The Libra Cluster
List of Installed Perl Modules
Note: You must use /usr/local/bin/perl to use these modules and not the default system perl
| Module | Version | Description |
|---|---|---|
| AnyDBM_File | 1.00 | provide framework for multiple DBMs |
| Apache::Htpasswd | 1.5.5 | Manage Unix crypt-style password file. |
| Archive::Tar | 1.04 | module for manipulations of tar archives |
| Archive::Tar::File | N/A | a subclass for in-memory extracted file from Archive::Tar |
| Attribute::Handlers | 0.77 | Simpler definition of attribute handlers |
| attributes | 0.05 | get/set subroutine or variable attributes |
| attrs | 1.01 | set/get attributes of a subroutine (deprecated) |
| AutoLoader | 5.59 | load subroutines only on demand |
| AutoSplit | 1.0307 | split a package for autoloading |
| autouse | 1.03 | postpone load of modules until a function is used |
| B | 1.01 | The Perl Compiler |
| B::Asmdata | 1.00 | Autogenerated data about Perl ops, used to generate bytecode |
| B::Assembler | 0.04 | Assemble Perl bytecode |
| B::Bblock | 1.00 | Walk basic blocks |
| B::Bytecode | 1.00 | Perl compiler's bytecode backend |
| B::C | N/A | Perl compiler's C backend |
| B::CC | 1.00 | Perl compiler's optimized C translation backend |
| B::Concise | 0.52 | Walk Perl syntax tree, printing concise info about ops |
| B::Debug | 1.00 | Walk Perl syntax tree, printing debug info about ops |
| B::Deparse | 0.63 | Perl compiler backend to produce perl code |
| B::Disassembler | N/A | Disassemble Perl bytecode |
| B::Lint | 1.01 | Perl lint |
| B::Showlex | 1.00 | Show lexical variables used in functions or files |
| B::Stackobj | 1.00 | Helper module for CC backend |
| B::Stash | N/A | show what stashes are loaded |
| B::Terse | 1.00 | Walk Perl syntax tree, printing terse info about ops |
| B::Xref | 1.01 | Generates cross reference reports for Perl programs |
| base | 1.03 | Establish IS-A relationship with base class at compile time |
| Benchmark | 1.04 | benchmark running times of Perl code |
| bigint | 0.02 | Transparent big integer support for Perl |
| bignum | 0.11 | Transparent BigNumber support for Perl |
| bigrat | 0.04 | Transparent BigNumber/BigRational support for Perl |
| Bio::Align::AlignI | N/A | An interface for describing sequence alignments. |
| Bio::Align::DNAStatistics | N/A | Calculate some statistics for a DNA alignment |
| Bio::Align::PairwiseStatistics | N/A | Base statistic object for Pairwise Alignments |
| Bio::Align::StatisticsI | N/A | Calculate some statistics for an alignment |
| Bio::Align::Utilities | N/A | A collection of utilities regarding converting and manipulating alignment objects |
| Bio::AlignIO | N/A | Handler for AlignIO Formats |
| Bio::AlignIO::bl2seq | N/A | bl2seq sequence input/output stream |
| Bio::AlignIO::clustalw | N/A | clustalw sequence input/output stream |
| Bio::AlignIO::emboss | N/A | Parse EMBOSS alignment output (from applications water and needle) |
| Bio::AlignIO::fasta | N/A | FastA MSA Sequence input/output stream |
| Bio::AlignIO::mase | N/A | mase sequence input/output stream |
| Bio::AlignIO::mega | N/A | Parse and Create MEGA format data files |
| Bio::AlignIO::meme | N/A | meme sequence input/output stream |
| Bio::AlignIO::msf | N/A | msf sequence input/output stream |
| Bio::AlignIO::nexus | N/A | NEXUS format sequence input/output stream |
| Bio::AlignIO::pfam | N/A | pfam sequence input/output stream |
| Bio::AlignIO::phylip | N/A | PHYLIP format sequence input/output stream |
| Bio::AlignIO::prodom | N/A | prodom sequence input/output stream |
| Bio::AlignIO::psi | N/A | Read/Write PSI-BLAST profile alignment files |
| Bio::AlignIO::selex | N/A | selex sequence input/output stream |
| Bio::AlignIO::stockholm | N/A | stockholm sequence input/output stream |
| Bio::AnalysisI | N/A | An interface to any (local or remote) analysis tool |
| Bio::AnalysisParserI | N/A | Generic analysis output parser interface |
| Bio::AnalysisResultI | N/A | Interface for analysis result objects |
| Bio::AnnotatableI | N/A | the base interface an annotatable object must implement |
| Bio::Annotation::AnnotationFactory | N/A | Instantiates a new Bio::AnnotationI (or derived class) through a factory |
| Bio::Annotation::Collection | N/A | Default Perl implementation of AnnotationCollectionI |
| Bio::Annotation::Comment | N/A | A comment object, holding text |
| Bio::Annotation::DBLink | N/A | DESCRIPTION of Object |
| Bio::Annotation::OntologyTerm | N/A | An ontology term adapted to AnnotationI |
| Bio::Annotation::Reference | N/A | Specialised DBLink object for Literature References |
| Bio::Annotation::SimpleValue | N/A | A simple scalar |
| Bio::Annotation::StructuredValue | N/A | A scalar with embedded structured |
| Bio::Annotation::TypeManager | N/A | Manages types for annotation collections |
| Bio::AnnotationCollectionI | N/A | Interface for annotation collections |
| Bio::AnnotationI | N/A | Annotation interface |
| Bio::Assembly::Contig | N/A | Perl module to hold and manipulate sequence assembly contigs. |
| Bio::Assembly::ContigAnalysis | N/A | Perform analysis on sequence assembly contigs. |
| Bio::Assembly::IO | N/A | Handler for Assembly::IO Formats |
| Bio::Assembly::IO::ace | N/A | module to load phrap ACE files. |
| Bio::Assembly::IO::phrap | N/A | driver to load phrap.out files. |
| Bio::Assembly::Scaffold | 0.0.1 | Perl module to hold and manipulate sequence assembly data. |
| Bio::Assembly::ScaffoldI | N/A | Abstract Inteface of Sequence Assemblies |
| Bio::Biblio | 0.0 | A Bibliographic Query Service module |
| Bio::Biblio::Article | N/A | Representation of a general article |
| Bio::Biblio::BiblioBase | N/A | An abstract base for other biblio classes |
| Bio::Biblio::Book | N/A | Representation of a book |
| Bio::Biblio::BookArticle | N/A | Representation of a book article |
| Bio::Biblio::IO | N/A | Handling the bibliographic references |
| Bio::Biblio::IO::medline2ref | 0.0 | A converter of a raw hash to MEDLINE citations |
| Bio::Biblio::IO::medlinexml | 0.0 | A converter of XML files with MEDLINE citations |
| Bio::Biblio::IO::pubmed2ref | 0.0 | A converter of a raw hash to PUBMED citations |
| Bio::Biblio::IO::pubmedxml | 0.0 | A converter of XML files with PUBMED citations |
| Bio::Biblio::Journal | N/A | Representation of a journal |
| Bio::Biblio::JournalArticle | N/A | Representation of a journal article |
| Bio::Biblio::MedlineArticle | N/A | Representation of a MEDLINE article |
| Bio::Biblio::MedlineBook | N/A | Representation of a MEDLINE book |
| Bio::Biblio::MedlineBookArticle | N/A | Representation of a MEDLINE book article |
| Bio::Biblio::MedlineJournal | N/A | Representation of a MEDLINE journal |
| Bio::Biblio::MedlineJournalArticle | N/A | Representation of a MEDLINE journal article |
| Bio::Biblio::Organisation | N/A | Representation of an organisation |
| Bio::Biblio::Patent | N/A | Representation of a patent |
| Bio::Biblio::Person | N/A | Representation of a person |
| Bio::Biblio::Proceeding | N/A | Representation of a conference proceeding |
| Bio::Biblio::Provider | N/A | Representation of a general provider |
| Bio::Biblio::PubmedArticle | N/A | Representation of a PUBMED article |
| Bio::Biblio::PubmedBookArticle | N/A | Representation of a PUBMED book article |
| Bio::Biblio::PubmedJournalArticle | N/A | Representation of a PUBMED journal article |
| Bio::Biblio::Ref | N/A | Representation of a bibliographic reference |
| Bio::Biblio::Service | N/A | Representation of a provider of type service |
| Bio::Biblio::TechReport | N/A | Representation of a technical report |
| Bio::Biblio::Thesis | N/A | Representation of thesis |
| Bio::Biblio::WebResource | N/A | Representation of a web resource |
| Bio::Cluster::ClusterFactory | N/A | Instantiates a new Bio::ClusterI (or derived class) through a factory |
| Bio::Cluster::FamilyI | N/A | Family Interface |
| Bio::Cluster::SequenceFamily | N/A | Sequence Family object |
| Bio::Cluster::UniGene | 1.1 | UniGene object |
| Bio::Cluster::UniGeneI | 1.0 | abstract interface of UniGene object |
| Bio::ClusterI | N/A | Cluster Interface |
| Bio::ClusterIO | N/A | Handler for Cluster Formats |
| Bio::ClusterIO::dbsnp | N/A | dbSNP input stream |
| Bio::ClusterIO::unigene | N/A | UniGene input stream |
| Bio::Coordinate::Chain | N/A | Mapping locations through a chain of coordinate mappers |
| Bio::Coordinate::Collection | N/A | Noncontinuous match between two coordinate sets |
| Bio::Coordinate::ExtrapolatingPair | N/A | Continuous match between two coordinate sets |
| Bio::Coordinate::GeneMapper | N/A | transformations between gene related coordinate systems |
| Bio::Coordinate::Graph | N/A | Finds shortest path between nodes in a graph |
| Bio::Coordinate::MapperI | N/A | Interface describing coordinate mappers |
| Bio::Coordinate::Pair | N/A | Continuous match between two coordinate sets |
| Bio::Coordinate::Result | N/A | Results from coordinate transformation |
| Bio::Coordinate::Result::Gap | N/A | An other name for Bio::Location::Simple |
| Bio::Coordinate::Result::Match | N/A | An other name for Bio::Location::Simple |
| Bio::Coordinate::ResultI | N/A | Interface to identify coordinate mapper results |
| Bio::Coordinate::Utils | N/A | Additional methods to create Bio::Coordinate objects |
| Bio::Das::FeatureTypeI | N/A | Simple interface to Sequence Ontology feature types |
| Bio::Das::SegmentI | 1 | DAS-style access to a feature database |
| Bio::DasI | N/A | DAS-style access to a feature database |
| Bio::DB::Ace | N/A | Database object interface to ACeDB servers |
| Bio::DB::Biblio::biofetch | 0.0 | A BioFetch-based access to a bibliographic citation retrieval |
| Bio::DB::Biblio::soap | N/A | A SOAP-based access to a bibliographic query service |
| Bio::DB::BiblioI | 0.0 | An interface to a Bibliographic Query Service |
| Bio::DB::BioFetch | 1.0 | Database object interface to BioFetch retrieval |
| Bio::DB::DBFetch | N/A | Database object for retrieving using the dbfetch script |
| Bio::DB::EMBL | N/A | Database object interface for EMBL entry retrieval |
| Bio::DB::Failover | N/A | A Bio::DB::RandomAccessI compliant class which wraps a priority list of DBs |
| Bio::DB::Fasta | 1.03 | Fast indexed access to a directory of fasta files |
| Bio::DB::FileCache | N/A | In file cache for BioSeq objects |
| Bio::DB::Flat | N/A | Interface for indexed flat files |
| Bio::DB::Flat::BDB | N/A | Interface for BioHackathon standard BDB-indexed flat file |
| Bio::DB::Flat::BDB::embl | N/A | embl adaptor for Open-bio standard BDB-indexed flat file |
| Bio::DB::Flat::BDB::fasta | N/A | fasta adaptor for Open-bio standard BDB-indexed flat file |
| Bio::DB::Flat::OBDAIndex | N/A | Binary search indexing system for sequence files |
| Bio::DB::GDB | N/A | Database object interface to GDB HTTP query |
| Bio::DB::GenBank | N/A | Database object interface to GenBank |
| Bio::DB::GenPept | N/A | Database object interface to GenPept |
| Bio::DB::GFF | N/A | Storage and retrieval of sequence annotation data |
| Bio::DB::GFF::Adaptor::ace | N/A | ace interface (for multiple inheritance) |
| Bio::DB::GFF::Adaptor::biofetch | N/A | Cache BioFetch objects in a Bio::DB::GFF database |
| Bio::DB::GFF::Adaptor::dbi | N/A | Database adaptor for DBI (SQL) databases |
| Bio::DB::GFF::Adaptor::dbi::caching_handle | N/A | Cache for database handles |
| Bio::DB::GFF::Adaptor::dbi::iterator | N/A | iterator for Bio::DB::GFF::Adaptor::dbi |
| Bio::DB::GFF::Adaptor::dbi::mysql | N/A | Database adaptor for a specific mysql schema |
| Bio::DB::GFF::Adaptor::dbi::mysqlace | N/A | Unholy union between mysql GFF database and acedb database |
| Bio::DB::GFF::Adaptor::dbi::mysqlopt | N/A | Deprecated database adaptor |
| Bio::DB::GFF::Adaptor::dbi::oracle | N/A | Database adaptor for a specific oracle schema |
| Bio::DB::GFF::Adaptor::dbi::oracleace | N/A | Unholy union between oracle GFF database and acedb database |
| Bio::DB::GFF::Adaptor::memory | N/A | Database adaptor for a specific mysql schema |
| Bio::DB::GFF::Adaptor::memory_iterator | N/A | iterator for Bio::DB::GFF::Adaptor::memory |
| Bio::DB::GFF::Aggregator | N/A | Aggregate GFF groups into composite features |
| Bio::DB::GFF::Aggregator::alignment | N/A | Alignment aggregator |
| Bio::DB::GFF::Aggregator::clone | N/A | Clone aggregator |
| Bio::DB::GFF::Aggregator::coding | N/A | The Coding Region Aggregator |
| Bio::DB::GFF::Aggregator::match | N/A | Match aggregator |
| Bio::DB::GFF::Aggregator::none | N/A | No aggregation |
| Bio::DB::GFF::Aggregator::processed_transcript | N/A | Sequence Ontology Transcript |
| Bio::DB::GFF::Aggregator::transcript | N/A | Transcript aggregator |
| Bio::DB::GFF::Aggregator::ucsc_acembly | N/A | UCSC acembly aggregator |
| Bio::DB::GFF::Aggregator::ucsc_ensgene | N/A | UCSC ensGene aggregator |
| Bio::DB::GFF::Aggregator::ucsc_genscan | N/A | UCSC genscan aggregator |
| Bio::DB::GFF::Aggregator::ucsc_refgene | N/A | UCSC refGene aggregator |
| Bio::DB::GFF::Aggregator::ucsc_sanger22 | N/A | UCSC sanger22 aggregator |
| Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo | N/A | UCSC sanger22pseudo aggregator |
| Bio::DB::GFF::Aggregator::ucsc_softberry | N/A | UCSC softberry aggregator |
| Bio::DB::GFF::Aggregator::ucsc_twinscan | N/A | UCSC twinscan aggregator |
| Bio::DB::GFF::Aggregator::ucsc_unigene | N/A | UCSC UniGene aggregator |
| Bio::DB::GFF::Featname | N/A | The name of a feature |
| Bio::DB::GFF::Feature | N/A | A relative segment identified by a feature type |
| Bio::DB::GFF::Homol | N/A | A segment of DNA that is homologous to another |
| Bio::DB::GFF::RelSegment | N/A | Sequence segment with relative coordinate support |
| Bio::DB::GFF::Segment | N/A | Simple DNA segment object |
| Bio::DB::GFF::Typename | N/A | The name of a feature type |
| Bio::DB::GFF::Util::Binning | N/A | binning utility for Bio::DB::GFF index |
| Bio::DB::GFF::Util::Rearrange | N/A | rearrange utility |
| Bio::DB::InMemoryCache | N/A | Abstract interface for a sequence database |
| Bio::DB::NCBIHelper | 0.8 | A collection of routines useful for queries to NCBI databases. |
| Bio::DB::Query::GenBank | 0.2 | Build a GenBank Entrez Query |
| Bio::DB::Query::WebQuery | 0.1 | Helper class for web-based sequence queryies |
| Bio::DB::QueryI | 0.1 | Object Interface to queryable sequence databases |
| Bio::DB::RandomAccessI | N/A | Abstract interface for a sequence database |
| Bio::DB::RefSeq | N/A | Database object interface for RefSeq retrieval |
| Bio::DB::Registry | 1.2 | Access to the Open Bio Database Access registry scheme |
| Bio::DB::SeqI | N/A | Abstract Interface for Sequence databases |
| Bio::DB::SwissProt | N/A | Database object interface to SwissProt retrieval |
| Bio::DB::Universal | N/A | Artificial database that delegates to specific databases |
| Bio::DB::UpdateableSeqI | N/A | An interface for writing to a database of sequences. |
| Bio::DB::WebDBSeqI | N/A | Object Interface to generalize Web Databases |
| Bio::DB::XEMBL | N/A | Database object interface for XEMBL entry retrieval |
| Bio::DB::XEMBLService | N/A | SOAP service definition for XEMBL |
| Bio::DBLinkContainerI | N/A | Abstract interface for any object wanting to use database cross references |
| Bio::DescribableI | N/A | interface for objects with human readable names and descriptions |
| Bio::Event::EventGeneratorI | N/A | This interface describes the basic event generator class. |
| Bio::Event::EventHandlerI | N/A | An Event Handler Interface |
| Bio::Expression::FeatureI | N/A | an interface class for DNA/RNA features |
| Bio::Expression::FeatureSet | N/A | a set of DNA/RNA features. ISA |
| Bio::Factory::AnalysisI | N/A | An interface to analysis tool factory |
| Bio::Factory::ApplicationFactoryI | N/A | Interface class for Application Factories |
| Bio::Factory::BlastHitFactory | N/A | Factory for Bio::Search::Hit::BlastHit objects |
| Bio::Factory::BlastResultFactory | N/A | Factory for Bio::Search::Result::BlastResult objects |
| Bio::Factory::DriverFactory | N/A | Base class for factory classes loading drivers |
| Bio::Factory::EMBOSS | N/A | EMBOSS appliaction factory class |
| Bio::Factory::FTLocationFactory | N/A | DESCRIPTION of Object |
| Bio::Factory::HitFactoryI | N/A | Interface for an object that builds Bio::Search::Hit::HitI objects |
| Bio::Factory::LocationFactoryI | N/A | DESCRIPTION of Interface |
| Bio::Factory::MapFactoryI | N/A | A Factory for getting markers |
| Bio::Factory::ObjectBuilderI | N/A | Interface for an object builder |
| Bio::Factory::ObjectFactory | N/A | Instantiates a new Bio::Root::RootI (or derived class) through a factory |
| Bio::Factory::ObjectFactoryI | N/A | A General object creator factory |
| Bio::Factory::ResultFactoryI | N/A | Interface for an object that builds Bio::Search::Result::ResultI objects |
| Bio::Factory::SeqAnalysisParserFactory | N/A | class capable of |
| Bio::Factory::SeqAnalysisParserFactoryI | N/A | interface describing objects capable |
| Bio::Factory::SequenceFactoryI | N/A | This interface allows for generic building of sequences in factories which create sequences (like SeqIO) |
| Bio::Factory::SequenceProcessorI | N/A | Interface for chained sequence processing algorithms |
| Bio::Factory::SequenceStreamI | N/A | Interface describing the basics of a Sequence Stream. |
| Bio::Factory::TreeFactoryI | N/A | Factory Interface for getting and writing trees |
| Bio::FeatureHolderI | N/A | the base interface an object with features must implement |
| Bio::Graphics | N/A | Generate GD images of Bio::Seq objects |
| Bio::Graphics::Feature | N/A | A simple feature object for use with Bio::Graphics::Panel |
| Bio::Graphics::FeatureFile | N/A | A set of Bio::Graphics features, stored in a file |
| Bio::Graphics::Glyph | N/A | Base class for Bio::Graphics::Glyph objects |
| Bio::Graphics::Glyph::alignment | N/A | The "alignment" glyph |
| Bio::Graphics::Glyph::anchored_arrow | N/A | The "anchored_arrow" glyph |
| Bio::Graphics::Glyph::arrow | N/A | The "arrow" glyph |
| Bio::Graphics::Glyph::box | N/A | The "box" glyph |
| Bio::Graphics::Glyph::cds | N/A | The "cds" glyph |
| Bio::Graphics::Glyph::crossbox | N/A | The "crossbox" glyph |
| Bio::Graphics::Glyph::diamond | N/A | The "diamond" glyph |
| Bio::Graphics::Glyph::dna | N/A | The "dna" glyph |
| Bio::Graphics::Glyph::dot | N/A | The "dot" glyph |
| Bio::Graphics::Glyph::ellipse | N/A | The "ellipse" glyph |
| Bio::Graphics::Glyph::ex | N/A | The "crossbox" glyph |
| Bio::Graphics::Glyph::extending_arrow | N/A | The "extending arrow" glyph |
| Bio::Graphics::Glyph::Factory | N/A | Factory for Bio::Graphics::Glyph objects |
| Bio::Graphics::Glyph::generic | N/A | The "generic" glyph |
| Bio::Graphics::Glyph::graded_segments | N/A | The "graded_segments" glyph |
| Bio::Graphics::Glyph::group | N/A | The "group" glyph |
| Bio::Graphics::Glyph::heterogeneous_segments | N/A | The "heterogeneous_segments" glyph |
| Bio::Graphics::Glyph::line | N/A | The "line" glyph |
| Bio::Graphics::Glyph::oval | N/A | The "oval" glyph |
| Bio::Graphics::Glyph::pinsertion | N/A | The "Drosophila P-element Insertion" glyph |
| Bio::Graphics::Glyph::primers | N/A | The "STS primers" glyph |
| Bio::Graphics::Glyph::processed_transcript | N/A | The sequence ontology transcript glyph |
| Bio::Graphics::Glyph::redgreen_box | N/A | The "redgreen_box" glyph |
| Bio::Graphics::Glyph::redgreen_segment | N/A | The "redgreen_segments" glyph |
| Bio::Graphics::Glyph::rndrect | N/A | The "round rect" glyph |
| Bio::Graphics::Glyph::ruler_arrow | N/A | The "ruler_arrow" glyph |
| Bio::Graphics::Glyph::segmented_keyglyph | N/A | The "segmented_keyglyph" glyph |
| Bio::Graphics::Glyph::segments | N/A | The "segments" glyph |
| Bio::Graphics::Glyph::span | N/A | The "span" glyph |
| Bio::Graphics::Glyph::splice_site | N/A | The "splice_site" glyph |
| Bio::Graphics::Glyph::toomany | N/A | The "too many to show" glyph |
| Bio::Graphics::Glyph::track | N/A | The "track" glyph |
| Bio::Graphics::Glyph::transcript | N/A | The "transcript" glyph |
| Bio::Graphics::Glyph::transcript2 | N/A | The "transcript2" glyph |
| Bio::Graphics::Glyph::translation | N/A | The "6-frame translation" glyph |
| Bio::Graphics::Glyph::triangle | N/A | The "triangle" glyph |
| Bio::Graphics::Glyph::xyplot | N/A | The xyplot glyph |
| Bio::Graphics::Panel | N/A | Generate GD images of Bio::Seq objects |
| Bio::IdCollectionI | N/A | interface for objects with multiple identifiers |
| Bio::IdentifiableI | N/A | interface for objects with identifiers |
| Bio::Index::Abstract | N/A | Abstract interface for indexing a flat file |
| Bio::Index::AbstractSeq | N/A | Base class for AbstractSeq s |
| Bio::Index::Blast | 0.1 | Indexes Blast reports and supports retrieval based on query accession(s) |
| Bio::Index::EMBL | 0.1 | Interface for indexing (multiple) EMBL/Swissprot |
| Bio::Index::Fasta | 0.2 | Interface for indexing (multiple) fasta files |
| Bio::Index::Fastq | 0.2 | Interface for indexing (multiple) fastq files |
| Bio::Index::GenBank | 0.1 | Interface for indexing (multiple) GenBank |
| Bio::Index::SwissPfam | 0.1 | Interface for indexing swisspfam files |
| Bio::Index::Swissprot | 0.1 | Interface for indexing (multiple) Swissprot |
| Bio::LiveSeq::AARange | 1.8 | AARange abstract class for LiveSeq |
| Bio::LiveSeq::Chain | 2.7 | DoubleChain DataStructure for Perl |
| Bio::LiveSeq::ChainI | 1.9 | Double linked chain data structure |
| Bio::LiveSeq::DNA | 1.4 | DNA object for LiveSeq |
| Bio::LiveSeq::Exon | 1.1 | Range abstract class for LiveSeq |
| Bio::LiveSeq::Gene | 2.3 | Range abstract class for LiveSeq |
| Bio::LiveSeq::Intron | 1 | Range abstract class for LiveSeq |
| Bio::LiveSeq::IO::BioPerl | 2.42 | Loader for LiveSeq from EMBL entries with BioPerl |
| Bio::LiveSeq::IO::Loader | 4.44 | Parent Loader for LiveSeq |
| Bio::LiveSeq::IO::SRS | N/A | Loader for LiveSeq from EMBL entries with SRS |
| Bio::LiveSeq::Mutation | N/A | Mutation event descriptor class |
| Bio::LiveSeq::Mutator | N/A | Package mutating LiveSequences |
| Bio::LiveSeq::Prim_Transcript | 1 | Prim_Transcript class for LiveSeq |
| Bio::LiveSeq::Range | 1.6 | Range abstract class for LiveSeq |
| Bio::LiveSeq::Repeat_Region | 1 | Repeat_Region class for LiveSeq |
| Bio::LiveSeq::Repeat_Unit | 1 | Repeat_Unit class for LiveSeq |
| Bio::LiveSeq::SeqI | 3.3 | Abstract sequence interface class for LiveSeq |
| Bio::LiveSeq::Transcript | 5.2 | Transcript class for LiveSeq |
| Bio::LiveSeq::Translation | 1.8 | Translation class for LiveSeq |
| Bio::LocatableSeq | N/A | A Sequence object with start/end points on it |
| Bio::Location::Atomic | N/A | Implementation of a Atomic Location on a Sequence |
| Bio::Location::AvWithinCoordPolicy | N/A | class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise |
| Bio::Location::CoordinatePolicyI | N/A | Abstract interface for objects implementing |
| Bio::Location::Fuzzy | N/A | Implementation of a Location on a Sequence |
| Bio::Location::FuzzyLocationI | N/A | Abstract interface of a Location on a Sequence |
| Bio::Location::NarrowestCoordPolicy | N/A | class implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range |
| Bio::Location::Simple | N/A | Implementation of a Simple Location on a Sequence |
| Bio::Location::Split | N/A | Implementation of a Location on a Sequence |
| Bio::Location::SplitLocationI | N/A | Abstract interface of a Location on a Sequence |
| Bio::Location::WidestCoordPolicy | N/A | class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable range |
| Bio::LocationI | N/A | Abstract interface of a Location on a Sequence |
| Bio::Map::CytoMap | N/A | A Bio::MapI compliant map implementation handling cytogenic bands |
| Bio::Map::CytoMarker | N/A | An object representing a marker. |
| Bio::Map::CytoPosition | 1 | Marker class with cytogenetic band storing attributes |
| Bio::Map::LinkageMap | N/A | A representation of a genetic linkage map. |
| Bio::Map::LinkagePosition | N/A | Create a Position for a Marker that will be placed |
| Bio::Map::MapI | N/A | Interface for describing Map objects in bioperl |
| Bio::Map::MappableI | N/A | An object that can be placed in a map |
| Bio::Map::Marker | N/A | An central map object representing a generic marker |
| Bio::Map::MarkerI | N/A | Interface for basic marker functionality |
| Bio::Map::Microsatellite | N/A | An object representing a Microsatellite marker. |
| Bio::Map::OrderedPosition | N/A | Abstracts the notion of a member |
| Bio::Map::OrderedPositionWithDistance | N/A | Abstracts the notion of a member |
| Bio::Map::Position | N/A | A single position of a Marker in a Map |
| Bio::Map::PositionI | N/A | Abstracts the notion of a position having |
| Bio::Map::SimpleMap | N/A | A MapI implementation handling the basics of a Map |
| Bio::MapIO | N/A | A Map Factory object |
| Bio::MapIO::mapmaker | N/A | A Mapmaker Map reader |
| Bio::Matrix::PhylipDist | N/A | A Phylip Distance Matrix object |
| Bio::Ontology::GOterm | N/A | representation of GO terms |
| Bio::Ontology::InterProTerm | N/A | Implementation of InterProI term interface |
| Bio::Ontology::Ontology | N/A | standard implementation of an Ontology |
| Bio::Ontology::OntologyEngineI | N/A | Interface a minimal Ontology implementation should satisfy |
| Bio::Ontology::OntologyI | N/A | Interface for an ontology implementation |
| Bio::Ontology::OntologyStore | N/A | A repository of ontologies |
| Bio::Ontology::Path | N/A | a path for an ontology term graph |
| Bio::Ontology::PathI | N/A | Interface for a path between ontology terms |
| Bio::Ontology::Relationship | N/A | a relationship for an ontology |
| Bio::Ontology::RelationshipFactory | N/A | Instantiates a new Bio::Ontology::RelationshipI (or derived class) through a factory |
| Bio::Ontology::RelationshipI | N/A | Interface for a relationship between ontology terms |
| Bio::Ontology::RelationshipType | N/A | a relationship type for an ontology |
| Bio::Ontology::SimpleGOEngine | N/A | a Ontology Engine for GO implementing OntologyEngineI |
| Bio::Ontology::SimpleOntologyEngine | N/A | Implementation of OntologyEngineI interface |
| Bio::Ontology::Term | N/A | interface for ontology terms |
| Bio::Ontology::TermFactory | N/A | Instantiates a new Bio::Ontology::TermI (or derived class) through a factory |
| Bio::Ontology::TermI | N/A | interface for ontology terms |
| Bio::OntologyIO | N/A | Parser factory for Ontology formats |
| Bio::OntologyIO::dagflat | N/A | a base class parser for GO flat-file type formats |
| Bio::OntologyIO::goflat | N/A | a parser for the Gene Ontology flat-file format |
| Bio::OntologyIO::Handlers::InterProHandler | N/A | XML handler class for InterProParser |
| Bio::OntologyIO::InterProParser | N/A | Parser for InterPro xml files. |
| Bio::OntologyIO::soflat | N/A | a parser for the Sequence Ontology flat-file format |
| Bio::Perl | N/A | Functional access to BioPerl for people who don't know objects |
| Bio::Phenotype::Correlate | N/A | Representation of a correlating phenotype in a given species |
| Bio::Phenotype::Measure | N/A | Representation of context/value(-range)/unit triplets |
| Bio::Phenotype::OMIM::MiniMIMentry | N/A | Representation of a Mini MIM entry |
| Bio::Phenotype::OMIM::OMIMentry | N/A | represents OMIM (Online Mendelian Inheritance in Man) database entries |
| Bio::Phenotype::OMIM::OMIMentryAllelicVariant | N/A | Representation of a allelic variant of the OMIM database |
| Bio::Phenotype::OMIM::OMIMparser | N/A | parser for the OMIM database |
| Bio::Phenotype::Phenotype | N/A | A class for modeling phenotypes |
| Bio::Phenotype::PhenotypeI | N/A | An interface for classes modeling phenotypes |
| Bio::PrimarySeq | N/A | Bioperl lightweight Sequence Object |
| Bio::PrimarySeqI | N/A | Interface definition for a Bio::PrimarySeq |
| Bio::Range | N/A | Pure perl RangeI implementation |
| Bio::RangeI | N/A | Range interface |
| Bio::Root::Err | 0.041 | Exception class for Perl 5 objects |
| Bio::Root::Exception | N/A | Generic exception objects for Bioperl |
| Bio::Root::Global | N/A | Global variables and utility functions |
| Bio::Root::HTTPget | N/A | module for fallback HTTP get operations when LWP:: is unavailable |
| Bio::Root::IO | N/A | module providing several methods often needed when dealing with file IO |
| Bio::Root::IOManager | 0.043 | Input and output manager for Perl5 objects. |
| Bio::Root::Object | 0.041 | A core Perl 5 object. |
| Bio::Root::Root | 1 | Hash-based implementation of Bio::Root::RootI |
| Bio::Root::RootI | 1 | Abstract interface to root object code |
| Bio::Root::Utilities | 0.05 | General-purpose utility module |
| Bio::Root::Vector | 0.04 | Interface for managing linked lists of Perl5 objects. |
| Bio::Root::Xref | 0.01 | A generic cross-reference object. |
| Bio::Search::BlastUtils | N/A | Utility functions for Bio::Search:: BLAST objects |
| Bio::Search::DatabaseI | N/A | Interface for a database used in a sequence search |
| Bio::Search::GenericDatabase | N/A | Generic implementation of Bio::Search::DatabaseI |
| Bio::Search::Hit::BlastHit | N/A | Bioperl BLAST Hit object |
| Bio::Search::Hit::Fasta | N/A | Hit object specific for Fasta-generated hits |
| Bio::Search::Hit::GenericHit | N/A | A generic implementation of the Bio::Search::Hit::HitI interface |
| Bio::Search::Hit::HitFactory | N/A | A factory to create Bio::Search::Hit::HitI objects |
| Bio::Search::Hit::HitI | N/A | Interface for a hit in a similarity search result |
| Bio::Search::Hit::HMMERHit | N/A | A Hit module for HMMER hits |
| Bio::Search::HSP::BlastHSP | N/A | Bioperl BLAST High-Scoring Pair object |
| Bio::Search::HSP::FastaHSP | N/A | HSP object for FASTA specific data |
| Bio::Search::HSP::GenericHSP | N/A | A "Generic" implementation of a High Scoring Pair |
| Bio::Search::HSP::HMMERHSP | N/A | A HSP object for HMMER results |
| Bio::Search::HSP::HSPFactory | N/A | A factory to create Bio::Search::HSP::HSPI objects |
| Bio::Search::HSP::HSPI | N/A | Interface for a High Scoring Pair in a similarity search result |
| Bio::Search::HSP::WABAHSP | N/A | HSP object suitable for describing WABA alignments |
| Bio::Search::Processor | N/A | DESCRIPTION of Object |
| Bio::Search::Result::BlastResult | N/A | A top-level BLAST Report object |
| Bio::Search::Result::GenericResult | N/A | Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results. |
| Bio::Search::Result::HMMERResult | N/A | A Result object for HMMER results |
| Bio::Search::Result::ResultFactory | N/A | A factory to create Bio::Search::Result::ResultI objects |
| Bio::Search::Result::ResultI | N/A | Abstract interface to Search Result objects |
| Bio::Search::Result::WABAResult | N/A | Result object for WABA alignment output |
| Bio::Search::SearchUtils | N/A | Utility functions for Bio::Search:: objects |
| Bio::SearchDist (Can't locate Bio/Ext/Align.pm in @INC | N/A | A perl wrapper around Sean Eddy's histogram object |
| Bio::SearchIO | N/A | Driver for parsing Sequence Database Searches (Blast,FASTA,...) |
| Bio::SearchIO::blast | N/A | Event generator for event based parsing of blast reports |
| Bio::SearchIO::blastxml | N/A | A SearchIO implementation of NCBI Blast XML parsing. |
| Bio::SearchIO::chado | N/A | chado sequence input/output stream |
| Bio::SearchIO::chadosxpr | N/A | chadosxpr sequence input/output stream |
| Bio::SearchIO::EventHandlerI | N/A | An abstract Event Handler for Search Result parsing |
| Bio::SearchIO::exonerate | N/A | parser for Exonerate |
| Bio::SearchIO::fasta | N/A | A SearchIO parser for FASTA results |
| Bio::SearchIO::FastHitEventBuilder | N/A | Event Handler for SearchIO events. |
| Bio::SearchIO::hmmer | N/A | A parser for HMMER output (hmmpfam, hmmsearch) |
| Bio::SearchIO::psiblast | N/A | Parser for traditional BLAST and PSI-BLAST reports |
| Bio::SearchIO::SearchResultEventBuilder | N/A | Event Handler for SearchIO events. |
| Bio::SearchIO::SearchWriterI | N/A | Interface for outputting parsed Search results |
| Bio::SearchIO::waba | N/A | SearchIO parser for Jim Kent WABA program |
| Bio::SearchIO::Writer::HitTableWriter | N/A | Tab-delimited data for Bio::Search::Hit::HitI objects |
| Bio::SearchIO::Writer::HSPTableWriter | N/A | Tab-delimited data for Bio::Search::HSP::HSPI objects |
| Bio::SearchIO::Writer::HTMLResultWriter | N/A | Object to implement writing a Bio::Search::ResultI in HTML. |
| Bio::SearchIO::Writer::ResultTableWriter | N/A | Outputs tab-delimited data for each Bio::Search::Result::ResultI object. |
| Bio::SearchIO::Writer::TextResultWriter | N/A | Object to implement writing a Bio::Search::ResultI in Text. |
| Bio::Seq | 1.1 | Sequence object, with features |
| Bio::Seq::BaseSeqProcessor | N/A | Base implementation for a SequenceProcessor |
| Bio::Seq::EncodedSeq | N/A | subtype of L |
| Bio::Seq::LargePrimarySeq | N/A | PrimarySeq object that stores sequence as |
| Bio::Seq::LargeSeq | N/A | SeqI compliant object that stores sequence as files in /tmp |
| Bio::Seq::PrimaryQual | N/A | Bioperl lightweight Quality Object |
| Bio::Seq::QualI | N/A | Interface definition for a Bio::Seq::Qual |
| Bio::Seq::RichSeq | N/A | Module implementing a sequence created from a rich |
| Bio::Seq::RichSeqI | N/A | RichSeq interface, mainly for database orientated sequences |
| Bio::Seq::SeqBuilder | N/A | Configurable object builder for sequence stream parsers |
| Bio::Seq::SeqFactory | N/A | Instantiates a new Bio::PrimarySeqI (or derived class) through a factory |
| Bio::Seq::SeqFastaSpeedFactory | N/A | Instantiates a new Bio::PrimarySeqI (or derived class) through a factory |
| Bio::Seq::SequenceTrace | N/A | Bioperl object packaging a sequence with its trace |
| Bio::Seq::SeqWithQuality | N/A | Bioperl object packaging a sequence with its quality |
| Bio::Seq::TraceI | N/A | Interface definition for a Bio::Seq::Trace |
| Bio::SeqAnalysisParserI | N/A | Sequence analysis output parser interface |
| Bio::SeqFeature::AnnotationAdaptor | N/A | integrates SeqFeatureIs annotation |
| Bio::SeqFeature::Collection | N/A | A container class for SeqFeatures |
| Bio::SeqFeature::CollectionI | N/A | An interface for a collection of SeqFeatureI objects. |
| Bio::SeqFeature::Computation | N/A | Computation SeqFeature |
| Bio::SeqFeature::FeaturePair | N/A | hold pair feature information e.g. blast hits |
| Bio::SeqFeature::Gene::Exon | N/A | a feature representing an exon |
| Bio::SeqFeature::Gene::ExonI | N/A | Interface for a feature representing an exon |
| Bio::SeqFeature::Gene::GeneStructure | N/A | A feature representing an arbitrarily |
| Bio::SeqFeature::Gene::GeneStructureI | N/A | A feature representing an arbitrarily |
| Bio::SeqFeature::Gene::Intron | N/A | DESCRIPTION of Object |
| Bio::SeqFeature::Gene::NC_Feature | N/A | DESCRIPTION of Object |
| Bio::SeqFeature::Gene::Poly_A_site | N/A | DESCRIPTION of Object |
| Bio::SeqFeature::Gene::Promoter | N/A | Describes a promotor |
| Bio::SeqFeature::Gene::Transcript | N/A | A feature representing a transcript |
| Bio::SeqFeature::Gene::TranscriptI | N/A | Interface for a feature representing a |
| Bio::SeqFeature::Gene::UTR | N/A | A feature representing an untranslated region |
| Bio::SeqFeature::Generic | N/A | Generic SeqFeature |
| Bio::SeqFeature::PositionProxy | N/A | handle features when truncation/revcom sequences span a feature |
| Bio::SeqFeature::Primer | N/A | Primer Generic SeqFeature |
| Bio::SeqFeature::Similarity | N/A | A sequence feature based on similarity |
| Bio::SeqFeature::SimilarityPair | N/A | Sequence feature based on the similarity |
| Bio::SeqFeatureI | N/A | Abstract interface of a Sequence Feature |
| Bio::SeqI | N/A | Abstract Interface of Sequence (with features) |
| Bio::SeqIO | N/A | Handler for SeqIO Formats |
| Bio::SeqIO::abi | N/A | abi trace sequence input/output stream |
| Bio::SeqIO::ace | N/A | ace sequence input/output stream |
| Bio::SeqIO::alf | N/A | alf trace sequence input/output stream |
| Bio::SeqIO::bsml | N/A | BSML sequence input/output stream |
| Bio::SeqIO::chado | N/A | chado sequence input/output stream |
| Bio::SeqIO::chadoitext | N/A | chadoitext sequence input/output stream |
| Bio::SeqIO::chadosxpr | N/A | chadosxpr sequence input/output stream |
| Bio::SeqIO::chadoxml | N/A | chadoxml sequence input/output stream |
| Bio::SeqIO::ctf | N/A | ctf trace sequence input/output stream |
| Bio::SeqIO::embl | N/A | EMBL sequence input/output stream |
| Bio::SeqIO::exp | N/A | exp trace sequence input/output stream |
| Bio::SeqIO::fasta | N/A | fasta sequence input/output stream |
| Bio::SeqIO::fastq | N/A | fastq sequence input/output stream |
| Bio::SeqIO::FTHelper | N/A | Helper class for Embl/Genbank feature tables |
| Bio::SeqIO::game | N/A | Parses GAME XML 0.1 and higher into and out of Bio::Seq objects. |
| Bio::SeqIO::game::featureHandler | N/A | GAME helper via PerlSAX helper. |
| Bio::SeqIO::game::idHandler | N/A | GAME helper via PerlSAX helper. |
| Bio::SeqIO::game::seqHandler | N/A | GAME helper via PerlSAX helper. |
| Bio::SeqIO::gcg | N/A | GCG sequence input/output stream |
| Bio::SeqIO::genbank | N/A | GenBank sequence input/output stream |
| Bio::SeqIO::largefasta | N/A | method i/o on very large fasta sequence files |
| Bio::SeqIO::locuslink | N/A | DESCRIPTION of Object |
| Bio::SeqIO::MultiFile | N/A | Treating a set of files as a single input stream |
| Bio::SeqIO::phd | N/A | .phd file input/output stream |
| Bio::SeqIO::pir | N/A | PIR sequence input/output stream |
| Bio::SeqIO::pln | N/A | pln trace sequence input/output stream |
| Bio::SeqIO::qual | N/A | .qual file input/output stream |
| Bio::SeqIO::raw | N/A | raw sequence file input/output stream |
| Bio::SeqIO::scf | N/A | .scf file input/output stream |
| Bio::SeqIO::swiss | N/A | Swissprot sequence input/output stream |
| Bio::SeqIO::ztr | N/A | ztr trace sequence input/output stream |
| Bio::SeqUtils | N/A | Additional methods for PrimarySeq objects |
| Bio::SimpleAlign | N/A | Multiple alignments held as a set of sequences |
| Bio::Species | N/A | Generic species object |
| Bio::Structure::Atom | N/A | Bioperl structure Object, describes an Atom |
| Bio::Structure::Chain | N/A | Bioperl structure Object, describes a chain |
| Bio::Structure::Entry | N/A | Bioperl structure Object, describes the whole entry |
| Bio::Structure::IO | N/A | Handler for Structure Formats |
| Bio::Structure::IO::pdb | N/A | PDB input/output stream |
| Bio::Structure::Model | N/A | Bioperl structure Object, describes a Model |
| Bio::Structure::Residue | N/A | Bioperl structure Object, describes a Residue |
| Bio::Structure::SecStr::DSSP::Res | N/A | Module for parsing/accessing dssp output |
| Bio::Structure::SecStr::STRIDE::Res | N/A | Module for parsing/accessing stride output |
| Bio::Structure::StructureI | N/A | Abstract Interface for a Structure objects |
| Bio::Symbol::Alphabet | N/A | DESCRIPTION of Object |
| Bio::Symbol::AlphabetI | N/A | A Symbol Alphabet |
| Bio::Symbol::DNAAlphabet | N/A | A ready made DNA alphabet |
| Bio::Symbol::ProteinAlphabet | N/A | A ready made Protein alphabet |
| Bio::Symbol::Symbol | N/A | A biological symbol |
| Bio::Symbol::SymbolI | N/A | Interface for a Symbol |
| Bio::Taxonomy | N/A | Conversion used bt the Taxonomy classes |
| Bio::Taxonomy::Taxon | N/A | Generic Taxonomic Entity object |
| Bio::Taxonomy::Tree | N/A | An Organism Level Implementation of TreeI interface. |
| Bio::Tools::AlignFactory | N/A | Base object for alignment factories |
| Bio::Tools::Alignment::Consed | 0.60 | A module to work with objects from consed .ace files |
| Bio::Tools::Alignment::Trim | 0.01 | A kludge to do specialized trimming of |
| Bio::Tools::AnalysisResult | N/A | Base class for analysis result objects and parsers |
| Bio::Tools::Blast | 0.09 | Bioperl BLAST sequence analysis object |
| Bio::Tools::Blast::HSP | N/A | Bioperl BLAST High-Scoring Segment Pair object |
| Bio::Tools::Blast::HTML | N/A | Bioperl Utility module for HTML formatting Blast reports |
| Bio::Tools::Blast::Sbjct | N/A | Bioperl BLAST "Hit" object |
| Bio::Tools::BPbl2seq | N/A | Lightweight BLAST parser for pair-wise sequence |
| Bio::Tools::BPlite | N/A | Lightweight BLAST parser |
| Bio::Tools::BPlite::HSP | N/A | Blast report High Scoring Pair (HSP) |
| Bio::Tools::BPlite::Iteration | N/A | object for parsing single iteration |
| Bio::Tools::BPlite::Sbjct | N/A | A Blast Subject (database search Hit) |
| Bio::Tools::BPpsilite | N/A | Lightweight BLAST parser for (iterated) psiblast reports |
| Bio::Tools::CodonTable | N/A | Bioperl codon table object |
| Bio::Tools::Coil | N/A | Bio::Tools::Coil |
| Bio::Tools::ECnumber | N/A | representation of EC numbers |
| Bio::Tools::EPCR | N/A | Parse ePCR output and make features |
| Bio::Tools::Eponine | N/A | Results of one Eponine run |
| Bio::Tools::Est2Genome | N/A | Parse est2genome output, makes simple Bio::SeqFeature::Generic objects |
| Bio::Tools::ESTScan | N/A | Results of one ESTScan run |
| Bio::Tools::FootPrinter | N/A | DESCRIPTION of Object |
| Bio::Tools::Gel | N/A | Calculates relative electrophoretic migration distances |
| Bio::Tools::Genemark | N/A | Results of one Genemark run |
| Bio::Tools::Genewise | N/A | Results of one Genewise run |
| Bio::Tools::Genomewise | N/A | Results of one Genomewise run |
| Bio::Tools::Genscan | N/A | Results of one Genscan run |
| Bio::Tools::GFF | N/A | A Bio::SeqAnalysisParserI compliant GFF format parser |
| Bio::Tools::Grail | N/A | Results of one Grail run |
| Bio::Tools::HMMER::Domain | N/A | One particular domain hit from HMMER |
| Bio::Tools::HMMER::Results | N/A | Object representing HMMER output results |
| Bio::Tools::HMMER::Set | N/A | Set of identical domains from HMMER matches |
| Bio::Tools::Hmmpfam | N/A | Bio::Tools::Hmmpfam |
| Bio::Tools::IUPAC | N/A | Generates unique Seq objects from an ambiguous Seq object |
| Bio::Tools::Lucy | 0.01 | Object for analyzing the output from Lucy, |
| Bio::Tools::MZEF | N/A | Results of one MZEF run |
| Bio::Tools::OddCodes | N/A | Object holding alternative alphabet coding for one protein sequence |
| Bio::Tools::Phylo::Molphy | N/A | DESCRIPTION of Object |
| Bio::Tools::Phylo::Molphy::Result | N/A | DESCRIPTION of Object |
| Bio::Tools::Phylo::PAML | N/A | Parses output from the PAML programs codeml, |
| Bio::Tools::Phylo::PAML::Result | N/A | A PAML result set object |
| Bio::Tools::Phylo::Phylip::ProtDist | N/A | DESCRIPTION of Object |
| Bio::Tools::Prediction::Exon | N/A | A predicted exon feature |
| Bio::Tools::Prediction::Gene | N/A | a predicted gene structure feature |
| Bio::Tools::Primer3 | N/A | Create input for and work with the output from the program primer3 |
| Bio::Tools::Prints | N/A | Parser for FingerPRINTScanII program |
| Bio::Tools::Profile | N/A | parse Profile output |
| Bio::Tools::Promoterwise | N/A | DESCRIPTION of Object |
| Bio::Tools::Pseudowise | N/A | Results of one Pseudowise run |
| Bio::Tools::pSW | N/A | pairwise Smith Waterman object |
| Bio::Tools::RepeatMasker | N/A | DESCRIPTION of Object |
| Bio::Tools::RestrictionEnzyme | N/A | Bioperl object for a restriction endonuclease |
| Bio::Tools::Run::RemoteBlast | N/A | Object for remote execution of the NCBI Blast |
| Bio::Tools::Run::StandAloneBlast | N/A | Object for the local execution of the |
| Bio::Tools::Run::WrapperBase | N/A | A Base object for wrappers around executables |
| Bio::Tools::Seg | N/A | parse Seg output (filter low complexity protein sequence) |
| Bio::Tools::SeqAnal | 0.011 | Bioperl sequence analysis base class. |
| Bio::Tools::SeqPattern | 0.011 | Bioperl object for a sequence pattern or motif |
| Bio::Tools::SeqStats | N/A | Object holding statistics for one particular sequence |
| Bio::Tools::SeqWords | N/A | Object holding n-mer statistics for one sequence |
| Bio::Tools::Sigcleave | 0.02 | Bioperl object for sigcleave analysis |
| Bio::Tools::Signalp | N/A | Bio::Tools::SignalP |
| Bio::Tools::Sim4::Exon | N/A | A single exon determined by an alignment |
| Bio::Tools::Sim4::Results | N/A | Results of one Sim4 run |
| Bio::Tools::StateMachine::AbstractStateMachine | N/A | Abstract state machine object |
| Bio::Tools::StateMachine::IOStateMachine | N/A | IO-based implementation of AbstractStateMachine |
| Bio::Tools::Tmhmm | N/A | parse TmHMM output (transmembrane HMM) |
| Bio::Tools::WWW | 0.014 | Bioperl manager for web resources related to biology. |
| Bio::Tree::AlleleNode | N/A | DESCRIPTION of Object |
| Bio::Tree::Node | N/A | A Simple Tree Node |
| Bio::Tree::NodeI | N/A | Interface describing a Tree Node |
| Bio::Tree::NodeNHX | N/A | A Simple Tree Node with support for NHX tags |
| Bio::Tree::RandomFactory | N/A | TreeFactory for generating Random Trees |
| Bio::Tree::Statistics | N/A | Calculate certain statistics for a Tree |
| Bio::Tree::Tree | N/A | An Implementation of TreeI interface. |
| Bio::Tree::TreeFunctionsI | N/A | Decorated Interface implementing basic Tree exploration methods |
| Bio::Tree::TreeI | N/A | A Tree object suitable for lots of things, designed |
| Bio::TreeIO | N/A | Parser for Tree files |
| Bio::TreeIO::newick | N/A | TreeIO implementation for parsing Newick/New Hampshire/PHYLIP format. |
| Bio::TreeIO::nhx | N/A | TreeIO implementation for parsing Newick/New Hampshire eXtendend (NHX) format. |
| Bio::TreeIO::tabtree | N/A | A simple output format which displays a tree as an ASCII drawing |
| Bio::TreeIO::TreeEventBuilder | N/A | Build Bio::Tree::Tree's and Bio::Tree::Node's from Events |
| Bio::UpdateableSeqI | N/A | Descendant of Bio::SeqI that allows updates |
| Bio::Variation::AAChange | N/A | Sequence change class for polypeptides |
| Bio::Variation::AAReverseMutate | N/A | point mutation and codon |
| Bio::Variation::Allele | N/A | Sequence object with allele-specific attributes |
| Bio::Variation::DNAMutation | N/A | DNA level mutation class |
| Bio::Variation::IO | N/A | Handler for sequence variation IO Formats |
| Bio::Variation::IO::flat | N/A | flat file sequence variation input/output stream |
| Bio::Variation::IO::xml | N/A | XML sequence variation input/output stream |
| Bio::Variation::RNAChange | N/A | Sequence change class for RNA level |
| Bio::Variation::SeqDiff | N/A | Container class for mutation/variant descriptions |
| Bio::Variation::SNP | N/A | submitted SNP |
| Bio::Variation::VariantI | 1 | Sequence Change SeqFeature abstract class |
| blib | 1.02 | Use MakeMaker's uninstalled version of a package |
| Bundle::CPAN | 1.58 | A bundle to play with all the other modules on CPAN |
| Bundle::DBI | 11.03 | A bundle to install DBI and required modules. |
| Bundle::LWP | 1.09 | A bundle to install all libwww-perl related modules |
| ByteLoader | 0.04 | load byte compiled perl code |
| bytes | 1.00 | Perl pragma to force byte semantics rather than character semantics |
| Carp | 1.01 | warn of errors (from perspective of caller) |
| Carp::Heavy | N/A | no user serviceable parts inside |
| CGI | 2.81 | Simple Common Gateway Interface Class |
| CGI::Apache | N/A | Backward compatibility module for CGI.pm |
| CGI::Carp | 1.23 | CGI routines for writing to the HTTPD (or other) error log |
| CGI::Cookie | 1.20 | Interface to Netscape Cookies |
| CGI::Fast | N/A | CGI Interface for Fast CGI |
| CGI::Pretty | 1.05_00 | module to produce nicely formatted HTML code |
| CGI::Push | 1.04 | Simple Interface to Server Push |
| CGI::Switch | N/A | Backward compatibility module for defunct CGI::Switch |
| CGI::Util | 1.3 | Internal utilities used by CGI module |
| charnames | 1.01 | define character names for C<\N{named}> string literal escapes |
| Class::ISA | 0.32 | report the search path for a class's ISA tree |
| Class::Loader | 2.02 | Load modules and create objects on demand. |
| Class::Struct | 0.61 | declare struct-like datatypes as Perl classes |
| Compress::Zlib | 1.22 | Interface to zlib compression library |
| Config | N/A | access Perl configuration information |
| constant | 1.04 | Perl pragma to declare constants |
| Convert::ASCII::Armor | N/A | Convert binary octets into ASCII armoured messages. |
| Convert::ASCII::Armour | 1.4 | Convert binary octets into ASCII armoured messages. |
| Convert::ASN1 | 0.17 | ASN.1 Encode/Decode library |
| Convert::PEM | 0.06 | Read/write encrypted ASN.1 PEM files |
| Convert::PEM::CBC | N/A | Cipher Block Chaining Mode implementation |
| Convert::PEM::ErrorHandler | N/A | Convert::PEM error handling |
| Crypt::Blowfish | 2.09 | Perl Blowfish encryption module |
| Crypt::CBC | 2.08 | Encrypt Data with Cipher Block Chaining Mode |
| Crypt::DES | 2.03 | Perl DES encryption module |
| Crypt::DES_EDE3 | 0.01 | Triple-DES EDE encryption/decryption |
| Crypt::RIPEMD160 | 0.04 | Perl extension for the RIPEMD-160 Hash function |
| Crypt::RIPEMD160::MAC | 0.01 | Perl extension for RIPEMD-160 MAC function |
| Cwd | 2.06 | get pathname of current working directory |
| Data::Dumper | 2.12 | stringified perl data structures, suitable for both printing and C |
| Data::Grove | 0.07 | support for deeply nested structures |
| Data::Grove::Parent | 0.07 | provide parent properties to Data::Grove objects |
| Data::Grove::Visitor | 0.07 | add visitor/callback methods to Data::Grove objects |
| DB | 1.0 | programmatic interface to the Perl debugging API (draft, subject to |
| DBD::DBM | 0.01 | a DBI driver for DBM & MLDBM files |
| DBD::File | 0.30 | Base class for writing DBI drivers |
| DBD::Oracle | N/A | Oracle database driver for the DBI module |
| DBD::Pg | 1.32 | PostgreSQL database driver for the DBI module |
| DBD::Proxy | N/A | A proxy driver for the DBI |
| DBD::Sponge | 11.10 | Create a DBI statement handle from Perl data |
| DBI | 1.42 | Database independent interface for Perl |
| DBI::Changes | N/A | List of significant changes to the DBI |
| DBI::Const::GetInfo::ANSI | N/A | ISO/IEC SQL/CLI Constants for GetInfo |
| DBI::Const::GetInfo::ODBC | N/A | ODBC Constants for GetInfo |
| DBI::Const::GetInfoReturn | N/A | Data and functions for describing GetInfo results |
| DBI::Const::GetInfoType | N/A | Data describing GetInfo type codes |
| DBI::DBD | 11.21 | Perl DBI Database Driver Writer's Guide |
| DBI::DBD::Metadata | N/A | Generate the code and data for some DBI metadata methods |
| DBI::FAQ | 0.38 | The Frequently Asked Questions for the Perl5 Database Interface |
| DBI::Profile | 1.07 | Performance profiling and benchmarking for the DBI |
| DBI::ProfileData | 1.0 | manipulate DBI::ProfileDumper data dumps |
| DBI::ProfileDumper | 1.0 | profile DBI usage and output data to a file |
| DBI::ProfileDumper::Apache | 1.0 | capture DBI profiling data from Apache/mod_perl |
| DBI::ProxyServer | N/A | a server for the DBD::Proxy driver |
| DBI::PurePerl | 1.96 | a DBI emulation using pure perl (no C/XS compilation required) |
| DBI::SQL::Nano | 0.01 | a very tiny SQL engine |
| DBI::W32ODBC | N/A | An experimental DBI emulation layer for Win32::ODBC |
| DB_File | 1.807 | Perl5 access to Berkeley DB version 1.x |
| Devel::DProf | N/A | a Perl code profiler |
| Devel::Peek | 1.0003 | A data debugging tool for the XS programmer |
| Devel::PPPort | 2.0002 | Perl/Pollution/Portability |
| Devel::SelfStubber | 1.03 | generate stubs for a SelfLoading module |
| diagnostics | 1.1 | Perl compiler pragma to force verbose warning diagnostics |
| Digest | 1.00 | Modules that calculate message digests |
| Digest::MD5 | 2.26 | Perl interface to the MD5 Algorithm |
| Digest::SHA1 | 2.04 | Perl interface to the SHA-1 Algorithm |
| DirHandle | 1.00 | supply object methods for directory handles |
| Dumpvalue | 1.11 | provides screen dump of Perl data. |
| DynaLoader | 1.04 | Dynamically load C libraries into Perl code |
| Encode | 1.75 | character encodings |
| Encode::Alias | 1.32 | alias definitions to encodings |
| Encode::Byte | 1.22 | Single Byte Encodings |
| Encode::CJKConstants | 1.00 | Internally used by Encode::??::ISO_2022_* |
| Encode::CN | 1.24 | China-based Chinese Encodings |
| Encode::CN::HZ | 1.04 | internally used by Encode::CN |
| Encode::Config | 1.06 | internally used by Encode |
| Encode::EBCDIC | 1.21 | EBCDIC Encodings |
| Encode::Encoder | 0.05 | Object Oriented Encoder |
| Encode::Encoding | 1.30 | Encode Implementation Base Class |
| Encode::Guess | 1.06 | Guesses encoding from data |
| Encode::JP | 1.25 | Japanese Encodings |
| Encode::JP::H2Z | 1.02 | internally used by Encode::JP::2022_JP* |
| Encode::JP::JIS7 | 1.08 | internally used by Encode::JP |
| Encode::KR | 1.22 | Korean Encodings |
| Encode::KR::2022_KR | 1.05 | internally used by Encode::KR |
| Encode::MIME::Header | 1.05 | MIME 'B' and 'Q' header encoding |
| Encode::PerlIO | N/A | a detailed document on Encode and PerlIO |
| Encode::Supported | N/A | Encodings supported by Encode |
| Encode::Symbol | 1.22 | Symbol Encodings |
| Encode::TW | 1.26 | Taiwan-based Chinese Encodings |
| Encode::Unicode | 1.37 | Various Unicode Transformation Formats |
| encoding | 1.35 | allows you to write your script in non-ascii or non-utf8 |
| English | 1.00 | use nice English (or awk) names for ugly punctuation variables |
| Env | 1.00 | perl module that imports environment variables as scalars or arrays |
| Errno | 1.09 | System errno constants |
| Exporter | 5.566 | Implements default import method for modules |
| Exporter::Heavy | 5.566 | Exporter guts |
| ExtUtils::Command | 1.04 | utilities to replace common UNIX commands in Makefiles etc. |
| ExtUtils::Command::MM | 0.01 | Commands for the MM's to use in Makefiles |
| ExtUtils::Constant | 0.12 | generate XS code to import C header constants |
| ExtUtils::Embed | 1.250601 | Utilities for embedding Perl in C/C++ applications |
| ExtUtils::F77 | N/A | Simple interface to F77 libs |
| ExtUtils::Install | 1.29 | install files from here to there |
| ExtUtils::Installed | 0.06 | Inventory management of installed modules |
| ExtUtils::Liblist | 1.00 | determine libraries to use and how to use them |
| ExtUtils::MakeMaker | 6.03 | create an extension Makefile |
| ExtUtils::Manifest | 1.38 | utilities to write and check a MANIFEST file |
| ExtUtils::Miniperl | N/A | write the C code for perlmain.c |
| ExtUtils::Mkbootstrap | 1.15 | make a bootstrap file for use by DynaLoader |
| ExtUtils::Mksymlists | 1.19 | write linker options files for dynamic extension |
| ExtUtils::MM | 0.04 | OS adjusted ExtUtils::MakeMaker subclass |
| ExtUtils::MM_Any | 0.04 | Platform agnostic MM methods |
| ExtUtils::MM_BeOS | 1.03 | methods to override UN*X behaviour in ExtUtils::MakeMaker |
| ExtUtils::MM_Cygwin | 1.04 | methods to override UN*X behaviour in ExtUtils::MakeMaker |
| ExtUtils::MM_DOS | 0.01 | DOS specific subclass of ExtUtils::MM_Unix |
| ExtUtils::MM_MacOS | 1.03 | methods to override UN*X behaviour in ExtUtils::MakeMaker |
| ExtUtils::MM_NW5 | 2.05 | methods to override UN*X behaviour in ExtUtils::MakeMaker |
| ExtUtils::MM_OS2 | 1.03 | methods to override UN*X behaviour in ExtUtils::MakeMaker |
| ExtUtils::MM_Unix | 1.33 | methods used by ExtUtils::MakeMaker |
| ExtUtils::MM_UWIN | 0.01 | U/WIN specific subclass of ExtUtils::MM_Unix |
| ExtUtils::MM_VMS | N/A | methods to override UN*X behaviour in ExtUtils::MakeMaker |
| ExtUtils::MM_Win32 | 1.05 | methods to override UN*X behaviour in ExtUtils::MakeMaker |
| ExtUtils::MM_Win95 | 0.02 | method to customize MakeMaker for Win9X |
| ExtUtils::MY | 0.01 | ExtUtils::MakeMaker subclass for customization |
| ExtUtils::Packlist | 0.04 | manage .packlist files |
| ExtUtils::testlib | 1.15 | add blib/* directories to @INC |
| Fatal | 1.03 | replace functions with equivalents which succeed or die |
| Fcntl | 1.04 | load the C Fcntl.h defines |
| fields | 1.02 | compile-time class fields |
| File::Basename | 2.71 | split a pathname into pieces |
| File::CheckTree | 4.2 | run many filetest checks on a tree |
| File::Compare | 1.1003 | Compare files or filehandles |
| File::Copy | 2.05 | Copy files or filehandles |
| File::DosGlob | 1.00 | DOS like globbing and then some |
| File::Find | 1.04 | Traverse a directory tree. |
| File::Glob | 1.01 | Perl extension for BSD glob routine |
| File::Listing | 1.11 | parse directory listing |
| File::Path | 1.05 | create or remove directory trees |
| File::Spec | 0.83 | portably perform operations on file names |
| File::Spec::Cygwin | 1.0 | methods for Cygwin file specs |
| File::Spec::Epoc | 1.00 | methods for Epoc file specs |
| File::Spec::Functions | 1.2 | portably perform operations on file names |
| File::Spec::Mac | 1.3 | File::Spec for Mac OS (Classic) |
| File::Spec::OS2 | 1.1 | methods for OS/2 file specs |
| File::Spec::Unix | 1.4 | File::Spec for Unix, base for other File::Spec modules |
| File::Spec::VMS | N/A | methods for VMS file specs |
| File::Spec::Win32 | 1.3 | methods for Win32 file specs |
| File::stat | 1.00 | by-name interface to Perl's built-in stat() functions |
| File::Temp | 0.13 | return name and handle of a temporary file safely |
| FileCache | 1.021 | keep more files open than the system permits |
| FileHandle | 2.01 | supply object methods for filehandles |
| filetest | 1.00 | Perl pragma to control the filetest permission operators |
| Filter::Simple | 0.78 | Simplified source filtering |
| Filter::Util::Call | 1.06 | Perl Source Filter Utility Module |
| FindBin | 1.43 | Locate directory of original perl script |
| FreezeThaw | 0.43 | converting Perl structures to strings and back. |
| Getopt::Long | 2.32 | Extended processing of command line options |
| Getopt::Std | 1.03 | Process single-character switches with switch clustering |
| Graph | 0.20101 | graph operations |
| Graph::Base | N/A | graph base class |
| Graph::BFS | N/A | graph breadth-first search |
| Graph::DFS | N/A | graph depth-first search |
| Graph::Directed | N/A | directed graphs |
| Graph::HeapElem | 0.01 | internal use only |
| Graph::Kruskal | 2.0 | Kruskal's Algorithm for Minimal Spanning Trees in Graphs |
| Graph::Reader | 1.02 | base class for Graph file format readers |
| Graph::Reader::Dot | 1.01 | class for reading a Graph instance from Dot format |
| Graph::Reader::HTK | 1.03 | read an HTK lattice in as an instance of Graph |
| Graph::Reader::XML | 1.03 | class for reading a Graph instance from XML |
| Graph::Traversal | N/A | graph traversal |
| Graph::Undirected | N/A | directed graphs |
| Graph::Weighted | 0.1301 | An abstract, weighted graph implementation |
| Graph::Weighted::Capacity | 0.0301 | A capacity graph implementation |
| Graph::Writer | 1.02 | base class for Graph file format writers |
| Graph::Writer::daVinci | 1.02 | write out directed graph in daVinci format |
| Graph::Writer::Dot | 1.02 | write out directed graph in Dot format |
| Graph::Writer::HTK | 1.02 | write an perl Graph out as an HTK lattice file |
| Graph::Writer::VCG | 1.03 | write out directed graph in VCG format |
| Graph::Writer::XML | 1.02 | write out directed graph as XML |
| Hash::Util | 0.04 | A selection of general-utility hash subroutines |
| Heap | 0.50 | Perl extensions for keeping data partially sorted |
| Heap::Binary | 0.01 | a Perl extension for keeping data partially sorted |
| Heap::Binomial | 0.01 | a Perl extension for keeping data partially sorted |
| Heap::Elem | 0.01 | Perl extension for elements to be put in Heaps |
| Heap::Elem::Num | 0.01 | Perl extension for Numeric Heap Elements |
| Heap::Elem::NumRev | 0.01 | Perl extension for Reversed Numeric Heap Elements |
| Heap::Elem::Ref | 0.01 | Perl extension for Object Reference Heap Elements |
| Heap::Elem::RefRev | 0.01 | Perl extension for reversed Object Reverence Heap Elements |
| Heap::Elem::Str | 0.01 | Perl extension for String Heap Elements |
| Heap::Elem::StrRev | 0.01 | Perl extension for Reversed String Heap Elements |
| Heap::Fibonacci | 0.01 | a Perl extension for keeping data partially sorted |
| HTML::Entities | 1.25 | Encode or decode strings with HTML entities |
| HTML::Filter | 2.09 | Filter HTML text through the parser |
| HTML::Form | 1.00 | Class that represents an HTML form element |
| HTML::HeadParser | 2.17 | Parse section of a HTML document |
| HTML::LinkExtor | 1.31 | Extract links from an HTML document |
| HTML::Parser | 3.28 | HTML parser class |
| HTML::PullParser | 2.06 | Alternative HTML::Parser interface |
| HTML::Tagset | 3.03 | data tables useful in parsing HTML |
| HTML::TokeParser | 2.24 | Alternative HTML::Parser interface |
| HTTP::Cookies | 1.30 | HTTP cookie jars |
| HTTP::Cookies::Microsoft | N/A | access to Microsoft cookies files |
| HTTP::Cookies::Netscape | 1.01 | access to Netscape cookies files |
| HTTP::Daemon | 1.26 | a simple http server class |
| HTTP::Date | 1.44 | date conversion routines |
| HTTP::Headers | 1.44 | Class encapsulating HTTP Message headers |
| HTTP::Headers::Util | 1.10 | Header value parsing utility functions |
| HTTP::Message | 1.25 | Class encapsulating HTTP messages |
| HTTP::Negotiate | 1.12 | choose a variant of a document to serve (HTTP content negotiation) |
| HTTP::Request | 1.30 | Class encapsulating HTTP Requests |
| HTTP::Request::Common | 1.19 | Construct common HTTP::Request objects |
| HTTP::Response | 1.36 | Class encapsulating HTTP Responses |
| HTTP::Status | 1.26 | HTTP Status code processing |
| I18N::Collate | 1.00 | compare 8-bit scalar data according to the current locale |
| I18N::Langinfo | 0.01 | query locale information |
| I18N::LangTags | 0.27 | functions for dealing with RFC3066-style language tags |
| I18N::LangTags::List | 0.25 | tags and names for human languages |
| if | 0.01 | C |
| Inline-API | N/A | How to bind a programming language to Perl using Inline.pm |
| Inline-FAQ | N/A | The Inline FAQ |
| Inline-Support | N/A | Support Information for Inline.pm and related modules. |
| Inline | 0.44 | Write Perl subroutines in other programming languages. |
| Inline::C | 0.44 | Write Perl Subroutines in C |
| Inline::C-Cookbook | N/A | A Cornucopia of Inline C Recipes |
| Inline::C::ParseRecDescent | N/A | The Classic Inline::C Parser |
| Inline::C::ParseRegExp | N/A | The New and Improved Inline::C Parser |
| Inline::Pdlpp | 0.2 | Write PDL Subroutines inline with PDL::PP |
| integer | 1.00 | Perl pragma to use integer arithmetic instead of floating point |
| IO | 1.20 | load various IO modules |
| IO::AtomicFile | 2.101 | write a file which is updated atomically |
| IO::Dir | 1.03 | supply object methods for directory handles |
| IO::File | 1.09 | supply object methods for filehandles |
| IO::Handle | 1.21 | supply object methods for I/O handles |
| IO::InnerFile | 2.102 | define a file inside another file |
| IO::Lines | 2.103 | IO:: interface for reading/writing an array of lines |
| IO::Pipe | 1.122 | supply object methods for pipes |
| IO::Poll | 0.06 | Object interface to system poll call |
| IO::Scalar | 2.104 | IO:: interface for reading/writing a scalar |
| IO::ScalarArray | 2.103 | IO:: interface for reading/writing an array of scalars |
| IO::Seekable | 1.08 | supply seek based methods for I/O objects |
| IO::Select | 1.15 | OO interface to the select system call |
| IO::Socket | 1.27 | Object interface to socket communications |
| IO::Socket::INET | 1.26 | Object interface for AF_INET domain sockets |
| IO::Socket::UNIX | 1.2 | Object interface for AF_UNIX domain sockets |
| IO::String | 1.02 | Emulate IO::File interface for in-core strings |
| IO::Stringy | 2.108 | I/O on in-core objects like strings and arrays |
| IO::Wrap | 2.102 | wrap raw filehandles in IO::Handle interface |
| IO::WrapTie | 2.102 | wrap tieable objects in IO::Handle interface |
| IPC::Msg | 1 | SysV Msg IPC object class |
| IPC::Open2 | 1.01 | open a process for both reading and writing |
| IPC::Open3 | 1.0104 | open a process for reading, writing, and error handling |
| IPC::Semaphore | 1 | SysV Semaphore IPC object class |
| IPC::SysV | 1.03 | SysV IPC constants |
| less | 0.01 | perl pragma to request less of something from the compiler |
| lib | 0.5564 | manipulate @INC at compile time |
| List::Util | 1.07 | A selection of general-utility list subroutines |
| locale | 1.00 | Perl pragma to use and avoid POSIX locales for built-in operations |
| Locale::Constants | 2.01 | constants for Locale codes |
| Locale::Country | 2.06 | ISO codes for country identification (ISO 3166) |
| Locale::Currency | 2.02 | ISO three letter codes for currency identification (ISO 4217) |
| Locale::Language | 2.02 | ISO two letter codes for language identification (ISO 639) |
| Locale::Maketext | 1.03 | framework for localization |
| Locale::Maketext::TPJ13 | N/A | article about software localization |
| Locale::Script | 2.02 | ISO codes for script identification (ISO 15924) |
| LWP | 5.69 | The World-Wide Web library for Perl |
| LWP::Authen::Ntlm | N/A | Library for enabling NTLM authentication (Microsoft) in LWP |
| LWP::ConnCache | 0.01 | Connection cache manager |
| LWP::Debug | N/A | debug routines for the libwww-perl library |
| LWP::DebugFile | N/A | N/A |
| LWP::MediaTypes | 1.27 | guess media type for a file or a URL |
| LWP::MemberMixin | N/A | Member access mixin class |
| LWP::Protocol | 1.39 | Base class for LWP protocols |
| LWP::RobotUA | 1.19 | a class for well-behaved Web robots |
| LWP::Simple | 1.36 | simple procedural interface to LWP |
| LWP::UserAgent | 2.003 | A WWW UserAgent class |
| lwpcook | N/A | The libwww-perl cookbook |
| lwptut | N/A | An LWP Tutorial |
| Mail::Address | 1.62 | Parse mail addresses |
| Mail::Cap | 1.62 | Parse mailcap files |
| Mail::Field | 1.62 | Base class for manipulation of mail header fields |
| Mail::Field::AddrList | 1.62 | object representation of e-mail address lists |
| Mail::Filter | 1.62 | Filter mail through multiple subroutines |
| Mail::Header | 1.62 | manipulate mail RFC822 compliant headers |
| Mail::Internet | 1.62 | manipulate Internet format (RFC 822) mail messages |
| Mail::Mailer | 1.62 | Simple interface to electronic mailing mechanisms |
| Mail::Send | 1.62 | Simple electronic mail interface |
| Mail::Util | 1.62 | mail utility functions |
| Math::BigFloat | 1.35 | Arbitrary size floating point math package |
| Math::BigInt | 1.60 | Arbitrary size integer math package |
| Math::BigInt::Calc | 0.30 | Pure Perl module to support Math::BigInt |
| Math::BigRat | 0.07 | arbitrarily big rationals |
| Math::Complex | 1.34 | complex numbers and associated mathematical functions |
| Math::Kleene | N/A | the theory behind it |
| Math::MatrixReal | 1.9 | Matrix of Reals |
| Math::Trig | 1.01 | trigonometric functions |
| Memoize | 1.01 | Make functions faster by trading space for time |
| Memoize::AnyDBM_File | 0.65 | glue to provide EXISTS for AnyDBM_File for Storable use |
| Memoize::Expire | 1.00 | Plug-in module for automatic expiration of memoized values |
| Memoize::ExpireFile | 1.01 | test for Memoize expiration semantics |
| Memoize::ExpireTest | 0.65 | test for Memoize expiration semantics |
| Memoize::NDBM_File | 0.65 | glue to provide EXISTS for NDBM_File for Storable use |
| Memoize::SDBM_File | 0.65 | glue to provide EXISTS for SDBM_File for Storable use |
| Memoize::Storable | 0.65 | store Memoized data in Storable database |
| MIME::Base64 | 2.12 | Encoding and decoding of base64 strings |
| MIME::QuotedPrint | 2.03 | Encoding and decoding of quoted-printable strings |
| MLDBM | 2.01 | store multi-level hash structure in single level tied hash |
| NDBM_File | 1.04 | Tied access to ndbm files |
| Net::Cmd | 2.24 | Network Command class (as used by FTP, SMTP etc) |
| Net::Config | 1.10 | Local configuration data for libnet |
| Net::Domain | 2.18 | Attempt to evaluate the current host's internet name and domain |
| Net::FTP | 2.71 | FTP Client class |
| Net::hostent | 1.00 | by-name interface to Perl's built-in gethost*() functions |
| Net::HTTP | 1.00 | Low-level HTTP connection (client) |
| Net::HTTP::NB | 0.02 | Non-blocking HTTP client |
| Net::libnetFAQ | N/A | libnet Frequently Asked Questions |
| Net::netent | 1.00 | by-name interface to Perl's built-in getnet*() functions |
| Net::Netrc | 2.12 | OO interface to users netrc file |
| Net::NNTP | 2.22 | NNTP Client class |
| Net::Ping | 2.20 | check a remote host for reachability |
| Net::POP3 | 2.24 | Post Office Protocol 3 Client class (RFC1939) |
| Net::protoent | 1.00 | by-name interface to Perl's built-in getproto*() functions |
| Net::servent | 1.00 | by-name interface to Perl's built-in getserv*() functions |
| Net::SMTP | 2.26 | Simple Mail Transfer Protocol Client |
| Net::Telnet | 3.03 | interact with TELNET port or other TCP ports |
| Net::Time | 2.09 | time and daytime network client interface |
| NEXT | 0.50 | Provide a pseudo-class NEXT that allows method redispatch |
| O | 1.00 | Generic interface to Perl Compiler backends |
| ODBM_File | 1.03 | Tied access to odbm files |
| Opcode | 1.05 | Disable named opcodes when compiling perl code |
| open | 1.01 | perl pragma to set default PerlIO layers for input and output |
| ops | 1.00 | Perl pragma to restrict unsafe operations when compiling |
| Oraperl | N/A | Perl access to Oracle databases for old oraperl scripts |
| overload | 1.00 | Package for overloading perl operations |
| Parse::RecDescent | 1.94 | Generate Recursive-Descent Parsers |
| PDL | 2.4.1 | the Perl Data Language |
| PDL::API | N/A | making piddles from Perl and C/XS code |
| PDL::AutoLoader | N/A | MatLab style AutoLoader for PDL |
| PDL::Bad | N/A | PDL does not process bad values |
| PDL::BadValues | N/A | Discussion of bad value support in PDL |
| PDL::Basic | N/A | Basic utility functions for PDL |
| PDL::CallExt | N/A | call functions in external shared libraries |
| PDL::Char | N/A | PDL subclass which allows reading and writing of fixed-length character strings as byte PDLs |
| PDL::Complex | N/A | handle complex numbers |
| PDL::Core | N/A | fundamental PDL functionality |
| PDL::Core::Dev | N/A | PDL development module |
| PDL::Dataflow | N/A | description of the dataflow philosophy |
| PDL::Dbg | N/A | functions to support debugging of PDL scripts |
| PDL::Delta | N/A | PDL changes between V1.0 and V2.0 |
| PDL::DiskCache | 1.1 | Non-memory-resident array object |
| PDL::Doc | N/A | support for PDL online documentation |
| PDL::Doc::Perldl | N/A | commands for accessing PDL doc database from 'perldl' shell |
| PDL::Exporter | N/A | PDL export control |
| PDL::FAQ | N/A | Frequently asked questions about PDL |
| PDL::FFT | N/A | FFTs for PDL |
| PDL::Filter::Linear | N/A | linear filtering for PDL |
| PDL::Filter::LinPred | N/A | Linear predictive filtering |
| PDL::Fit::Gaussian | N/A | routines for fitting gaussians |
| PDL::Fit::Linfit | N/A | routines for fitting data with linear combinations of functions. |
| PDL::Fit::LM | N/A | Levenber-Marquardt fitting routine for PDL |
| PDL::Fit::Polynomial | N/A | routines for fitting with polynomials |
| PDL::Func | N/A | useful functions |
| PDL::Gaussian | N/A | Gaussian distributions. |
| PDL::Graphics2D | N/A | An object oriented interface to PDL graphics |
| PDL::Graphics::IIS | N/A | Display PDL images on IIS devices (saoimage/ximtool) |
| PDL::Graphics::LUT | N/A | provides access to a number of look-up tables |
| PDL::Graphics::PGPLOT | N/A | PGPLOT enhanced interface for PDL |
| PDL::Graphics::PGPLOT::Window | N/A | A OO interface to PGPLOT windows |
| PDL::Graphics::PGPLOTOptions | N/A | Setting PGPLOT options |
| PDL::Graphics::State | N/A | A package to keep track of plotting commands |
| PDL::Graphics::TriD | N/A | PDL 3D interface |
| PDL::Graphics::TriD::ButtonControl | N/A | default event handler subroutines |
| PDL::Graphics::TriD::Contours | N/A | 3D Surface contours for TriD |
| PDL::Graphics::TriD::Labels | N/A | Text tools |
| PDL::Graphics::TriD::MathGraph | N/A | Mathematical Graph objects for PDL |
| PDL::Graphics::TriD::Objects | N/A | Simple Graph Objects for TriD |
| PDL::Graphics::TriD::Rout | N/A | Helper routines for Three-dimensional graphics |
| PDL::Graphics::TriD::Tk | N/A | A Tk widget interface to the PDL::Graphics::TriD. |
| PDL::Graphics::TriD::VRML | N/A | TriD VRML backend |
| PDL::GSL::DIFF | N/A | PDL interface to numerical differentiation routines in GSL |
| PDL::GSL::INTEG | N/A | PDL interface to numerical integration routines in GSL |
| PDL::GSL::INTERP | N/A | PDL interface to Interpolation routines in GSL |
| PDL::GSL::RNG | N/A | PDL interface to RNG and randist routines in GSL |
| PDL::GSLSF::AIRY | N/A | PDL interface to GSL Special Functions |
| PDL::GSLSF::BESSEL | N/A | PDL interface to GSL Special Functions |
| PDL::GSLSF::CLAUSEN | N/A | PDL interface to GSL Special Functions |
| PDL::GSLSF::COULOMB | N/A | PDL interface to GSL Special Functions |
| PDL::GSLSF::COUPLING | N/A | PDL interface to GSL Special Functions |
| PDL::GSLSF::DAWSON | N/A | PDL interface to GSL Special Functions |
| PDL::GSLSF::DEBYE | N/A | PDL interface to GSL Special Functions |
| PDL::GSLSF::DILOG | N/A | PDL interface to GSL Special Functions |
| PDL::GSLSF::ELEMENTARY | N/A | PDL interface to GSL Special Functions |
| PDL::GSLSF::ELLINT | N/A | PDL interface to GSL Special Functions |
| PDL::GSLSF::ELLJAC | N/A | PDL interface to GSL Special Functions |
| PDL::GSLSF::ERF | N/A | PDL interface to GSL Special Functions |
| PDL::GSLSF::EXP | N/A | PDL interface to GSL Special Functions |
| PDL::GSLSF::EXPINT | N/A | PDL interface to GSL Special Functions |
| PDL::GSLSF::FERMI_DIRAC | N/A | PDL interface to GSL Special Functions |
| PDL::GSLSF::GAMMA | N/A | PDL interface to GSL Special Functions |
| PDL::GSLSF::GEGENBAUER | N/A | PDL interface to GSL Special Functions |
| PDL::GSLSF::HYPERG | N/A | PDL interface to GSL Special Functions |
| PDL::GSLSF::LAGUERRE | N/A | PDL interface to GSL Special Functions |
| PDL::GSLSF::LEGENDRE | N/A | PDL interface to GSL Special Functions |
| PDL::GSLSF::LOG | N/A | PDL interface to GSL Special Functions |
| PDL::GSLSF::POLY | N/A | PDL interface to GSL Special Functions |
| PDL::GSLSF::POW_INT | N/A | PDL interface to GSL Special Functions |
| PDL::GSLSF::PSI | N/A | PDL interface to GSL Special Functions |
| PDL::GSLSF::SYNCHROTRON | N/A | PDL interface to GSL Special Functions |
| PDL::GSLSF::TRANSPORT | N/A | PDL interface to GSL Special Functions |
| PDL::GSLSF::TRIG | N/A | PDL interface to GSL Special Functions |
| PDL::GSLSF::ZETA | N/A | PDL interface to GSL Special Functions |
| PDL::Image2D | N/A | Miscellaneous 2D image processing functions |
| PDL::ImageND | N/A | useful image processing in N dimensions |
| PDL::ImageRGB | N/A | some utility functions for RGB image data handling |
| PDL::Impatient | N/A | PDL for the impatient (quick overview) |
| PDL::Index | N/A | an index of PDL documentation |
| PDL::Indexing | N/A | how to index piddles. |
| PDL::Internals | N/A | description of some aspects of the current internals |
| PDL::Intro | N/A | Introduction to the Perl Data Language |
| PDL::IO::Dumper | data dumping for structs with PDLs | |
| PDL::IO::FastRaw | N/A | A simple, fast and convenient io format for PerlDL. |
| PDL::IO::FITS | N/A | Simple FITS support for PDL |
| PDL::IO::FlexRaw | N/A | A flexible binary i/o format for PerlDL. |
| PDL::IO::Misc | N/A | misc IO routines for PDL |
| PDL::IO::NDF | 1.02 | PDL Module for reading and writing Starlink |
| PDL::IO::Pic | N/A | image I/O for PDL |
| PDL::IO::Pnm | N/A | pnm format I/O for PDL |
| PDL::IO::Storable | N/A | helper functions to make PDL usable with Storable |
| PDL::Lite | 2.4.1 | minimum PDL module OO loader |
| PDL::LiteF | 2.4.1 | minimum PDL module function loader |
| PDL::Lvalue | N/A | declare PDL lvalue subs |
| PDL::Math | N/A | extended mathematical operations and special functions |
| PDL::Matrix | 0.5 | a convenience matrix class for column-major access |
| PDL::MatrixOps | N/A | PDL::MatrixOps |
| PDL::NiceSlice | 1.0.1 | toward a nicer slicing syntax for PDL |
| PDL::Objects | N/A | Object-Orientation, what is it and how to exploit it |
| PDL::Ops | N/A | Fundamental mathematical operators |
| PDL::Opt::Simplex | N/A | Simplex optimization routines |
| PDL::Options | 0.92 | simplifies option passing by hash in PerlDL |
| PDL::pdldoc | N/A | shell interface to PDL documentation |
| PDL::perldl | N/A | Simple shell for PDL |
| PDL::Philosophy | N/A | what's behind PDL? |
| PDL::Pod::Parser | 1 | base class for creating pod filters and translators |
| PDL::Pod::Select | 1 | function to extract selected sections of pod documentation |
| PDL::Pod::Usage | 1 | print a usage message using a script's embedded pod documentation |
| PDL::PP | 2.2 | Generate PDL routines from concise descriptions |
| PDL::PP-Inline | N/A | Write PDL Subroutines inline with PDL::PP |
| PDL::PP::Dump | N/A | dump pp_xxx calls to stdout |
| PDL::PP::Signature | N/A | Internal module to handle signatures |
| PDL::pptemplate | N/A | script to generate Makefile.PL and PP file skeleton |
| PDL::Primitive | N/A | primitive operations for pdl |
| PDL::Reduce | N/A | a C |
| PDL::Slatec | N/A | PDL interface to the slatec numerical programming library |
| PDL::Slices | N/A | Stupid index tricks |
| PDL::Tests | N/A | tests for some PP features |
| PDL::Tips | N/A | Small tidbits of useful arcana. Programming tidbits and such. |
| PDL::Transform | N/A | Image transformations and N-D functions |
| PDL::Transform::Cartography | 0.5 | Useful cartographic projections |
| PDL::Types | N/A | define fundamental PDL Datatypes |
| PDL::Ufunc | N/A | primitive ufunc operations for pdl |
| PerlIO | 1.01 | On demand loader for PerlIO layers and root of PerlIO::* name space |
| PerlIO::encoding | 0.06 | encoding layer |
| PerlIO::scalar | 0.01 | support module for in-memory IO. |
| PerlIO::via | 0.01 | Helper class for PerlIO layers implemented in perl |
| PerlIO::via::QuotedPrint | 0.04 | PerlIO layer for quoted-printable strings |
| Pod::Checker | 1.3 | check pod documents for syntax errors |
| Pod::Find | 0.22 | find POD documents in directory trees |
| Pod::Functions | 1.01 | Group Perl's functions a la perlfunc.pod |
| Pod::Html | 1.04 | module to convert pod files to HTML |
| Pod::InputObjects | 1.13 | objects representing POD input paragraphs, commands, etc. |
| Pod::LaTeX | 0.54 | Convert Pod data to formatted Latex |
| Pod::Man | 1.34 | Convert POD data to formatted *roff input |
| Pod::ParseLink | 1.06 | Parse an LE |
| Pod::Parser | 1.13 | base class for creating POD filters and translators |
| Pod::ParseUtils | 0.22 | helpers for POD parsing and conversion |
| pod::perl | N/A | Practical Extraction and Report Language |
| pod::perl5004delta | N/A | what's new for perl5.004 |
| pod::perl5005delta | N/A | what's new for perl5.005 |
| pod::perl561delta | N/A | what's new for perl v5.6.x |
| pod::perl56delta | N/A | what's new for perl v5.6.0 |
| pod::perl570delta | N/A | what's new for perl v5.7.0 |
| pod::perl571delta | N/A | what's new for perl v5.7.1 |
| pod::perl572delta | N/A | what's new for perl v5.7.2 |
| pod::perlaix | N/A | Perl version 5 on IBM Unix (AIX) systems |
| pod::perlamiga | N/A | Perl under Amiga OS |
| pod::perlapi | N/A | autogenerated documentation for the perl public API |
| pod::perlapio | N/A | perl's IO abstraction interface. |
| pod::perlapollo | N/A | Perl version 5 on Apollo DomainOS |
| pod::perlbeos | N/A | Perl version 5 on BeOS |
| pod::perlbook | N/A | Perl book information |
| pod::perlboot | N/A | Beginner's Object-Oriented Tutorial |
| pod::perlbot | N/A | Bag'o Object Tricks (the BOT) |
| pod::perlbs2000 | N/A | building and installing Perl for BS2000. |
| pod::perlcall | N/A | Perl calling conventions from C |
| pod::perlclib | N/A | Internal replacements for standard C library functions |
| pod::perlcn | N/A | 简体中文 Perl 指南 |
| pod::perlcompile | N/A | Introduction to the Perl Compiler-Translator |
| pod::perlcygwin | N/A | Perl for Cygwin |
| pod::perldata | N/A | Perl data types |
| pod::perldbmfilter | N/A | Perl DBM Filters |
| pod::perldebguts | N/A | Guts of Perl debugging |
| pod::perldebtut | N/A | Perl debugging tutorial |
| pod::perldebug | N/A | Perl debugging |
| pod::perldelta | N/A | what is new for perl v5.8.0 |
| pod::perldgux | N/A | Perl under DG/UX. |
| pod::perldiag | N/A | various Perl diagnostics |
| pod::perldos | N/A | N/A |
| pod::perldsc | N/A | Perl Data Structures Cookbook |
| pod::perlebcdic | N/A | Considerations for running Perl on EBCDIC platforms |
| pod::perlembed | N/A | how to embed perl in your C program |
| pod::perlepoc | N/A | Perl for EPOC |
| pod::perlfaq | N/A | frequently asked questions about Perl ($Date: 2002/03/11 21:32:23 $) |
| pod::perlfaq1 | N/A | General Questions About Perl ($Revision: 1.8 $, $Date: 2002/04/07 18:46:13 $) |
| pod::perlfaq2 | N/A | Obtaining and Learning about Perl ($Revision: 1.13 $, $Date: 2002/04/26 16:56:35 $) |
| pod::perlfaq3 | N/A | Programming Tools ($Revision: 1.22 $, $Date: 2002/05/06 13:11:13 $) |
| pod::perlfaq4 | N/A | Data Manipulation ($Revision: 1.25 $, $Date: 2002/05/30 07:04:25 $) |
| pod::perlfaq5 | N/A | Files and Formats ($Revision: 1.18 $, $Date: 2002/05/30 07:04:25 $) |
| pod::perlfaq6 | N/A | Regular Expressions ($Revision: 1.12 $, $Date: 2002/06/01 22:31:09 $) |
| pod::perlfaq7 | N/A | General Perl Language Issues ($Revision: 1.8 $, $Date: 2002/03/26 15:48:32 $) |
| pod::perlfaq8 | N/A | System Interaction ($Revision: 1.8 $, $Date: 2002/05/16 12:41:42 $) |
| pod::perlfaq9 | N/A | Networking ($Revision: 1.9 $, $Date: 2002/04/07 18:46:13 $) |
| pod::perlfilter | N/A | Source Filters |
| pod::perlfork | N/A | Perl's fork() emulation |
| pod::perlform | N/A | Perl formats |
| pod::perlfreebsd | N/A | Perl version 5 on FreeBSD systems |
| pod::perlfunc | N/A | Perl builtin functions |
| pod::perlguts | N/A | Introduction to the Perl API |
| pod::perlhack | N/A | How to hack at the Perl internals |
| pod::perlhist | N/A | the Perl history records |
| pod::perlhpux | N/A | Perl version 5 on Hewlett-Packard Unix (HP-UX) systems |
| pod::perlhurd | N/A | Perl version 5 on Hurd |
| pod::perlintern | N/A | autogenerated documentation of purely B |
| pod::perlintro | N/A | a brief introduction and overview of Perl |
| pod::perliol | N/A | C API for Perl's implementation of IO in Layers. |
| pod::perlipc | N/A | Perl interprocess communication (signals, fifos, pipes, safe subprocesses, sockets, and semaphores) |
| pod::perlirix | N/A | Perl version 5 on Irix systems |
| pod::perljp | N/A | 泣塑胳 Perl ガイド |
| pod::perlko | N/A | Perl苞 茄惫绢 牢内爹 |
| pod::perllexwarn | N/A | Perl Lexical Warnings |
| pod::perllocale | N/A | Perl locale handling (internationalization and localization) |
| pod::perllol | N/A | Manipulating Arrays of Arrays in Perl |
| pod::perlmachten | N/A | Perl version 5 on Power MachTen systems |
| pod::perlmacos | N/A | Perl under Mac OS (Classic) |
| pod::perlmint | N/A | Perl version 5 on Atari MiNT |
| pod::perlmod | N/A | Perl modules (packages and symbol tables) |
| pod::perlmodinstall | N/A | Installing CPAN Modules |
| pod::perlmodlib | N/A | constructing new Perl modules and finding existing ones |
| pod::perlmodstyle | N/A | Perl module style guide |
| pod::perlmpeix | N/A | Perl/iX for HP e3000 MPE |
| pod::perlnewmod | N/A | preparing a new module for distribution |
| pod::perlnumber | N/A | semantics of numbers and numeric operations in Perl |
| pod::perlobj | N/A | Perl objects |
| pod::perlop | N/A | Perl operators and precedence |
| pod::perlopentut | N/A | tutorial on opening things in Perl |
| pod::perlos2 | N/A | Perl under OS/2, DOS, Win0.3*, Win0.95 and WinNT. |
| pod::perlos390 | N/A | building and installing Perl for OS/390 and z/OS |
| pod::perlothrtut | N/A | old tutorial on threads in Perl |
| pod::perlpacktut | N/A | tutorial on C |
| pod::perlplan9 | N/A | Plan 9-specific documentation for Perl |
| pod::perlpod | N/A | the Plain Old Documentation format |
| pod::perlpodspec | N/A | Plain Old Documentation: format specification and notes |
| pod::perlport | N/A | Writing portable Perl |
| pod::perlqnx | N/A | Perl version 5 on QNX |
| pod::perlre | N/A | Perl regular expressions |
| pod::perlref | N/A | Perl references and nested data structures |
| pod::perlreftut | N/A | Mark's very short tutorial about references |
| pod::perlrequick | N/A | Perl regular expressions quick start |
| pod::perlretut | N/A | Perl regular expressions tutorial |
| pod::perlrun | N/A | how to execute the Perl interpreter |
| pod::perlsec | N/A | Perl security |
| pod::perlsolaris | N/A | Perl version 5 on Solaris systems |
| pod::perlstyle | N/A | Perl style guide |
| pod::perlsub | N/A | Perl subroutines |
| pod::perlsyn | N/A | Perl syntax |
| pod::perlthrtut | N/A | tutorial on threads in Perl |
| pod::perltie | N/A | how to hide an object class in a simple variable |
| pod::perltoc | N/A | perl documentation table of contents |
| pod::perltodo | N/A | Perl TO-DO List |
| pod::perltooc | N/A | Tom's OO Tutorial for Class Data in Perl |
| pod::perltoot | N/A | Tom's object-oriented tutorial for perl |
| pod::perltrap | N/A | Perl traps for the unwary |
| pod::perltru64 | N/A |