-
-
29 Sep 2009 16:43:11 UTC
- Browse (raw)
- Changes
- How to Contribute
- Issues
- Testers (660 / 23 / 0)
- Kwalitee
Bus factor: 2- License: unknown
24 month- Download (9.98MB)
- MetaCPAN Explorer
- Permissions
- Subscribe to distribution
- This version
- Latest version
Changes for version 1.6.0_1
- Bio::Align::DNAStatistics
- fix divide by zero problem [jason]
- Bio::AlignIO::*
- bug 2813 - fix faulty logic to detect end-of-stream [cjfields]
- Bio::AlignIO::stockholm
- bug 2796 - fix faulty logic to detect end-of-stream [cjfields]
- Bio::Assembly::Tools::ContigSpectrum
- function to score contig spectrum [fangly]
- Bio::DB::EUtilities
- small updates [cjfields]
- Bio::DB::Fasta
- berkeleydb database now autoindexes wig files and locks correctly
- lstein
- berkeleydb database now autoindexes wig files and locks correctly
- Bio::DB::HIV
- various small updates for stability; tracking changes to LANL database interface [maj]
- Bio::DB::SeqFeature (lots of updates and changes)
- add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain]
- bug 2835 - patch [Dan Bolser]
- bug RT 44535 - patch FeatureFileLoader [Cathy Gresham]
- Bio::DB::SwissProt
- bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders]
- Bio::Factory::FTLocationFactory
- mailing list bug fix [cjfields]
- Bio::LocatableSeq
- performance work on column_from_residue_number [hartzell]
- Bio::Matrix::IO::phylip
- bug 2800 - patch to fix phylip parsing [Wei Zou]
- Bio::Nexml
- Google Summer of Code project from Chase Miller - parsers for Nexml file format [maj, chmille4]
- Bio::PopGen
- Make Individual, Population, Marker objects AnnotatableI [maj]
- simplify LD code [jason]
- Bio::RangeI
- deal with empty intersection [jason]
- Bio::Restriction
- significant overhaul of Bio::Restriction system: complete support for external and non-palindromic cutters. [maj]
- Bio::Root::Build
- CPANPLUS support, no automatic installation [sendu]
- Bio::Root::IO
- allow IO::String (regression fix) [cjfields]
- catch unintentional undef values [cjfields]
- throw if non-fh is passed to -fh [maj]
- Bio::Root::Root/RootI
- small debugging and core fixes [cjfields]
- Bio::Root::Test
- bug RT 48813 - fix for Strawberry Perl bug [kmx]
- Bio::Root::Utilities
- bug 2737 - better warnings [cjfields]
- Bio::Search
- tiling completely refactored, HOWTO added [maj] NOTE : Bio::Search::Hit::* classes do not use this code directly; we will deprecate usage of the older tiling code in the next BioPerl release
- small fixes [cjfields]
- Bio::SearchIO
- Infernal 1.0 output now parsed [cjfields]
- new parser for gmap -f9 output [hartzell]
- bug 2852 - fix infinite loop in some output [cjfields]
- blastxml output now passes all TODO tests [cjfields]
- bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
- RT 44782 - GbrowseGFF writer now catches evalues [Allen Day]
- bug 2575 - add two columns of additional output to HSPTableWriter [cjfields]
- Bio::Seq::LargePrimarySeq
- delete tempdirs [cjfields]
- bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
- Bio::Seq::Quality
- extract regions based on quality threshold value [Dan Bolser, heikki]
- bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi)
- Bio::SeqFeature::Lite
- various Bio::DB::SeqFeature-related fixes [lstein]
- Bio::SeqFeature::Tools::TypeMapper
- additional terms for GenBank to SO map [scain]
- Bio::SeqIO::chadoxml
- bug 2785 - patch to get this working for bp_seqconvert [cjfields]
- Bio::SeqIO::embl
- support for CDS records [dave_messina, Sylvia]
- Bio::SeqIO::fastq
- complete refactoring to handle all FASTQ variants, perform validation, write output. API now conforms with other Bio* parsers and the rest of Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
- cjfields
- complete refactoring to handle all FASTQ variants, perform validation, write output. API now conforms with other Bio* parsers and the rest of Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
- Bio::SeqIO::genbank
- bug 2784 - fix DBSOURCE issue [Phillip Garland]
- bug RT 44536 - support for UniProt/UniProtKB tests [cjfields]
- Bio::SeqIO::largefasta
- parser returns a Bio::Seq::LargePrimarySeq [jhannah]
- Bio::SeqIO::raw
- add option for 'single' and 'multiple'
- Bio::SeqIO::scf
- bug 2881 - fix scf round-tripping [Adam Sj¿gren]
- Bio::SeqUtils
- bug 2766, 2810 - copy over tags from features, doc fixes [David Jackson]
- Bio::SimpleAlign
- bug 2793 - patch for add_seq index issue [jhannah, maj]
- bug 2801 - throw if args are required [cjfields]
- bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types
- Tristan Lefebure, maj
- bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi]
- fix POD and add get_SeqFeatures filter [maj]
- Bio::Tools::dpAlign
- add support for LocatableSeq [ymc]
- to be moved to a separate distribution [cjfields, rbuels]
- Bio::Tools::EUtilities
- fix for two bugs from mail list [Adam Whitney, cjfields]
- add generic ItemContainerI interface for containing same methods
- cjfields
- Bio::Tools::HMM
- fix up code, add more warnings [cjfields]
- to be moved to a separate distribution [cjfields, rbuels]
- Bio::Tools::Primer3
- bug 2862 - fenceposting issue fixed [maj]
- Bio::Tools::Run::RemoteBlast
- tests for remote RPS-BLAST [mcook]
- Bio::Tools::SeqPattern
- bug 2844 - backtranslate method [rbuels, jhannah, bvecchi]
- Bio::Tools::tRNAscanSE
- use 'gene' and 'exon' for proper SO, ensure ID is unique [jason]
- Bio::Tree::*
- bug 2456 - fix reroot_tree(), added create_node_on_branch() [maj]
- Bio::Tree::Statistics
- several methods for calculating Fitch-based score, internal trait values, statratio(), sum of leaf distances [heikki]
- Bio::Tree::Tree
- bug 2869 - add docs indicating edge case where nodes can be prematurely garbage-collected [cjfields]
- add as_text() function to create Tree as a string in specified format
- maj
- Bio::Tree::TreeFunctionsI
- bug 2877 - fix bug where bootstrap assigned to the wrong node [Tristan Lefebure, maj]
- Bio::TreeIO::newick
- fix small semicolon issue [cjfields]
- scripts
- update to bp_seqfeature_load for SQLite [lstein]
- hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
- fastam9_to_table - fix for MPI output [jason]
- gccalc - total stats [jason]
- General Stuff
- POD cleanup re: FEEDBACK section [maj, cjfields]
- cleanup or fix dead links [cjfields]
- Use of no_* methods (indicating 'number of something') is deprecated in favor of num_* [cjfields]
- lots of new tests for the above bugs and refactors [everyone!]
- new template for Komodo text editor [cjfields]
Changes for version 1.6.1
- No change from last alpha except VERSION and doc updates [cjfields]
Documentation
extracts BioPerl documentation and indexes it in a database for easy retrievalcheck modules and scripts for authors not in AUTHORS filecheck NAME in module POD has fully qualified object namevalidate URLs located in module code and PODconvert cvs log messages to changelogscheck modules and scripts for dependencies not in coreCheck modules and scripts for use of deprecated modules and methods, indicates presence in a file to STDERR. Optionally accepts new modules and adds them to a newly formatted deprecation file.information about modules in BioPerl corecheck the POD documentation syntax in modules and scriptsinstall script to create symbolic linksModules
An interface for describing sequence alignments.Calculate some statistics for a DNA alignmentBase statistic object for Pairwise AlignmentsCalculate Protein Alignment statistics (mostly distances)Calculate some statistics for an alignmentA collection of utilities regarding converting and manipulating alignment objectsHandler for AlignIO FormatsBio::HandlerI-based generic data handler class for alignment-based dataARP MSA Sequence input/output streambl2seq sequence input/output streamclustalw sequence input/output streamParse EMBOSS alignment output (from applications water and needle)fasta MSA Sequence input/output streamLargemultifasta MSA Sequence input/output streamMultiple Alignment Format sequence input streammase sequence input/output streamParse and Create MEGA format data filesmeme sequence input/output streamMetafasta MSA Sequence input/output streammsf sequence input/output streamNEXUS format sequence input/output streampfam sequence input/output streamPHYLIP format sequence input/output streampo MSA Sequence input/output streamproda sequence input/output streamprodom sequence input/output streamRead/Write PSI-BLAST profile alignment filesselex sequence input/output streamstockholm sequence input/output streamXMFA MSA Sequence input/output streamAn interface to any (local or remote) analysis toolGeneric analysis output parser interfaceInterface for analysis result objectsthe base interface an annotatable object must implementInstantiates a new Bio::AnnotationI (or derived class) through a factoryDefault Perl implementation of AnnotationCollectionIA comment object, holding textuntyped links between databasesAn ontology term adapted to AnnotationISpecialised DBLink object for Literature ReferencesRelationship (pairwise) with other objects SeqI and NodeI;A simple scalarA scalar with embedded structured informationAnnotationI with tree-like hierarchal key-value relationships ('structured tags') that can be represented as simple text.Provides an object which represents a target (ie, a similarity hit) from one object to something in another databaseProvide a tree as an annotation to a Bio::AnnotatableI objectManages types for annotation collectionsInterface for annotation collectionsAnnotation interfacePerl module to hold and manipulate sequence assembly contigs.Perform analysis on sequence assembly contigs.Handler for Assembly::IO Formatsmodule to load ACE files from various assembly programsdriver to load phrap.out files.Driver to read and write assembly files in the TIGR Assembler v2 default format.Perl module to hold and manipulate sequence assembly data.Abstract Inteface of Sequence AssembliesPerl module to hold and manipulate singlets from sequence assembly contigs.create and manipulate contig spectraA Bibliographic Query Service moduleRepresentation of a general articleAn abstract base for other biblio classesRepresentation of a bookRepresentation of a book articleHandling the bibliographic referencesA converter of a raw hash to MEDLINE citationsA converter of XML files with MEDLINE citationsA converter of a raw hash to PUBMED citationsA converter of XML files with PUBMED citationsRepresentation of a journalRepresentation of a journal articleRepresentation of a MEDLINE articleRepresentation of a MEDLINE bookRepresentation of a MEDLINE book articleRepresentation of a MEDLINE journalRepresentation of a MEDLINE journal articleRepresentation of an organisationRepresentation of a patentRepresentation of a personRepresentation of a conference proceedingRepresentation of a general providerRepresentation of a PUBMED articleRepresentation of a PUBMED book articleRepresentation of a PUBMED journal articleRepresentation of a bibliographic referenceRepresentation of a provider of type serviceRepresentation of a technical reportRepresentation of thesisRepresentation of a web resourceInstantiates a new Bio::ClusterI (or derived class) through a factoryFamily InterfaceSequence Family objectUniGene objectabstract interface of UniGene objectCluster InterfaceHandler for Cluster FormatsdbSNP input streamUniGene input streamfor reading and writing codon usage tables to filefor access to the Codon usage Database at http://www.kazusa.or.jp/codon.Mapping locations through a chain of coordinate mappersNoncontinuous match between two coordinate setsContinuous match between two coordinate setstransformations between gene related coordinate systemsFinds shortest path between nodes in a graphInterface describing coordinate mappersContinuous match between two coordinate setsResults from coordinate transformationAnother name for Bio::Location::SimpleAnother name for Bio::Location::SimpleInterface to identify coordinate mapper resultsAdditional methods to create Bio::Coordinate objectsDatabase object interface to ACeDB serversA BioFetch-based access to a bibliographic citation retrievalAccess to PubMed's bibliographic query serviceA SOAP-based access to a bibliographic query serviceAn interface to a Bibliographic Query ServiceDatabase object interface to BioFetch retrievalfor access to the Codon usage Database at http://www.kazusa.or.jp/codon.Database object for retrieving using the dbfetch scriptDatabase object interface for EMBL entry retrievalwebagent which interacts with and retrieves data from NCBI's eUtilsDatabase object interface to Entrez GeneDESCRIPTION of Object*** DESCRIPTION of ClassA Bio::DB::RandomAccessI compliant class which wraps a prioritized list of DBsFast indexed access to a directory of fasta filesIn file cache for BioSeq objectsInterface for indexed flat filesInterface for BioHackathon standard BDB-indexed flat fileembl adaptor for Open-bio standard BDB-indexed flat filefasta adaptor for Open-bio standard BDB-indexed flat filegenbank adaptor for Open-bio standard BDB-indexed flat fileswissprot adaptor for Open-bio standard BDB-indexed flat fileBinarySearch search indexing system for sequence filesStorage and retrieval of sequence annotation dataace interface (for multiple inheritance)Bio::DB::GFF database adaptor for in-memory databasesiterator for Bio::DB::GFF::Adaptor::berkeleydbCache BioFetch objects in a Bio::DB::GFF databaseCache BioFetch objects in a Bio::DB::GFF databaseDatabase adaptor for DBI (SQL) databasesCache for database handlesiterator for Bio::DB::GFF::Adaptor::dbiDatabase adaptor for a specific mysql schemaUnholy union between mysql GFF database and acedb databaseDatabase adaptor for an integraded CMap/GBrowse mysql schemaDeprecated database adaptorDatabase adaptor for a specific oracle schemaUnholy union between oracle GFF database and acedb databaseDatabase adaptor for a specific postgres schemaDatabase adaptor for a specific postgres schema with a TSearch2 implementationBio::DB::GFF database adaptor for in-memory databasesutility methods for serializing and deserializing GFF featuresiterator for Bio::DB::GFF::Adaptor::memoryAggregate GFF groups into composite featuresAlignment aggregatorClone aggregatorThe Coding Region AggregatorSequence Ontology GeeneMatch aggregatorNo aggregationAn aggregator for orf regionsSequence Ontology TranscriptSequence Ontology TranscriptTranscript aggregatorUCSC acembly aggregatorUCSC ensGene aggregatorUCSC genscan aggregatorUCSC refGene aggregatorUCSC sanger22 aggregatorUCSC sanger22pseudo aggregatorUCSC softberry aggregatorUCSC twinscan aggregatorUCSC UniGene aggregatorThe name of a featureA relative segment identified by a feature typeA segment of DNA that is homologous to anotherSequence segment with relative coordinate supportSimple DNA segment objectThe name of a feature typebinning utility for Bio::DB::GFF indexrearrange utilityDatabase object interface to GenBankDatabase object interface to GenPepthelper base class for parameter-based remote server access and response retrieval.Database object interface to the Los Alamos HIV Sequence DatabaseAdds HIV-specific annotations to Bio::SeqIO streamsRoutines and packages used by Bio::DB::HIV and Bio::DB::Query::HIVQueryAbstract interface for a sequence databaseA RandomAccessI-like abstract interface for retrieving location data from a sequence database and returning Bio::LocationI objectsTerm retrieval from a Web MeSH databaseA collection of routines useful for queries to NCBI databases.Fast indexed access to a directory of quality filesBuild a GenBank Entrez QueryQuery interface to the Los Alamos HIV Sequence DatabaseHelper class for web-based sequence queryiesObject Interface to queryable sequence databasesAbstract interface for a sequence databaseDatabase object interface for RefSeq retrievalA RandomAccessI-like abstract interface for retrieving Reference data from a sequence database and returning Bio::Annotation::Reference objectsAccess to the Open Bio Database Access registry schemeNormalized feature for use with Bio::DB::SeqFeature::StoreNormalized feature for use with Bio::DB::SeqFeature::StoreInterface for normalized featuresInterface for normalized features whose hierarchy is stored in a tableLocation-based access to genome annotation dataStorage and retrieval of sequence annotation datautility methods for creating and iterating over SeqFeature recordsMysql implementation of Bio::DB::SeqFeature::StoreSQLite implementation of Bio::DB::SeqFeature::StoreMysql implementation of Bio::DB::SeqFeature::Storefeature file loader for Bio::DB::SeqFeature::StoreGFF2 file loader for Bio::DB::SeqFeature::StoreGFF3 file loader for Bio::DB::SeqFeature::StoreInternal utility for Bio::DB::SeqFeature::Storefetch and store objects from a BerkeleyDBStorage and retrieval of sequence annotation data in Berkeleydb filesStorage and retrieval of sequence annotation data in Berkeleydb filesIn-memory implementation of Bio::DB::SeqFeature::StoreDatabase object interface to SeqHoundAbstract Interface for Sequence databasesfront end to querying databases for identifier versionsinterface to NCBI Sequence Revision History pageDatabase object interface to SwissProt retrievalAccess to a Transcription Factor Binding Site databaseAn implementation of Bio::DB::TFBS which uses local flat files for transfac proAccess to a taxonomy databaseTaxonomy Entrez driverAn implementation of Bio::DB::Taxonomy which uses local flat filesAn implementation of Bio::DB::Taxonomy that accepts lists of words to build a databaseArtificial database that delegates to specific databasesAn interface for writing to a database of sequences.Object Interface to generalize Web Databases for retrieving sequencesAbstract interface for any object wanting to use database cross referencesSimple interface to Sequence Ontology feature typesDAS-style access to a feature databaseDAS-style access to a feature databaseinterface for objects with human readable names and descriptionsThis interface describes the basic event generator class.An Event Handler InterfaceDESCRIPTION of ObjectDESCRIPTION of Objecta set of DNA/RNA features. ISA Bio::Expression::FeatureIutility class for Mas50 FeatureGroupan interface class for DNA/RNA featuresutility class for Mas50 FeatureSetDESCRIPTION of Objectan interface class for DNA/RNA probesDESCRIPTION of ObjectAn interface to analysis tool factoryInterface class for Application FactoriesBase class for factory classes loading driversA FeatureTable Location ParserA factory interface for generating locations from a stringA Factory for getting markersInterface for an object builderInstantiates a new Bio::Root::RootI (or derived class) through a factoryA General object creator factoryclass capable of creating SeqAnalysisParserI compliant parsersinterface describing objects capable of creating SeqAnalysisParserI compliant parsersThis interface allows for generic building of sequences in factories which create sequences (like SeqIO)Interface for chained sequence processing algorithmsInterface describing the basics of a Sequence Stream.Factory Interface for getting and writing trees from/to a data streamthe base interface an object with features must implementHandler for FeatureIOread/write features from UCSC BED formatread/write GFF feature filesread write features in GTF formatread features from InterPro XMLread/write features in PTT formatread/write features from NCBI vecscreen -f 3 outputInterface class for handler methods which interact with any event-driven parsers (drivers).interface for objects with multiple identifiersinterface for objects with identifiersAbstract interface for indexing a flat filebase class for AbstractSeqIndexes Blast reports and supports retrieval based on query accession(s)Indexes tabular Blast reports (-m 9 format) and supports retrieval based on query accession(s)Interface for indexing (multiple) EMBL/Swissprot .dat files (i.e. flat file EMBL/Swissprot format).Interface for indexing (multiple) fasta filesInterface for indexing (multiple) fastq filesInterface for indexing one or more GenBank files (i.e. flat file GenBank format).indexes HMMER reports and supports retreival based on queryInterface for indexing (multiple) fasta qual filesIndexes Stockholm format alignments (such as those from Pfam and Rfam. Retrieves raw stream data using the ID or a Bio::SimpleAlign (via Bio::AlignIO)Interface for indexing swisspfam filesInterface for indexing one or more Swissprot files.AARange abstract class for LiveSeqDoubleChain DataStructure for PerlDouble linked chain data structureDNA object for LiveSeqRange abstract class for LiveSeqRange abstract class for LiveSeqLoader for LiveSeq from EMBL entries with BioPerlParent Loader for LiveSeqRange abstract class for LiveSeqMutation event descriptor classPackage mutating LiveSequencesPrim_Transcript class for LiveSeqRange abstract class for LiveSeqRepeat_Region class for LiveSeqRepeat_Unit class for LiveSeqAbstract sequence interface class for LiveSeqTranscript class for LiveSeqTranslation class for LiveSeqA Bio::PrimarySeq object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq.Implementation of a Atomic Location on a Sequenceclass implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwiseAbstract interface for objects implementing a certain policy of computing integer-valued coordinates of a LocationImplementation of a Location on a Sequence which has unclear start and/or end locationsAbstract interface of a Location on a Sequence which has unclear start/end locationclass implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable rangeImplementation of a Simple Location on a SequenceImplementation of a Location on a Sequence which has multiple locations (start/end points)Abstract interface of a Location on a Sequence which has multiple locations (start/end points)class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable rangeAbstract interface of a Location on a SequenceAn central map object representing a cloneA MapI implementation handling the contigs of a Physical Map (such as FPC)A Bio::MapI compliant map implementation handling cytogenic bandsAn object representing a marker.Marker class with cytogenetic band storing attributesAn Entity InterfaceAn central map object representing a markerAn gene modelled as a mappable element.A MapI implementation to represent the area around a geneA typed position, suitable for modelling the various regions of a gene.Represents being relative to named sub-regions of a gene.A representation of a genetic linkage map.Create a Position for a Marker that will be placed on a Bio::Map::LinkageMapInterface for describing Map objects in bioperlAn object representing a generic map element that can have multiple locations in several maps.An object that can be placed in a mapAn central map object representing a generic marker that can have multiple location in several maps.Interface for basic marker functionalityAn object representing a Microsatellite marker.Abstracts the notion of a member of an ordered list of markers. Each marker is a certain distance from the one in the ordered list before it.Abstracts the notion of a member of an ordered list of markers. Each marker is a certain distance from the one in the ordered list before it.A class for handling a Physical Map (such as FPC)A single position of a Marker, or the range over which that marker lies, in a MapA Position Handler ImplementationA Position Handler InterfaceAbstracts the notion of a position having a value in the context of a marker and a MapA position with a sequence.An object representing the predictions of something that can have multiple locations in several maps.Represents what a Position's coordiantes are relative to.Interface for describing what a Position's coordiantes are relative to.A MapI implementation handling the basics of a MapA transcription factor modelled as a mappable elementA Map Factory objectA FPC Map readerA Mapmaker Map readerA generic matrix implementationA factory for Matrix parsingA parser for the mlagan substitution matrixA parser for PHYLIP distance matriciesA parser for PAM/BLOSUM matriciesAn interface for describing a MatrixA generic matrix with mlagan fieldsPSM parserPSM mast parser implementationmotif fasta format parserPSM meme parser implementationPSM psiblast parserPSM transfac parserA PSM site occuranceInstanceSite interface, holds an instance of a PSMSiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) with log-odds scoring information.handle combination of site matricieshandle combination of site matriciesPSM mast parser implementationhandles the header data from a PSM fileabstract interface to handler of site matriciesSiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-oddsSiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-oddsA Phylip Distance Matrix objectObject which can hold scoring matrix informationCodon Evolution ModelsKeep track of where to find ontologies. Allows lookups by name.representation of GO termsImplementation of InterProI term interfaceAn Ontology Engine for OBO style flat file format from the Gene Ontology Consortiumrepresentation of OBO termsstandard implementation of an OntologyInterface a minimal Ontology implementation should satisfyInterface for an ontology implementationA repository of ontologiesa path for an ontology term graphInterface for a path between ontology termsa relationship for an ontologyInstantiates a new Bio::Ontology::RelationshipI (or derived class) through a factoryInterface for a relationship between ontology termsa relationship type for an ontologyGraph adaptor for Bio::Ontology::SimpleGOEngineGraph adaptor (v02.x) for Bio::Ontology::SimpleGOEngineImplementation of OntologyEngineI interfaceimplementation of the interface for ontology termsInstantiates a new Bio::Ontology::TermI (or derived class) through a factoryinterface for ontology termsParser factory for Ontology formatsXML handler class for InterProParserparse an InterPro XML file and persist the resulting terms to a Biosql databaseParser for InterPro xml files.a base class parser for GO flat-file type formatsa parser for the Gene Ontology flat-file formata parser for OBO flat-file format from Gene Ontology Consortiuma base class parser for simple hierarchy-by-indentation type formatsa parser for the Sequence Ontology flat-file formatSimple interface class for any parameter-related data such as IDs, database name, program arguments, and other odds and ends.Functional access to BioPerl for people who don't know objectsRepresentation of a correlating phenotype in a given speciesA MeSH termContext for a MeSH termRepresentation of context/value(-range)/unit tripletsRepresentation of a Mini MIM entryrepresents OMIM (Online Mendelian Inheritance in Man) database entriesRepresentation of a allelic variant of the OMIM databaseparser for the OMIM databaseA class for modeling phenotypesAn interface for classes modeling phenotypesModule to compute with Phylogenetic NetworksModule to sequentially generate Phylogenetic NetworksModule to sequentially generate Phylogenetic NetworksInterface between PhyloNetwork and GraphVizModule to generate random Phylogenetic NetworksModule to sequentially generate Phylogenetic TreesModule to sequentially generate Phylogenetic TreesModule to sequentially generate Phylogenetic TreesModule to compute with vectors of arbitrary dimensionAn implementation of GenotypeI which is just an allele containerA marker and alleles for a specific individualInput individual,marker,allele informationA parser for HapMap output dataA parser for Phase format dataExtract individual allele data from PrettyBase formatAn implementation of an Individual who has Genotype or Sequence ResultsAn individual who has Genotype or Sequence ResultsA genetic marker which one uses to generate genotypesA Population Genetic conceptual markerA collection of methods for calculating statistics about a population or sets of populationsA population of individualsInterface for PopulationsA Coalescent simulation factoryA simple genetic drift simulationPopulation Genetics statistical testsHaplotype tag object.Utilities for working with PopGen data and objectsBioperl lightweight Sequence ObjectInterface definition for a Bio::PrimarySeqA base module for fast 'pull' parsingPure perl RangeI implementationRange interfacecutting sequences with restriction enzymesA single restriction endonuclease (cuts DNA at specific locations)A single restriction endonucleaseA single restriction endonucleaseSet of restriction endonucleasesInterface class for restriction endonucleaseHandler for sequence variation IO Formatsbairoch enzyme setbase enzyme setitype2 enzyme setprototype enzyme setwithrefm enzyme setA common Module::Build subclass base for BioPerl distributionsGeneric exception objects for Bioperlmodule for fallback HTTP get operations when LWP:: is unavailablemodule providing several methods often needed when dealing with file IOHash-based implementation of Bio::Root::RootIAbstract interface to root object codeobject serialisation methodsA common base for all Bioperl test scripts.Perl extension to test Bioperl methods for warningsGeneral-purpose utility moduleprovide global, distribution-level versioningAn object for Blast statisticsUtility functions for Bio::Search:: BLAST objectsInterface for a database used in a sequence searchGeneric implementation of Bio::Search::DatabaseIAn object for statisticsBioperl BLAST High-Scoring Pair objectA parser and HSP object for BlastN hspsHSP object for FASTA specific dataA "Generic" implementation of a High Scoring PairA HSP object for HMMER resultsA factory to create Bio::Search::HSP::HSPI objectsInterface for a High Scoring Pair in a similarity search resultA parser and HSP object for hmmpfam hspsA HSP object for model-based searchesA HSP for PSL outputBioperl BLAST High-Scoring Pair objectBio::Search::HSP::HSPI interface for pull parsers.HSP object suitable for describing WABA alignmentsBlast-specific subclass of Bio::Search::Hit::GenericHitA parser and hit object for BLASTN hitsHit object specific for Fasta-generated hitsA generic implementation of the Bio::Search::Hit::HitI interfaceA Hit module for HMMER hitsA factory to create Bio::Search::Hit::HitI objectsInterface for a hit in a similarity search resultA parser and hit object for hmmpfam hitsA model-based implementation of the Bio::Search::Hit::HitI interfaceBioperl BLAST Hit objectBio::Search::Hit::HitI interface for pull parsers.A generic implementation of the Bio::Search::Iteration::IterationI interface.Abstract interface to an iteration from an iterated search result, such as PSI-BLAST.DESCRIPTION of ObjectA parser and result object for BLASTN resultsBlast-specific subclass of Bio::Search::Result::GenericResultCrossMatch-specific subclass of Bio::Search::Result::GenericResultGeneric Implementation of Bio::Search::Result::ResultI interface applicable to most search results.A Result object for HMMER resultsA parser and result object for hmmpfam resultsBio::Search::Result::ResultI interface for 'pull' parsersA factory to create Bio::Search::Result::ResultI objectsAbstract interface to Search Result objectsResult object for WABA alignment outputUtility functions for Bio::Search:: objectsA Base object for statisticsutilities for manipulating closed intervals for an HSP tiling algorithmAn implementation of an HSP tiling algorithm, with methods to obtain frequently-requested statisticsAbstract interface for an HSP tiling moduleA perl wrapper around Sean Eddy's histogram objectDriver for parsing Sequence Database Searches (BLAST, FASTA, ...)An abstract Event Handler for Search Result parsingEvent Handler for SearchIO events.Event Handler for SearchIO events.Event Handler for SearchIO events.Interface for outputting parsed Search resultsBSML output writerInterface for outputting parsed search results in Gbrowse GFF formatTab-delimited data for Bio::Search::HSP::HSPI objectswrite a Bio::Search::ResultI in HTMLTab-delimited data for Bio::Search::Hit::HitI objectsOutputs tab-delimited data for each Bio::Search::Result::ResultI object.Object to implement writing a Bio::Search::ResultI in Text.XML Handler for NCBI Blast XML parsing.XML Handler for NCBI Blast PSIBLAST XML parsing.a parser for axt format reportsEvent generator for event based parsing of blast reportsA parser for BLAST outputDriver module for SearchIO for parsing NCBI -m 8/9 formatA SearchIO implementation of NCBI Blast XML parsing.CrossMatch-specific subclass of Bio::SearchIOSearchIO-based ERPIN parserparser for ExonerateA SearchIO parser for FASTA resultsEvent generator for parsing gmap reports (Z format)A parser for HMMER output (hmmpfam, hmmsearch)A parser for HMMER outputSearchIO-based Infernal parsera driver module for Bio::SearchIO to parse megablast reports (format 0)A parser for PSL output (UCSC)SearchIO-based RNAMotif parserparser for Sim4 alignmentsSearchIO parser for Jim Kent WABA program alignment outputParsing of wise output as alignmentsSequence object, with featuresBase implementation for a SequenceProcessorsubtype of Bio::LocatableSeq to store DNA that encodes a proteinLocatableSeq object that stores sequence as files in the tempdirPrimarySeq object that stores sequence as files in the tempdir (as found by File::Temp) or the default method in Bio::Root::RootSeqI compliant object that stores sequence as files in /tmpInterface class for sequences that cache their residues in a temporary fileGeneric superclass for sequence objects with residue-based meta informationarray-based generic implementation of a sequence class with residue-based meta informationInterface for sequence objects with residue-based meta informationBioperl lightweight Quality ObjectA representation of a sequence and two primers flanking a target regionInterface definition for a Bio::Seq::QualImplementation of sequence with residue quality and trace valuesModule implementing a sequence created from a rich sequence database entryinterface for sequences from rich data sources, mostly databasesConfigurable object builder for sequence stream parsersInstantiates a new Bio::PrimarySeqI (or derived class) through a factoryInstantiates a new Bio::PrimarySeqI (or derived class) through a factoryBioperl object packaging a sequence with its quality. Deprecated class, use Bio::Seq::Quality instead!Bioperl object packaging a sequence with its traceInterface definition for a Bio::Seq::TraceSequence analysis output parser interfaceevolve a sequence by point mutationsthe interface for evolving sequencesFactory object to instantiate sequence evolving classesPLEASE PUT SOMETHING HEREintegrates SeqFeatureIs annotationA container class for SeqFeatures suitable for performing operations such as finding features within a range, that match a certain feature type, etc.An interface for a collection of SeqFeatureI objects.Computation SeqFeaturehold pair feature information e.g. blast hitsa feature representing an exonInterface for a feature representing an exonA feature representing an arbitrarily complex structure of a geneA feature representing an arbitrarily complex structure of a geneAn intron featuresuperclass for non-coding featurespoly A featureDescribes a promoterA feature representing a transcriptInterface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site.A feature representing an untranslated region that is part of a transcriptional unitGeneric SeqFeatureLightweight Bio::SeqFeatureI classhandle features when truncation/revcom sequences span a featurePrimer Generic SeqFeaturePerl object for small inhibitory RNAs.Perl object for small inhibitory RNA (SiRNA) oligo pairsA sequence feature based on similaritySequence feature based on the similarity of two sequences.generates unique persistent names for featuresmaps $seq_feature-gtprimary_tagmaps $seq_feature-gtprimary_tagturns flat list of genbank-sourced features into a nested SeqFeatureI hierarchya strongly typed SeqFeatureAbstract interface of a Sequence Feature[Developers] Abstract Interface of Sequence (with features)Handler for SeqIO FormatsHelper class for Embl/Genbank feature tablesBio::HandlerI-based data handler for GenBank/EMBL/UniProt (and other) sequence dataTreating a set of files as a single input streamabi trace sequence input/output streamace sequence input/output streamAGAVE sequence output stream.alf trace sequence input/output streamasciitree sequence input/output streamBSML sequence input/output streamBSML sequence input/output stream using SAXchadoxml sequence output streamchaos sequence input/output streamchaosxml sequence input/output streamctf trace sequence input/output streamEMBL sequence input/output streamEMBL sequence input/output streamEntrez Gene ASN1 parsersequence input/output stream from a MSExcel-formatted tableexp trace sequence input/output streamfasta sequence input/output streamfastq sequence input/output streamFlyBase variant of chadoxml with sequence output streama class for parsing and writing game-XMLa class for handling feature elementsPerlSAX handler for game-XMLa base class for game-XML parsinga class for writing game-XMLa class for handling game-XML sequencesGenBank handler-based push parserGCG sequence input/output streamGenBank sequence input/output streamInterProScan XML input/output streamKEGG sequence input/output streammethod i/o on very large fasta sequence filesLasergene sequence file input/output streamLocusLink input/output streammetafasta sequence input/output stream.phd file input/output streamPIR sequence input/output streampln trace sequence input/output stream.qual file input/output streamraw sequence file input/output stream.scf file input/output streamDNA strider sequence input/output streamSwissprot sequence input/output streamSwissProt/UniProt handler-based push parsernearly raw sequence file input/output stream. Reads/writes id"\t"sequence"\n"sequence input/output stream from a delimited tableTIGR XML sequence input/output streamParse TIGR (new) XMLreading/writing sequences in NCBI TinySeq formatXML event handlers to support NCBI TinySeq XML parsingztr trace sequence input/output streamAdditional methods for PrimarySeq objectsMultiple alignments held as a set of sequencesA simple interface to any (local or remote) analysis toolGeneric species objectBioperl structure Object, describes an AtomBioperl structure Object, describes a chainBioperl structure Object, describes the whole entryHandler for Structure FormatsPDB input/output streamBioperl structure Object, describes a ModelBioperl structure Object, describes a ResidueModule for parsing/accessing dssp outputModule for parsing/accessing stride outputAbstract Interface for a Structure objectsBSANE/BioCORBA compliant symbol list alphabetA Symbol AlphabetA ready made DNA alphabetA ready made Protein alphabetA biological symbolInterface for a SymbolA node in a represented taxonomyrepresenting Taxonomy.interface to define how to access NCBI TaxonoyA node in a represented taxonomyGeneric Taxonomic Entity objectAn Organism Level Implementation of TreeI interface.Base object for alignment factoriesA module to work with objects from consed .ace filesA kludge to do specialized trimming of sequence based on quality.a wrapper around ESEfinder servera wrapper around Domcut servera wrapper around the ELM server which predicts short functional motifs on amino acid sequencesa wrapper around GOR4 protein secondary structure prediction servera wrapper around the HNN protein secondary structure prediction servera wrapper around Mitoprot servera wrapper around NetPhos servera wrapper around the Scansite servera wrapper around the Sopma protein secondary structure prediction serverabstract superclass for SimpleAnalysis implementationsBase class for analysis result objects and parsersparser for Blat programCodon table objectparser for Coil outputrepresentation of EC numbers (Enzyme Classification)parse EMBOSS palindrome outputParse ePCR output and make featuresa parser for ERPIN outputResults of one ESTScan runNCBI eutil XML parserslightweight implementation of HistoryI interface (not bound to filehandles, extraneous methods, etc).eutil data object interfaceManipulation of NCBI eutil-based parameters for remote database requests.lightweight implementation of HistoryI interface (not bound to filehandles, extraneous methods, etc).simple extension of EUtilDataI interface class for classes which hold NCBI server history datainterface class for storing einfo dataclass for storing einfo field dataclass for storing einfo link datageneral API for accessing data retrieved from elink queriesclass for EUtils LinkSetsclass for EUtils UrlLinksparse and collect esearch, epost, espell, egquery informationcontainer class for egquery dataclass for handlign data output (XML) from esummary.data object for document summary data from esummarysimple layered object for DocSum item dataabtract interface methods for accessing Item information from any Item-containing class. This pertains to either DocSums or to Items themselves (which can be layered)Results of one Eponine runParse est2genome output, makes simple Bio::SeqFeature::Generic objectsparse results of one Fgenesh runwrite sequence features in FootPrinter formatA Bio::SeqAnalysisParserI compliant GFF format parserCalculates relative electrophoretic migration distancesResults of one geneid runResults of one Genemark runResults of one Genewise runResults of one Genomewise runResults of one Genscan runparser for Glimmer 2.X/3.X prokaryotic and GlimmerM/GlimmerHMM eukaryotic gene predictionsResults of one Grail runModule for determining the sequence format of the contents of a file, a string, or through a filehandle.One particular domain hit from HMMERObject representing HMMER output resultsSet of identical domains from HMMER matchesParser for Hmmpfam programGenerates unique Seq objects from an ambiguous Seq objectA parser for Infernal outputObject for analyzing the output from Lucy, a vector and quality trimming program from TIGRResults of one MZEF runParses output from Transfac's match(TM)Object holding alternative alphabet coding for one protein sequenceParses output from GERPParses output from gumbyparser for Molphy outputcontainer for data parsed from a ProtML runParses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00A container for NSSite Model Result from PAMLA PAML result set objectparser for ProtDist outputA predicted exon featurea predicted gene structure featurebase class for common assessor thingsinterface for assessing primer pairsposition of a single primertwo primers on left and right sideCreate input for and work with the output from the program primer3Parser for FingerPRINTScanII programparse Profile outputparser for Promoterwise tab format outputParser for ps_scan resultsubmit to and parse output from protparam ;Results of one Pseudowise runA Parser for qrna outputA parser for RNAMotif outputA set of routines useful for generating random data in different distributionsa parser for RepeatMasker outputAn object for the parameters used to run programsA Base object for the parameters used to run programsObject for remote execution of the NCBI Blast via HTTPObject for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). There is experimental support for WU-Blast and NCBI rpsblast.Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). With experimental support for NCBI rpsblast.Object for the local execution of WU-Blast.A Base object for wrappers around executablesparse seg outputrepresent a sequence pattern or motifObject holding statistics for one particular sequenceObject holding n-mer statistics for a sequencePerl object for designing small inhibitory RNAs.Perl object implementing the Saigo group's rules for designing small inhibitory RNAsPerl object implementing the tuschl group's rules for designing small inhibitory RNAsBioperl object for sigcleave analysisparser for Signalp outputenhanced parser for Signalp outputA single exon determined by an alignmentResults of one Sim4 runA single exon determined by an alignmentResults of a Spidey runa parser for Tandem Repeats Finder outputResults of one TargetP runparse TMHMM output (TransMembrane HMM)Perl extension to do pairwise dynamic programming sequence alignmentParse ipcress output and make featuresParse isPcr output and make featurescalculate the isoelectric point of a proteinpairwise Smith Waterman objectA parser for tRNAscan-SE outputA Node with Alleles attachedA Tree Node with support for annotationTesting compatibility of phylogenetic trees with nested taxa.Construct a tree using distance based methodsDrawing phylogenetic trees in Encapsulated PostScript (EPS) format.A Simple Tree NodeInterface describing a Tree NodeA Simple Tree Node with support for NHX tagsTreeFactory for generating Random TreesCalculate certain statistics for a TreeAn Implementation of TreeI interface.Decorated Interface implementing basic Tree exploration methodsA Tree object suitable for lots of things, designed originally for Phylogenetic Trees.Parser for Tree filesBuild Bio::Tree::Tree's and Bio::Tree::Node's from EventsA TreeIO driver module for parsing Algorithm::Cluster::treecluster() outputParser for lintree output treesTreeIO implementation for parsing Newick/New Hampshire/PHYLIP format.A TreeIO driver module for parsing Nexus tree output from PAUPTreeIO implementation for parsing Newick/New Hampshire eXtendend (NHX) format.Bio::TreeIO driver for Pagel formatTreeIO implementation for parsing PhyloXML format.A simple output format that converts a Tree object to an SVG outputA simple output format which displays a tree as an ASCII drawingDescendant of Bio::SeqI that allows updatesSequence change class for polypeptidespoint mutation and codon information from single amino acid changesSequence object with allele-specific attributesDNA level mutation classHandler for sequence variation IO Formatsflat file sequence variation input/output streamXML sequence variation input/output streamSequence change class for RNA levelsubmitted SNPContainer class for mutation/variant descriptionsSequence Change SeqFeature abstract classA base class for Web (any protocol) accessPerl Modules for Biologyget BioPerl method and package information from a Berkeley DBProvides
in Bio/AnalysisI.pmin Bio/DB/HIV/HIVQueryHelper.pmin Bio/DB/Fasta.pmin Bio/DB/SeqFeature/Store/berkeleydb.pmin Bio/DB/GFF/Adaptor/dbi/caching_handle.pmin Bio/DB/GFF.pmin Bio/DB/Qual.pmin Bio/DB/SeqFeature/Store/berkeleydb.pmin Bio/DB/SeqFeature/Store/memory.pmin Bio/DB/Fasta.pmin Bio/Search/Tiling/MapTileUtils.pmin Bio/DB/Qual.pmin Bio/DB/GFF/Adaptor/berkeleydb.pmin Bio/DB/HIV/HIVQueryHelper.pmin Bio/DB/HIV/HIVQueryHelper.pmin Bio/DB/HIV/HIVQueryHelper.pmin Bio/DB/HIV/HIVQueryHelper.pmExamples
- examples/Bio-DB-GFF/load_ucsc.pl
- examples/align/align_on_codons.pl
- examples/align/aligntutorial.pl
- examples/align/clustalw.pl
- examples/align/simplealign.pl
- examples/biblio/biblio-eutils-example.pl
- examples/biblio/biblio-soap-example.pl
- examples/biblio/biblio_soap.pl
- examples/bioperl.pl
- examples/cluster/dbsnp.pl
- examples/contributed/nmrpdb_parse.pl
- examples/contributed/prosite2perl.pl
- examples/contributed/rebase2list.pl
- examples/db/dbfetch
- examples/db/est_tissue_query.pl
- examples/db/gb2features.pl
- examples/db/getGenBank.pl
- examples/db/get_seqs.pl
- examples/db/rfetch.pl
- examples/db/use_registry.pl
- examples/generate_random_seq.pl
- examples/liveseq/change_gene.pl
- examples/longorf.pl
- examples/make_primers.pl
- examples/popgen/parse_calc_stats.pl
- examples/quality/svgtrace.pl
- examples/rev_and_trans.pl
- examples/revcom_dir.pl
- examples/root/README
- examples/root/exceptions1.pl
- examples/root/exceptions2.pl
- examples/root/exceptions3.pl
- examples/root/exceptions4.pl
- examples/searchio/blast_example.pl
- examples/searchio/custom_writer.pl
- examples/searchio/hitwriter.pl
- examples/searchio/hspwriter.pl
- examples/searchio/htmlwriter.pl
- examples/searchio/psiblast_features.pl
- examples/searchio/psiblast_iterations.pl
- examples/searchio/rawwriter.pl
- examples/searchio/resultwriter.pl
- examples/searchio/waba2gff.pl
- examples/searchio/waba2gff3.pl
- examples/sirna/TAG
- examples/sirna/rnai_finder.cgi
- examples/structure/structure-io.pl
- examples/subsequence.cgi
- examples/tk/gsequence.pl
- examples/tk/hitdisplay.pl
- examples/tools/extract_genes.pl
- examples/tools/gb_to_gff.pl
- examples/tools/gff2ps.pl
- examples/tools/parse_codeml.pl
- examples/tools/psw.pl
- examples/tools/reverse-translate.pl
- examples/tools/run_genscan.pl
- examples/tools/run_primer3.pl
- examples/tools/seq_pattern.pl
- examples/tools/standaloneblast.pl
- examples/tree/paup2phylip.pl
As a valued partner and proud supporter of MetaCPAN, StickerYou
is happy to offer a 10% discount on all Custom Stickers,
Business Labels, Roll Labels, Vinyl Lettering or Custom Decals.
StickerYou.com is your one-stop shop to make
your business stick. Use code METACPAN10 at
checkout to apply your discount.