeq::Chain - DoubleChain DataStructure for Perl  [view source]
• Bio::LiveSeq::ChainI - Double linked chain data structure  [view source]
• Bio::LiveSeq::DNA - DNA object for LiveSeq  [view source]
• Bio::LiveSeq::Exon - Range abstract class for LiveSeq  [view source]
• Bio::LiveSeq::Gene - Range abstract class for LiveSeq  [view source]
• Bio::LiveSeq::Intron - Range abstract class for LiveSeq  [view source]
• Bio::LiveSeq::IO::BioPerl - Loader for LiveSeq from EMBL entries with BioPerl  [view source]
• Bio::LiveSeq::IO::Loader - Parent Loader for LiveSeq  [view source]
• Bio::LiveSeq::Mutation - Mutation event descriptor class  [view source]
• Bio::LiveSeq::Mutator - Package mutating LiveSequences  [view source]
• Bio::LiveSeq::Prim_Transcript - Prim_Transcript class for LiveSeq  [view source]
• Bio::LiveSeq::Range - Range abstract class for LiveSeq  [view source]
• Bio::LiveSeq::Repeat_Region - Repeat_Region class for LiveSeq  [view source]
• Bio::LiveSeq::Repeat_Unit - Repeat_Unit class for LiveSeq  [view source]
• Bio::LiveSeq::SeqI - Abstract sequence interface class for LiveSeq  [view source]
• Bio::LiveSeq::Transcript - Transcript class for LiveSeq  [view source]
• Bio::LiveSeq::Translation - Translation class for LiveSeq  [view source]
• Bio::Location::Atomic - Implementation of a Atomic Location on a Sequence  [view source]
• Bio::Location::AvWithinCoordPolicy - class implementing  [view source]
• Bio::Location::CoordinatePolicyI - Abstract interface for objects implementing  [view source]
• Bio::Location::Fuzzy - Implementation of a Location on a Sequence  [view source]
• Bio::Location::FuzzyLocationI - Abstract interface of a Location on a Sequence  [view source]
• Bio::Location::NarrowestCoordPolicy - class implementing  [view source]
• Bio::Location::Simple - Implementation of a Simple Location on a Sequence  [view source]
• Bio::Location::Split - Implementation of a Location on a Sequence  [view source]
• Bio::Location::SplitLocationI - Abstract interface of a Location on a Sequence  [view source]
• Bio::Location::WidestCoordPolicy - class implementing  [view source]
• Bio::LocationI - Abstract interface of a Location on a Sequence  [view source]
• Bio::Map::Clone - An central map object representing a clone  [view source]
• Bio::Map::Contig - A MapI implementation handling the contigs of a  [view source]
• Bio::Map::CytoMap - A Bio::MapI compliant map implementation handling cytogenic bands  [view source]
• Bio::Map::CytoMarker - An object representing a marker.  [view source]
• Bio::Map::CytoPosition - Marker class with cytogenetic band storing attributes  [view source]
• Bio::Map::EntityI - An Entity Interface  [view source]
• Bio::Map::FPCMarker - An central map object representing a marker  [view source]
• Bio::Map::Gene - An gene modelled as a mappable element.  [view source]
• Bio::Map::GeneMap - A MapI implementation to represent the area around a gene  [view source]
• Bio::Map::GenePosition - A typed position, suitable for modelling the various  [view source]
• Bio::Map::GeneRelative - Represents being relative to named sub-regions of a  [view source]
• Bio::Map::LinkageMap - A representation of a genetic linkage map.  [view source]
• Bio::Map::LinkagePosition - Create a Position for a Marker that will be placed  [view source]
• Bio::Map::MapI - Interface for describing Map objects in bioperl  [view source]
• Bio::Map::Mappable - An object representing a generic map element  [view source]
• Bio::Map::MappableI - An object that can be placed in a map  [view source]
• Bio::Map::Marker - An central map object representing a generic marker  [view source]
• Bio::Map::MarkerI - Interface for basic marker functionality  [view source]
• Bio::Map::Microsatellite - An object representing a Microsatellite marker.  [view source]
• Bio::Map::OrderedPosition - Abstracts the notion of a member  [view source]
• Bio::Map::OrderedPositionWithDistance - Abstracts the notion of a member  [view source]
• Bio::Map::Physical - A class for handling a Physical Map (such as FPC)  [view source]
• Bio::Map::Position - A single position of a Marker, or the range over which  [view source]
• Bio::Map::PositionHandler - A Position Handler Implementation  [view source]
• Bio::Map::PositionHandlerI - A Position Handler Interface  [view source]
• Bio::Map::PositionI - Abstracts the notion of a position having a value in the context of a marker and a Map  [view source]
• Bio::Map::PositionWithSequence - A position with a sequence.  [view source]
• Bio::Map::Prediction - An object representing the predictions of something  [view source]
• Bio::Map::Relative - Represents what a Position's coordiantes are relative to.  [view source]
• Bio::Map::RelativeI - Interface for describing what a Position's coordiantes are  [view source]
• Bio::Map::SimpleMap - A MapI implementation handling the basics of a Map  [view source]
• Bio::Map::TranscriptionFactor - A transcription factor modelled as a mappable  [view source]
• Bio::MapIO - A Map Factory object  [view source]
• Bio::MapIO::fpc - A FPC Map reader  [view source]
• Bio::MapIO::mapmaker - A Mapmaker Map reader  [view source]
• Bio::Matrix::Generic - A generic matrix implementation  [view source]
• Bio::Matrix::IO - A factory for Matrix parsing  [view source]
• Bio::Matrix::IO::mlagan - A parser for the mlagan substitution matrix  [view source]
• Bio::Matrix::IO::phylip - A parser for PHYLIP distance matricies  [view source]
• Bio::Matrix::IO::scoring - A parser for PAM/BLOSUM matricies  [view source]
• Bio::Matrix::MatrixI - An interface for describing a Matrix  [view source]
• Bio::Matrix::Mlagan - A generic matrix with mlagan fields  [view source]
• Bio::Matrix::PhylipDist - A Phylip Distance Matrix object  [view source]
• Bio::Matrix::PSM::InstanceSite - A PSM site occurance  [view source]
• Bio::Matrix::PSM::InstanceSiteI - InstanceSite interface, holds an instance of a PSM  [view source]
• Bio::Matrix::PSM::IO - PSM parser  [view source]
• Bio::Matrix::PSM::IO::mast - PSM mast parser implementation  [view source]
• Bio::Matrix::PSM::IO::masta - motif fasta format parser  [view source]
• Bio::Matrix::PSM::IO::meme - PSM meme parser implementation  [view source]
• Bio::Matrix::PSM::IO::psiblast - PSM psiblast parser  [view source]
• Bio::Matrix::PSM::IO::transfac - PSM transfac parser  [view source]
• Bio::Matrix::PSM::ProtMatrix - SiteMatrixI implementation, holds a  [view source]
• Bio::Matrix::PSM::ProtPsm - handle combination of site matricies  [view source]
• Bio::Matrix::PSM::Psm - handle combination of site matricies  [view source]
• Bio::Matrix::PSM::PsmHeader - PSM mast parser implementation  [view source]
• Bio::Matrix::PSM::PsmHeaderI - handles the header data from a PSM file  [view source]
• Bio::Matrix::PSM::PsmI - abstract interface to handler of site matricies  [view source]
• Bio::Matrix::PSM::SiteMatrix - SiteMatrixI implementation, holds a  [view source]
• Bio::Matrix::PSM::SiteMatrixI - SiteMatrixI implementation, holds a  [view source]
• Bio::Matrix::Scoring - Object which can hold scoring matrix information  [view source]
• Bio::MolEvol::CodonModel - Codon Evolution Models  [view source]
• Bio::Nexml::Factory - A factory module for creating BioPerl and Bio::Phylo objects from/to nexml documents  [view source]
• Bio::NexmlIO - stream handler for NeXML documents  [view source]
• Bio::Ontology::DocumentRegistry - Keep track of where to find ontologies.  [view source]
• Bio::Ontology::GOterm - representation of GO terms  [view source]
• Bio::Ontology::InterProTerm - Implementation of InterProI term interface  [view source]
• Bio::Ontology::OBOEngine - An Ontology Engine for OBO style flat file  [view source]
• Bio::Ontology::OBOterm - representation of OBO terms  [view source]
• Bio::Ontology::Ontology - standard implementation of an Ontology  [view source]
• Bio::Ontology::OntologyEngineI - Interface a minimal Ontology implementation should satisfy  [view source]
• Bio::Ontology::OntologyI - Interface for an ontology implementation  [view source]
• Bio::Ontology::OntologyStore - A repository of ontologies  [view source]
• Bio::Ontology::Path - a path for an ontology term graph  [view source]
• Bio::Ontology::PathI - Interface for a path between ontology terms  [view source]
• Bio::Ontology::Relationship - a relationship for an ontology  [view source]
• Bio::Ontology::RelationshipFactory - Instantiates a new  [view source]
• Bio::Ontology::RelationshipI - Interface for a relationship between ontology terms  [view source]
• Bio::Ontology::RelationshipType - a relationship type for an ontology  [view source]
• Bio::Ontology::SimpleGOEngine::GraphAdaptor - Graph adaptor for  [view source]
• Bio::Ontology::SimpleGOEngine::GraphAdaptor02 - Graph adaptor (v02.x) for  [view source]
• Bio::Ontology::SimpleOntologyEngine - Implementation of OntologyEngineI interface  [view source]
• Bio::Ontology::Term - implementation of the interface for ontology terms  [view source]
• Bio::Ontology::TermFactory - Instantiates a new  [view source]
• Bio::Ontology::TermI - interface for ontology terms  [view source]
• Bio::OntologyIO - Parser factory for Ontology formats  [view source]
• Bio::OntologyIO::dagflat - a base class parser for GO flat-file type formats  [view source]
• Bio::OntologyIO::goflat - a parser for the Gene Ontology flat-file format  [view source]
• Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler - parse an InterPro XML file and persist the resulting terms to a Biosql database  [view source]
• Bio::OntologyIO::Handlers::InterProHandler - XML handler class for InterProParser  [view source]
• Bio::OntologyIO::InterProParser - Parser for InterPro xml files.  [view source]
• Bio::OntologyIO::obo - a parser for OBO flat-file format from Gene Ontology Consortium  [view source]
• Bio::OntologyIO::simplehierarchy - a base class parser for simple hierarchy-by-indentation  [view source]
• Bio::OntologyIO::soflat - a parser for the Sequence Ontology flat-file format  [view source]
• Bio::ParameterBaseI - Simple interface class for any parameter-related data such  [view source]
• Bio::Perl - Functional access to BioPerl for people who don't know objects  [view source]
• Bio::Phenotype::Correlate - Representation of a correlating phenotype in a given species  [view source]
• Bio::Phenotype::Measure - Representation of context/value(-range)/unit triplets  [view source]
• Bio::Phenotype::MeSH::Term - A MeSH term  [view source]
• Bio::Phenotype::MeSH::Twig - Context for a MeSH term  [view source]
• Bio::Phenotype::OMIM::MiniMIMentry - Representation of a Mini MIM entry  [view source]
• Bio::Phenotype::OMIM::OMIMentry - represents OMIM (Online Mendelian  [view source]
• Bio::Phenotype::OMIM::OMIMentryAllelicVariant - Representation of a allelic  [view source]
• Bio::Phenotype::OMIM::OMIMparser - parser for the OMIM database  [view source]
• Bio::Phenotype::Phenotype - A class for modeling phenotypes  [view source]
• Bio::Phenotype::PhenotypeI - An interface for classes modeling phenotypes  [view source]
• Bio::PhyloNetwork - Module to compute with Phylogenetic Networks  [view source]
• Bio::PhyloNetwork::Factory - Module to sequentially generate  [view source]
• Bio::PhyloNetwork::FactoryX - Module to sequentially generate  [view source]
• Bio::PhyloNetwork::GraphViz - Interface between PhyloNetwork and GraphViz  [view source]
• Bio::PhyloNetwork::muVector - Module to compute with vectors of arbitrary  [view source]
• Bio::PhyloNetwork::RandomFactory - Module to generate random  [view source]
• Bio::PhyloNetwork::TreeFactory - Module to sequentially generate  [view source]
• Bio::PhyloNetwork::TreeFactoryMulti - Module to sequentially generate  [view source]
• Bio::PhyloNetwork::TreeFactoryX - Module to sequentially generate  [view source]
• Bio::PopGen::Genotype - An implementation of GenotypeI which is just an allele container  [view source]
• Bio::PopGen::GenotypeI - A marker and alleles for a specific individual  [view source]
• Bio::PopGen::Individual - An implementation of an Individual who has  [view source]
• Bio::PopGen::IndividualI - An individual who has Genotype or Sequence Results  [view source]
• Bio::PopGen::IO - Input individual,marker,allele information  [view source]
• Bio::PopGen::IO::hapmap - A parser for HapMap output data  [view source]
• Bio::PopGen::IO::phase - A parser for Phase format data  [view source]
• Bio::PopGen::IO::prettybase - Extract individual allele data from PrettyBase format  [view source]
• Bio::PopGen::Marker - A genetic marker which one uses to generate genotypes  [view source]
• Bio::PopGen::MarkerI - A Population Genetic conceptual marker  [view source]
• Bio::PopGen::PopStats - A collection of methods for calculating  [view source]
• Bio::PopGen::Population - A population of individuals  [view source]
• Bio::PopGen::PopulationI - Interface for Populations  [view source]
• Bio::PopGen::Simulation::Coalescent - A Coalescent simulation factory  [view source]
• Bio::PopGen::Simulation::GeneticDrift - A simple genetic drift simulation  [view source]
• Bio::PopGen::Statistics - Population Genetics statistical tests  [view source]
• Bio::PopGen::TagHaplotype - Haplotype tag object.  [view source]
• Bio::PopGen::Utilities - Utilities for working with PopGen data and objects  [view source]
• Bio::PrimarySeq - Bioperl lightweight Sequence Object  [view source]
• Bio::PrimarySeqI - Interface definition for a Bio::PrimarySeq  [view source]
• Bio::PullParserI - A base module for fast 'pull' parsing  [view source]
• Bio::Range - Pure perl RangeI implementation  [view source]
• Bio::RangeI - Range interface  [view source]
• Bio::Restriction::Analysis - cutting sequences with restriction  [view source]
• Bio::Restriction::Enzyme - A single restriction endonuclease  [view source]
• Bio::Restriction::Enzyme::MultiCut - A single restriction endonuclease  [view source]
• Bio::Restriction::Enzyme::MultiSite - A single restriction endonuclease  [view source]
• Bio::Restriction::EnzymeCollection - Set of restriction endonucleases  [view source]
• Bio::Restriction::EnzymeI - Interface class for restriction endonuclease  [view source]
• Bio::Restriction::IO - Handler for sequence variation IO Formats  [view source]
• Bio::Restriction::IO::bairoch - bairoch enzyme set  [view source]
• Bio::Restriction::IO::base - base enzyme set  [view source]
• Bio::Restriction::IO::itype2 - itype2 enzyme set  [view source]
• Bio::Restriction::IO::prototype - prototype enzyme set  [view source]
• Bio::Restriction::IO::withrefm - withrefm enzyme set  [view source]
• Bio::Root::Build - A common Module::Build subclass base for BioPerl distributions  [view source]
• Bio::Root::Exception - Generic exception objects for Bioperl  [view source]
• Bio::Root::HTTPget - module for fallback HTTP get operations when  [view source]
• Bio::Root::IO - module providing several methods often needed when dealing with file IO  [view source]
• Bio::Root::Root - Hash-based implementation of Bio::Root::RootI  [view source]
• Bio::Root::RootI - Abstract interface to root object code  [view source]
• Bio::Root::Storable - object serialisation methods  [view source]
• Bio::Root::Test - A common base for all Bioperl test scripts.  [view source]
• Bio::Root::Test::Warn - Perl extension to test Bioperl methods for warnings  [view source]
• Bio::Root::Utilities - General-purpose utility module  [view source]
• Bio::Root::Version - provide global, distribution-level versioning  [view source]
• Bio::Search::BlastStatistics - An object for Blast statistics  [view source]
• Bio::Search::BlastUtils - Utility functions for Bio::Search:: BLAST objects  [view source]
• Bio::Search::DatabaseI - Interface for a database used in a sequence search  [view source]
• Bio::Search::GenericDatabase - Generic implementation of Bio::Search::DatabaseI  [view source]
• Bio::Search::GenericStatistics - An object for statistics  [view source]
• Bio::Search::Hit::BlastHit - Blast-specific subclass of Bio::Search::Hit::GenericHit  [view source]
• Bio::Search::Hit::BlastPullHit - A parser and hit object for BLASTN hits  [view source]
• Bio::Search::Hit::Fasta - Hit object specific for Fasta-generated hits  [view source]
• Bio::Search::Hit::GenericHit - A generic implementation of the Bio::Search::Hit::HitI interface  [view source]
• Bio::Search::Hit::HitFactory - A factory to create Bio::Search::Hit::HitI objects  [view source]
• Bio::Search::Hit::HitI - Interface for a hit in a similarity search result  [view source]
• Bio::Search::Hit::hmmer3Hit - DESCRIPTION of Object  [view source]
• Bio::Search::Hit::HMMERHit - A Hit module for HMMER hits  [view source]
• Bio::Search::Hit::HmmpfamHit - A parser and hit object for hmmpfam hits  [view source]
• Bio::Search::Hit::ModelHit - A model-based implementation of the Bio::Search::Hit::HitI interface  [view source]
• Bio::Search::Hit::PsiBlastHit - Bioperl BLAST Hit object  [view source]
• Bio::Search::Hit::PullHitI - Bio::Search::Hit::HitI interface for pull parsers.  [view source]
• Bio::Search::HSP::BlastHSP - Bioperl BLAST High-Scoring Pair object  [view source]
• Bio::Search::HSP::BlastPullHSP - A parser and HSP object for BlastN hsps  [view source]
• Bio::Search::HSP::FastaHSP - HSP object for FASTA specific data  [view source]
• Bio::Search::HSP::GenericHSP - A "Generic" implementation of a High Scoring Pair  [view source]
• Bio::Search::HSP::hmmer3HSP - DESCRIPTION of Object  [view source]
• Bio::Search::HSP::HMMERHSP - A HSP object for HMMER results  [view source]
• Bio::Search::HSP::HmmpfamHSP - A parser and HSP object for hmmpfam hsps  [view source]
• Bio::Search::HSP::HSPFactory - A factory to create Bio::Search::HSP::HSPI objects  [view source]
• Bio::Search::HSP::ModelHSP - A HSP object for model-based searches  [view source]
• Bio::Search::HSP::PsiBlastHSP - Bioperl BLAST High-Scoring Pair object  [view source]
• Bio::Search::HSP::PSLHSP - A HSP for PSL output  [view source]
• Bio::Search::HSP::PullHSPI - Bio::Search::HSP::HSPI interface for pull parsers.  [view source]
• Bio::Search::HSP::WABAHSP - HSP object suitable for describing WABA alignments  [view source]
• Bio::Search::Iteration::GenericIteration - A generic implementation of the Bio::Search::Iteration::IterationI interface.  [view source]
• Bio::Search::Iteration::IterationI - Abstract interface to an  [view source]
• Bio::Search::Processor - DESCRIPTION of Object  [view source]
• Bio::Search::Result::BlastPullResult - A parser and result object for BLASTN  [view source]
• Bio::Search::Result::BlastResult - Blast-specific subclass of Bio::Search::Result::GenericResult  [view source]
• Bio::Search::Result::CrossMatchResult - CrossMatch-specific subclass of Bio::Search::Result::GenericResult  [view source]
• Bio::Search::Result::GenericResult - Generic Implementation of  [view source]
• Bio::Search::Result::hmmer3Result - DESCRIPTION of Object  [view source]
• Bio::Search::Result::HMMERResult - A Result object for HMMER results  [view source]
• Bio::Search::Result::HmmpfamResult - A parser and result object for hmmpfam  [view source]
• Bio::Search::Result::PullResultI - Bio::Search::Result::ResultI interface for  [view source]
• Bio::Search::Result::ResultFactory - A factory to create Bio::Search::Result::ResultI objects  [view source]
• Bio::Search::Result::ResultI - Abstract interface to Search Result objects  [view source]
• Bio::Search::Result::WABAResult - Result object for WABA alignment output  [view source]
• Bio::Search::SearchUtils - Utility functions for Bio::Search:: objects  [view source]
• Bio::Search::StatisticsI - A Base object for statistics  [view source]
• Bio::Search::Tiling::MapTileUtils - utilities for manipulating closed intervals for an HSP tiling algorithm  [view source]
• Bio::Search::Tiling::MapTiling - An implementation of an HSP tiling  [view source]
• Bio::Search::Tiling::TilingI - Abstract interface for an HSP tiling module  [view source]
• Bio::SearchDist - A perl wrapper around Sean Eddy's histogram object  [view source]
• Bio::SearchIO - Driver for parsing Sequence Database Searches  [view source]
• Bio::SearchIO::axt - a parser for axt format reports  [view source]
• Bio::SearchIO::blast - Event generator for event based parsing of  [view source]
• Bio::SearchIO::blast_pull - A parser for BLAST output  [view source]
• Bio::SearchIO::blasttable - Driver module for SearchIO for parsing NCBI -m 8/9 format  [view source]
• Bio::SearchIO::blastxml - A SearchIO implementation of NCBI Blast XML parsing.  [view source]
• Bio::SearchIO::cross_match - CrossMatch-specific subclass of Bio::SearchIO  [view source]
• Bio::SearchIO::erpin - SearchIO-based ERPIN parser  [view source]
• Bio::SearchIO::EventHandlerI - An abstract Event Handler for Search Result parsing  [view source]
• Bio::SearchIO::exonerate - parser for Exonerate  [view source]
• Bio::SearchIO::fasta - A SearchIO parser for FASTA results  [view source]
• Bio::SearchIO::FastHitEventBuilder - Event Handler for SearchIO events.  [view source]
• Bio::SearchIO::gmap_f9 - Event generator for parsing gmap reports (Z format)  [view source]
• Bio::SearchIO::hmmer - A parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam)  [view source]
• Bio::SearchIO::hmmer2 - A parser for HMMER output (hmmpfam, hmmsearch)  [view source]
• Bio::SearchIO::hmmer3 - DESCRIPTION of Object  [view source]
• Bio::SearchIO::hmmer_pull - A parser for HMMER output  [view source]
• Bio::SearchIO::infernal - SearchIO-based Infernal parser  [view source]
• Bio::SearchIO::IteratedSearchResultEventBuilder - Event Handler for  [view source]
• Bio::SearchIO::megablast - a driver module for Bio::SearchIO to parse  [view source]
• Bio::SearchIO::psl - A parser for PSL output (UCSC)  [view source]
• Bio::SearchIO::rnamotif - SearchIO-based RNAMotif parser  [view source]
• Bio::SearchIO::SearchResultEventBuilder - Event Handler for SearchIO events.  [view source]
• Bio::SearchIO::SearchWriterI - Interface for outputting parsed Search results  [view source]
• Bio::SearchIO::sim4 - parser for Sim4 alignments  [view source]
• Bio::SearchIO::waba - SearchIO parser for Jim Kent WABA program  [view source]
• Bio::SearchIO::wise - Parsing of wise output as alignments  [view source]
• Bio::SearchIO::Writer::BSMLResultWriter - BSML output writer  [view source]
• Bio::SearchIO::Writer::GbrowseGFF - Interface for outputting parsed search results in Gbrowse GFF format  [view source]
• Bio::SearchIO::Writer::HitTableWriter - Tab-delimited data for Bio::Search::Hit::HitI objects  [view source]
• Bio::SearchIO::Writer::HSPTableWriter - Tab-delimited data for Bio::Search::HSP::HSPI objects  [view source]
• Bio::SearchIO::Writer::HTMLResultWriter - write a Bio::Search::ResultI in HTML  [view source]
• Bio::SearchIO::Writer::ResultTableWriter - Outputs tab-delimited data for each Bio::Search::Result::ResultI object.  [view source]
• Bio::SearchIO::Writer::TextResultWriter - Object to implement writing  [view source]
• Bio::SearchIO::XML::BlastHandler - XML Handler for NCBI Blast XML parsing.  [view source]
• Bio::SearchIO::XML::PsiBlastHandler - XML Handler for NCBI Blast PSIBLAST XML parsing.  [view source]
• Bio::Seq - Sequence object, with features  [view source]
• Bio::Seq::BaseSeqProcessor - Base implementation for a SequenceProcessor  [view source]
• Bio::Seq::EncodedSeq - subtype of L to store DNA that encodes a protein  [view source]
• Bio::Seq::LargeLocatableSeq - LocatableSeq object that stores sequence as  [view source]
• Bio::Seq::LargePrimarySeq - PrimarySeq object that stores sequence as  [view source]
• Bio::Seq::LargeSeq - SeqI compliant object that stores sequence as  [view source]
• Bio::Seq::LargeSeqI - Interface class for sequences that cache their  [view source]
• Bio::Seq::Meta - Generic superclass for sequence objects with  [view source]
• Bio::Seq::Meta::Array - array-based generic implementation of a  [view source]
• Bio::Seq::MetaI - Interface for sequence objects with residue-based  [view source]
• Bio::Seq::PrimaryQual - Bioperl lightweight Quality Object  [view source]
• Bio::Seq::PrimedSeq - A representation of a sequence and two primers  [view source]
• Bio::Seq::QualI - Interface definition for a Bio::Seq::Qual  [view source]
• Bio::Seq::Quality - Implementation of sequence with residue quality  [view source]
• Bio::Seq::RichSeq - Module implementing a sequence created from a rich  [view source]
• Bio::Seq::RichSeqI - interface for sequences from rich data sources, mostly databases  [view source]
• Bio::Seq::SeqBuilder - Configurable object builder for sequence stream parsers  [view source]
• Bio::Seq::SeqFactory - Instantiates a new Bio::PrimarySeqI (or derived class) through a factory  [view source]
• Bio::Seq::SeqFastaSpeedFactory - Instantiates a new Bio::PrimarySeqI (or derived class) through a factory  [view source]
• Bio::Seq::SequenceTrace - Bioperl object packaging a sequence with its trace  [view source]
• Bio::Seq::SeqWithQuality - Bioperl object packaging a sequence with its quality.  [view source]
• Bio::Seq::TraceI - Interface definition for a Bio::Seq::Trace  [view source]
• Bio::SeqAnalysisParserI - Sequence analysis output parser interface  [view source]
• Bio::SeqEvolution::DNAPoint - evolve a sequence by point mutations  [view source]
• Bio::SeqEvolution::EvolutionI - the interface for evolving sequences  [view source]
• Bio::SeqEvolution::Factory - Factory object to instantiate sequence evolving classes  [view source]
• Bio::SeqFeature::Annotated - PLEASE PUT SOMETHING HERE  [view source]
• Bio::SeqFeature::AnnotationAdaptor - integrates SeqFeatureIs annotation  [view source]
• Bio::SeqFeature::Collection - A container class for SeqFeatures  [view source]
• Bio::SeqFeature::CollectionI - An interface for a collection of SeqFeatureI objects.  [view source]
• Bio::SeqFeature::Computation - Computation SeqFeature  [view source]
• Bio::SeqFeature::FeaturePair - hold pair feature information e.g. blast hits  [view source]
• Bio::SeqFeature::Gene::Exon - a feature representing an exon  [view source]
• Bio::SeqFeature::Gene::ExonI - Interface for a feature representing an exon  [view source]
• Bio::SeqFeature::Gene::GeneStructure - A feature representing an arbitrarily complex structure of a gene  [view source]
• Bio::SeqFeature::Gene::GeneStructureI - A feature representing an arbitrarily  [view source]
• Bio::SeqFeature::Gene::Intron - An intron feature  [view source]
• Bio::SeqFeature::Gene::NC_Feature - superclass for non-coding features  [view source]
• Bio::SeqFeature::Gene::Poly_A_site - poly A feature  [view source]
• Bio::SeqFeature::Gene::Promoter - Describes a promoter  [view source]
• Bio::SeqFeature::Gene::Transcript - A feature representing a transcript  [view source]
• Bio::SeqFeature::Gene::TranscriptI - Interface for a feature representing a  [view source]
• Bio::SeqFeature::Gene::UTR - A feature representing an untranslated region  [view source]
• Bio::SeqFeature::Generic - Generic SeqFeature  [view source]
• Bio::SeqFeature::Lite - Lightweight Bio::SeqFeatureI class  [view source]
• Bio::SeqFeature::PositionProxy - handle features when truncation/revcom sequences span a feature  [view source]
• Bio::SeqFeature::Primer - Primer Generic SeqFeature  [view source]
• Bio::SeqFeature::Similarity - A sequence feature based on similarity  [view source]
• Bio::SeqFeature::SimilarityPair - Sequence feature based on the similarity  [view source]
• Bio::SeqFeature::SiRNA::Oligo - Perl object for small inhibitory RNAs.  [view source]
• Bio::SeqFeature::SiRNA::Pair - Perl object for small inhibitory RNA  [view source]
• Bio::SeqFeature::Tools::FeatureNamer - generates unique persistent names for features  [view source]
• Bio::SeqFeature::Tools::IDHandler - maps $seq_feature-Eprimary_tag  [view source]
• Bio::SeqFeature::Tools::TypeMapper - maps $seq_feature-Eprimary_tag  [view source]
• Bio::SeqFeature::Tools::Unflattener - turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy  [view source]
• Bio::SeqFeature::TypedSeqFeatureI - a strongly typed SeqFeature  [view source]
• Bio::SeqFeatureI - Abstract interface of a Sequence Feature  [view source]
• Bio::SeqI - [Developers] Abstract Interface of Sequence (with features)  [view source]
• Bio::SeqIO - Handler for SeqIO Formats  [view source]
• Bio::SeqIO::abi - abi trace sequence input/output stream  [view source]
• Bio::SeqIO::ace - ace sequence input/output stream  [view source]
• Bio::SeqIO::agave - AGAVE sequence output stream.  [view source]
• Bio::SeqIO::alf - alf trace sequence input/output stream  [view source]
• Bio::SeqIO::asciitree - asciitree sequence input/output stream  [view source]
• Bio::SeqIO::bsml - BSML sequence input/output stream  [view source]
• Bio::SeqIO::bsml_sax - BSML sequence input/output stream using SAX  [view source]
• Bio::SeqIO::chadoxml - chadoxml sequence output stream  [view source]
• Bio::SeqIO::chaos - chaos sequence input/output stream  [view source]
• Bio::SeqIO::chaosxml - chaosxml sequence input/output stream  [view source]
• Bio::SeqIO::ctf - ctf trace sequence input/output stream  [view source]
• Bio::SeqIO::embl - EMBL sequence input/output stream  [view source]
• Bio::SeqIO::embldriver - EMBL sequence input/output stream  [view source]
• Bio::SeqIO::entrezgene - Entrez Gene ASN1 parser  [view source]
• Bio::SeqIO::excel - sequence input/output stream from a  [view source]
• Bio::SeqIO::exp - exp trace sequence input/output stream  [view source]
• Bio::SeqIO::fasta - fasta sequence input/output stream  [view source]
• Bio::SeqIO::fastq - fastq sequence input/output stream  [view source]
• Bio::SeqIO::flybase_chadoxml - FlyBase variant of chadoxml with sequence output stream  [view source]
• Bio::SeqIO::FTHelper - Helper class for Embl/Genbank feature tables  [view source]
• Bio::SeqIO::game - a class for parsing and writing game-XML  [view source]
• Bio::SeqIO::game::featHandler - a class for handling feature elements  [view source]
• Bio::SeqIO::game::gameHandler - PerlSAX handler for game-XML  [view source]
• Bio::SeqIO::game::gameSubs - a base class for game-XML parsing  [view source]
• Bio::SeqIO::game::gameWriter - a class for writing game-XML  [view source]
• Bio::SeqIO::game::seqHandler - a class for handling game-XML sequences  [view source]
• Bio::SeqIO::gbdriver - GenBank handler-based push parser  [view source]
• Bio::SeqIO::gbxml - GenBank sequence input/output stream using SAX  [view source]
• Bio::SeqIO::gcg - GCG sequence input/output stream  [view source]
• Bio::SeqIO::genbank - GenBank sequence input/output stream  [view source]
• Bio::SeqIO::Handler::GenericRichSeqHandler - Bio::HandlerI-based  [view source]
• Bio::SeqIO::interpro - InterProScan XML input/output stream  [view source]
• Bio::SeqIO::kegg - KEGG sequence input/output stream  [view source]
• Bio::SeqIO::largefasta - method i/o on very large fasta sequence files  [view source]
• Bio::SeqIO::lasergene - Lasergene sequence file input/output stream  [view source]
• Bio::SeqIO::locuslink - LocusLink input/output stream  [view source]
• Bio::SeqIO::mbsout - input stream for output by Teshima et al.'s mbs.  [view source]
• Bio::SeqIO::metafasta - metafasta sequence input/output stream  [view source]
• Bio::SeqIO::msout - input stream for output by Hudson's ms  [view source]
• Bio::SeqIO::MultiFile - Treating a set of files as a single input stream  [view source]
• Bio::SeqIO::nexml - NeXML sequence input/output stream  [view source]
• Bio::SeqIO::phd - phd file input/output stream  [view source]
• Bio::SeqIO::pir - PIR sequence input/output stream  [view source]
• Bio::SeqIO::pln - pln trace sequence input/output stream  [view source]
• Bio::SeqIO::qual - .qual file input/output stream  [view source]
• Bio::SeqIO::raw - raw sequence file input/output stream  [view source]
• Bio::SeqIO::scf - .scf file input/output stream  [view source]
• Bio::SeqIO::seqxml - SeqXML sequence input/output stream  [view source]
• Bio::SeqIO::strider - DNA strider sequence input/output stream  [view source]
• Bio::SeqIO::swiss - Swissprot sequence input/output stream  [view source]
• Bio::SeqIO::swissdriver - SwissProt/UniProt handler-based push parser  [view source]
• Bio::SeqIO::tab - nearly raw sequence file input/output  [view source]
• Bio::SeqIO::table - sequence input/output stream from a delimited table  [view source]
• Bio::SeqIO::tigr - TIGR XML sequence input/output stream  [view source]
• Bio::SeqIO::tigrxml - Parse TIGR (new) XML  [view source]
• Bio::SeqIO::tinyseq - reading/writing sequences in NCBI TinySeq format  [view source]
• Bio::SeqIO::tinyseq::tinyseqHandler - XML event handlers to support NCBI TinySeq XML parsing  [view source]
• Bio::SeqIO::ztr - ztr trace sequence input/output stream  [view source]
• Bio::SeqUtils - Additional methods for PrimarySeq objects  [view source]
• Bio::SimpleAlign - Multiple alignments held as a set of sequences  [view source]
• Bio::SimpleAnalysisI - A simple interface to any (local or remote) analysis tool  [view source]
• Bio::Species - Generic species object.  [view source]
• Bio::Structure::Atom - Bioperl structure Object, describes an Atom  [view source]
• Bio::Structure::Chain - Bioperl structure Object, describes a chain  [view source]
• Bio::Structure::Entry - Bioperl structure Object, describes the whole entry  [view source]
• Bio::Structure::IO - Handler for Structure Formats  [view source]
• Bio::Structure::IO::pdb - PDB input/output stream  [view source]
• Bio::Structure::Model - Bioperl structure Object, describes a Model  [view source]
• Bio::Structure::Residue - Bioperl structure Object, describes a Residue  [view source]
• Bio::Structure::SecStr::DSSP::Res - Module for parsing/accessing dssp output  [view source]
• Bio::Structure::SecStr::STRIDE::Res - Module for parsing/accessing stride output  [view source]
• Bio::Structure::StructureI - Abstract Interface for a Structure objects  [view source]
• Bio::Symbol::Alphabet - BSANE/BioCORBA compliant symbol list alphabet  [view source]
• Bio::Symbol::AlphabetI - A Symbol Alphabet  [view source]
• Bio::Symbol::DNAAlphabet - A ready made DNA alphabet  [view source]
• Bio::Symbol::ProteinAlphabet - A ready made Protein alphabet  [view source]
• Bio::Symbol::Symbol - A biological symbol  [view source]
• Bio::Symbol::SymbolI - Interface for a Symbol  [view source]
• Bio::Taxon - A node in a represented taxonomy  [view source]
• Bio::Taxonomy - representing Taxonomy.  [view source]
• Bio::Taxonomy::FactoryI - interface to define how to access NCBI Taxonoy  [view source]
• Bio::Taxonomy::Node - A node in a represented taxonomy  [view source]
• Bio::Taxonomy::Taxon - Generic Taxonomic Entity object  [view source]
• Bio::Taxonomy::Tree - An Organism Level Implementation of TreeI interface.  [view source]
• Bio::Tools::AlignFactory - Base object for alignment factories  [view source]
• Bio::Tools::Alignment::Consed - A module to work with objects from consed .ace files  [view source]
• Bio::Tools::Alignment::Trim - A kludge to do specialized trimming of  [view source]
• Bio::Tools::Analysis::DNA::ESEfinder - a wrapper around ESEfinder  [view source]
• Bio::Tools::Analysis::Protein::Domcut - a wrapper around Domcut server  [view source]
• Bio::Tools::Analysis::Protein::ELM - a wrapper around the ELM server which predicts short functional motifs on amino acid sequences  [view source]
• Bio::Tools::Analysis::Protein::GOR4 - a wrapper around GOR4 protein  [view source]
• Bio::Tools::Analysis::Protein::HNN - a wrapper around the HNN protein  [view source]
• Bio::Tools::Analysis::Protein::Mitoprot - a wrapper around Mitoprot  [view source]
• Bio::Tools::Analysis::Protein::NetPhos - a wrapper around NetPhos server  [view source]
• Bio::Tools::Analysis::Protein::Scansite - a wrapper around the Scansite server  [view source]
• Bio::Tools::Analysis::Protein::Sopma - a wrapper around the  [view source]
• Bio::Tools::Analysis::SimpleAnalysisBase - abstract superclass for  [view source]
• Bio::Tools::AnalysisResult - Base class for analysis result objects and parsers  [view source]
• Bio::Tools::Blat - parser for Blat program  [view source]
• Bio::Tools::CodonTable - Codon table object  [view source]
• Bio::Tools::Coil - parser for Coil output  [view source]
• Bio::Tools::dpAlign - Perl extension to do pairwise dynamic programming sequence alignment  [view source]
• Bio::Tools::ECnumber - representation of EC numbers (Enzyme Classification)  [view source]
• Bio::Tools::EMBOSS::Palindrome - parse EMBOSS palindrome output  [view source]
• Bio::Tools::EPCR - Parse ePCR output and make features  [view source]
• Bio::Tools::Eponine - Results of one Eponine run  [view source]
• Bio::Tools::ERPIN - a parser for ERPIN output  [view source]
• Bio::Tools::Est2Genome - Parse est2genome output, makes simple Bio::SeqFeature::Generic objects  [view source]
• Bio::Tools::ESTScan - Results of one ESTScan run  [view source]
• Bio::Tools::EUtilities - NCBI eutil XML parsers  [view source]
• Bio::Tools::EUtilities::EUtilDataI - eutil data object interface  [view source]
• Bio::Tools::EUtilities::EUtilParameters - Manipulation of NCBI eutil-based  [view source]
• Bio::Tools::EUtilities::History - lightweight implementation of HistoryI  [view source]
• Bio::Tools::EUtilities::HistoryI - simple extension of EUtilDataI interface  [view source]
• Bio::Tools::EUtilities::Info - interface class for storing einfo data  [view source]
• Bio::Tools::EUtilities::Info::FieldInfo - class for storing einfo field data  [view source]
• Bio::Tools::EUtilities::Info::LinkInfo - class for storing einfo link data  [view source]
• Bio::Tools::EUtilities::Link - general API for accessing data retrieved from elink queries  [view source]
• Bio::Tools::EUtilities::Link::LinkSet - class for EUtils LinkSets  [view source]
• Bio::Tools::EUtilities::Link::UrlLink - class for EUtils UrlLinks  [view source]
• Bio::Tools::EUtilities::Query - parse and collect esearch, epost, espell,  [view source]
• Bio::Tools::EUtilities::Query::GlobalQuery - container class for egquery data  [view source]
• Bio::Tools::EUtilities::Summary - class for handling data output (XML) from  [view source]
• Bio::Tools::EUtilities::Summary::DocSum - data object for document summary data  [view source]
• Bio::Tools::EUtilities::Summary::Item - simple layered object for DocSum item data  [view source]
• Bio::Tools::EUtilities::Summary::ItemContainerI - abtract interface methods  [view source]
• Bio::Tools::Fgenesh - parse results of one Fgenesh run  [view source]
• Bio::Tools::FootPrinter - write sequence features in FootPrinter format  [view source]
• Bio::Tools::Gel - Calculates relative electrophoretic migration distances  [view source]
• Bio::Tools::Geneid - Results of one geneid run  [view source]
• Bio::Tools::Genemark - Results of one Genemark run  [view source]
• Bio::Tools::Genewise - Results of one Genewise run  [view source]
• Bio::Tools::Genomewise - Results of one Genomewise run  [view source]
• Bio::Tools::Genscan - Results of one Genscan run  [view source]
• Bio::Tools::GFF - A Bio::SeqAnalysisParserI compliant GFF format parser  [view source]
• Bio::Tools::Glimmer - parser for Glimmer 2.X/3.X prokaryotic and  [view source]
• Bio::Tools::Grail - Results of one Grail run  [view source]
• Bio::Tools::GuessSeqFormat - Module for determining the sequence  [view source]
• Bio::Tools::HMMER::Domain - One particular domain hit from HMMER  [view source]
• Bio::Tools::HMMER::Results - Object representing HMMER output results  [view source]
• Bio::Tools::HMMER::Set - Set of identical domains from HMMER matches  [view source]
• Bio::Tools::Hmmpfam - Parser for Hmmpfam program  [view source]
• Bio::Tools::Infernal - A parser for Infernal output  [view source]
• Bio::Tools::ipcress - Parse ipcress output and make features  [view source]
• Bio::Tools::isPcr - Parse isPcr output and make features  [view source]
• Bio::Tools::IUPAC - Generates unique Seq objects from an ambiguous Seq object  [view source]
• Bio::Tools::Lucy - Object for analyzing the output from Lucy,  [view source]
• Bio::Tools::Match - Parses output from Transfac's match(TM)  [view source]
• Bio::Tools::MZEF - Results of one MZEF run  [view source]
• Bio::Tools::OddCodes - Object holding alternative alphabet coding for  [view source]
• Bio::Tools::Phylo::Gerp - Parses output from GERP  [view source]
• Bio::Tools::Phylo::Gumby - Parses output from gumby  [view source]
• Bio::Tools::Phylo::Molphy - parser for Molphy output  [view source]
• Bio::Tools::Phylo::Molphy::Result - container for data parsed from a ProtML run  [view source]
• Bio::Tools::Phylo::PAML - Parses output from the PAML programs codeml,  [view source]
• Bio::Tools::Phylo::PAML::Codeml - Parses output from the PAML program codeml.  [view source]
• Bio::Tools::Phylo::PAML::ModelResult - A container for NSSite Model Result from PAML  [view source]
• Bio::Tools::Phylo::PAML::Result - A PAML result set object  [view source]
• Bio::Tools::Phylo::Phylip::ProtDist - parser for ProtDist output  [view source]
• Bio::Tools::pICalculator - calculate the isoelectric point of a protein  [view source]
• Bio::Tools::Prediction::Exon - A predicted exon feature  [view source]
• Bio::Tools::Prediction::Gene - a predicted gene structure feature  [view source]
• Bio::Tools::Primer3 - Create input for and work with the output from  [view source]
• Bio::Tools::Primer::Assessor::Base - base class for common assessor things  [view source]
• Bio::Tools::Primer::AssessorI - interface for assessing primer pairs  [view source]
• Bio::Tools::Primer::Feature - position of a single primer  [view source]
• Bio::Tools::Primer::Pair - two primers on left and right side  [view source]
• Bio::Tools::Prints - Parser for FingerPRINTScanII program  [view source]
• Bio::Tools::Profile - parse Profile output  [view source]
• Bio::Tools::Promoterwise - parser for Promoterwise tab format output  [view source]
• Bio::Tools::PrositeScan - Parser for ps_scan result  [view source]
• Bio::Tools::Protparam - submit to and parse output from protparam ;  [view source]
• Bio::Tools::Pseudowise - Results of one Pseudowise run  [view source]
• Bio::Tools::pSW - pairwise Smith Waterman object  [view source]
• Bio::Tools::QRNA - A Parser for qrna output  [view source]
• Bio::Tools::RandomDistFunctions - A set of routines useful for  [view source]
• Bio::Tools::RepeatMasker - a parser for RepeatMasker output  [view source]
• Bio::Tools::RNAMotif - A parser for RNAMotif output  [view source]
• Bio::Tools::Run::GenericParameters - An object for the parameters used to run programs  [view source]
• Bio::Tools::Run::ParametersI - A Base object for the parameters used to run programs  [view source]
• Bio::Tools::Run::RemoteBlast - Object for remote execution of the NCBI Blast  [view source]
• Bio::Tools::Run::StandAloneBlast - Object for the local execution  [view source]
• Bio::Tools::Run::StandAloneNCBIBlast - Object for the local execution  [view source]
• Bio::Tools::Run::StandAloneWUBlast - Object for the local execution  [view source]
• Bio::Tools::Run::WrapperBase - A Base object for wrappers around executables  [view source]
• Bio::Tools::Seg - parse C output  [view source]
• Bio::Tools::SeqPattern - represent a sequence pattern or motif  [view source]
• Bio::Tools::SeqPattern::Backtranslate - Bio::Tools::SeqPattern::Backtranslate documentation  [view source]
• Bio::Tools::SeqStats - Object holding statistics for one  [view source]
• Bio::Tools::SeqWords - Object holding n-mer statistics for a sequence  [view source]
• Bio::Tools::Sigcleave - Bioperl object for sigcleave analysis  [view source]
• Bio::Tools::Signalp - parser for Signalp output  [view source]
• Bio::Tools::Signalp::ExtendedSignalp - enhanced parser for Signalp output  [view source]
• Bio::Tools::Sim4::Exon - A single exon determined by an alignment  [view source]
• Bio::Tools::Sim4::Results - Results of one Sim4 run  [view source]
• Bio::Tools::SiRNA::Ruleset::saigo - Perl object implementing the Saigo  [view source]
• Bio::Tools::SiRNA::Ruleset::tuschl - Perl object implementing the  [view source]
• Bio::Tools::Spidey::Exon - A single exon determined by an alignment  [view source]
• Bio::Tools::Spidey::Results - Results of a Spidey run  [view source]
• Bio::Tools::TandemRepeatsFinder - a parser for Tandem Repeats Finder output  [view source]
• Bio::Tools::TargetP - Results of one TargetP run  [view source]
• Bio::Tools::Tmhmm - parse TMHMM output (TransMembrane HMM)  [view source]
• Bio::Tools::tRNAscanSE - A parser for tRNAscan-SE output  [view source]
• Bio::Tree::AlleleNode - A Node with Alleles attached  [view source]
• Bio::Tree::AnnotatableNode - A Tree Node with support for annotation  [view source]
• Bio::Tree::Compatible - Testing compatibility of phylogenetic trees  [view source]
• Bio::Tree::DistanceFactory - Construct a tree using distance based methods  [view source]
• Bio::Tree::Draw::Cladogram - Drawing phylogenetic trees in  [view source]
• Bio::Tree::Node - A Simple Tree Node  [view source]
• Bio::Tree::NodeI - Interface describing a Tree Node  [view source]
• Bio::Tree::NodeNHX - A Simple Tree Node with support for NHX tags  [view source]
• Bio::Tree::RandomFactory - TreeFactory for generating Random Trees  [view source]
• Bio::Tree::Statistics - Calculate certain statistics for a Tree  [view source]
• Bio::Tree::Tree - An Implementation of TreeI interface.  [view source]
• Bio::Tree::TreeFunctionsI - Decorated Interface implementing basic Tree exploration methods  [view source]
• Bio::Tree::TreeI - A Tree object suitable for lots of things, designed  [view source]
• Bio::TreeIO - Parser for Tree files  [view source]
• Bio::TreeIO::cluster - A TreeIO driver module for parsing Algorithm::Cluster::treecluster() output  [view source]
• Bio::TreeIO::lintree - Parser for lintree output trees  [view source]
• Bio::TreeIO::newick - TreeIO implementation for parsing  [view source]
• Bio::TreeIO::nexml - A TreeIO driver module for parsing NeXML tree files  [view source]
• Bio::TreeIO::nexus - A TreeIO driver module for parsing Nexus tree output from PAUP  [view source]
• Bio::TreeIO::nhx - TreeIO implementation for parsing  [view source]
• Bio::TreeIO::pag - Bio::TreeIO driver for Pagel format  [view source]
• Bio::TreeIO::phyloxml - TreeIO implementation for parsing PhyloXML format.  [view source]
• Bio::TreeIO::svggraph - A simple output format that converts a Tree object to an SVG output  [view source]
• Bio::TreeIO::tabtree - A simple output format which displays a tree as an ASCII drawing  [view source]
• Bio::TreeIO::TreeEventBuilder - Build Bio::Tree::Tree's and  [view source]
• Bio::UpdateableSeqI - Descendant of Bio::SeqI that allows updates  [view source]
• Bio::Variation::AAChange - Sequence change class for polypeptides  [view source]
• Bio::Variation::AAReverseMutate - point mutation and codon  [view source]
• Bio::Variation::Allele - Sequence object with allele-specific attributes  [view source]
• Bio::Variation::DNAMutation - DNA level mutation class  [view source]
• Bio::Variation::IO - Handler for sequence variation IO Formats  [view source]
• Bio::Variation::IO::flat - flat file sequence variation input/output stream  [view source]
• Bio::Variation::IO::xml - XML sequence variation input/output stream  [view source]
• Bio::Variation::RNAChange - Sequence change class for RNA level  [view source]
• Bio::Variation::SeqDiff - Container class for mutation/variant descriptions  [view source]
• Bio::Variation::SNP - submitted SNP  [view source]
• Bio::Variation::VariantI - Sequence Change SeqFeature abstract class  [view source]
• Bio::WebAgent - A base class for Web (any protocol) access  [view source]