BioPerl Dependencies NOTE : This file was auto-generated by the helper script maintenance/dependencies.pl. Do not edit directly! The following packages are used by BioPerl. While not all are required for BioPerl to operate properly, some functionality will be missing without them. You can easily choose to install all of these during the normal installation process. Note that the PPM version of the BioPerl packages always tries to install all dependencies. The DBD::mysql, DB_File and XML::Parser modules require other applications or databases: MySQL, Berkeley DB, and expat respectively. NB: This list of packages is not authoritative. See the 'requires', 'build_requires' and 'recommends' sections of Build.PL instead. ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | AcePerl | * Ace - Interface to ACEDB (Popular | None | | | Genome DB) | | | | * Ace::Sequence::Homol - NA | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::DB::Ace - Ace | | * Bio::DB::GFF::Adaptor::ace - Ace | | * Bio::DB::GFF::Adaptor::dbi::mysqlace - Ace::Sequence::Homol | | * Bio::DB::GFF::Adaptor::dbi::oracleace - Ace::Sequence::Homol | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Algorithm-Munkres | * Algorithm::Munkres - Solution to | None | | | classical Assignment Problem | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::PhyloNetwork - Algorithm::Munkres | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Archive-Tar | * Archive::Tar - Read, write and | None | | | manipulate tar files | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::Root::Build - Archive::Tar | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Array-Compare | * Array::Compare - Class to compare | None | | | two arrays | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::PhyloNetwork - Array::Compare | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Bio-ASN1-EntrezGene | * Bio::ASN1::EntrezGene - Parser | None | | | for NCBI Entrez Gene (ASN.1- | | | | format) | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::SeqIO::entrezgene - Bio::ASN1::EntrezGene | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Compress-Zlib | * Compress::Zlib - Interface to | None | | | zlib compression library | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::DB::SeqFeature::Store - Compress::Zlib | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Convert-Binary-C | * Convert::Binary::C - Binary Data | None | | | Conversion using C Types | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::SeqIO::strider - Convert::Binary::C | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | DBI | * DBI - Generic Database Interface | None | | | (see DBD modules) | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::DB::GFF::Adaptor::dbi - DBI | | * Bio::DB::GFF::Adaptor::dbi::caching_handle - DBI | | * Bio::DB::SeqFeature::Store::DBI::mysql - DBI | | * Bio::DB::SeqFeature::Store::DBI::Pg - DBI | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Data-Stag | * Data::Stag - NA | None | | | * Data::Stag::XMLWriter - NA | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::Annotation::TagTree - Data::Stag | | * Bio::SeqIO::chaosxml - Data::Stag::XMLWriter | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Graph | * Graph::Directed - NA | None | | | * Graph::Undirected - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::PhyloNetwork - Graph::Directed | | * Bio::Ontology::SimpleGOEngine::GraphAdaptor - Graph::Directed | | * Bio::Assembly::Tools::ContigSpectrum - Graph::Undirected | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | HTML-Parser | * HTML::HeadParser - Parse <HEAD> | None | | | section of HTML documents | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::Tools::Analysis::DNA::ESEfinder - HTML::HeadParser | | * Bio::Tools::Analysis::Protein::ELM - HTML::HeadParser | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | IO-String | * IO::String - IO::File interface | None | | | for in-core strings | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::PhyloNetwork - IO::String | | * Bio::DB::CUTG - IO::String | | * Bio::DB::SeqHound - IO::String | | * Bio::DB::WebDBSeqI - IO::String | | * Bio::Index::Blast - IO::String | | * Bio::Index::BlastTable - IO::String | | * Bio::Index::Hmmer - IO::String | | * Bio::SearchIO::Writer::BSMLResultWriter - IO::String | | * Bio::SeqIO::game::gameWriter - IO::String | | * Bio::Tools::Analysis::DNA::ESEfinder - IO::String | | * Bio::Tools::Analysis::Protein::Domcut - IO::String | | * Bio::Tools::Analysis::Protein::ELM - IO::String | | * Bio::Tools::Analysis::Protein::GOR4 - IO::String | | * Bio::Tools::Analysis::Protein::HNN - IO::String | | * Bio::Tools::Analysis::Protein::Mitoprot - IO::String | | * Bio::Tools::Analysis::Protein::NetPhos - IO::String | | * Bio::Tools::Analysis::Protein::Scansite - IO::String | | * Bio::Tools::Analysis::Protein::Sopma - IO::String | | * Bio::Tools::Phylo::Molphy - IO::String | | * Bio::Tools::Phylo::PAML - IO::String | | * Bio::Tools::Run::RemoteBlast - IO::String | | * Bio::TreeIO::cluster - IO::String | | * Bio::TreeIO::nexus - IO::String | | * Bio::Variation::IO::xml - IO::String | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Math-Random | * Math::Random - Random Number | None | | | Generators | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::PhyloNetwork::RandomFactory - Math::Random | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Memoize | * Memoize - Automatically cache | None | | | results of functions | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::DB::SeqFeature::Store::DBI::mysql - Memoize | | * Bio::DB::SeqFeature::Store::DBI::Pg - Memoize | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Module-Build | * Module::Build - Build, test, and | 0.2805 | | | install Perl modules | | | | * Module::Build::PPMMaker - NA | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::Root::Build - Module::Build | | * Bio::Root::Test - Module::Build | | * Bio::Root::Build - Module::Build::PPMMaker | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | PostScript | * PostScript::TextBlock - Objects | None | | | used by PS::Document | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::Tree::Draw::Cladogram - PostScript::TextBlock | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | SVG | * SVG - Generate SVG images and | 2.26 | | | files | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::Draw::Pictogram - SVG | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | SVG-Graph | * SVG::Graph - Series of Modules to | None | | | produce SVG graphs | | | | * SVG::Graph::Data - NA | | | | * SVG::Graph::Data::Node - NA | | | | * SVG::Graph::Data::Tree - NA | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::TreeIO::svggraph - SVG::Graph | | * Bio::TreeIO::svggraph - SVG::Graph::Data | | * Bio::TreeIO::svggraph - SVG::Graph::Data::Node | | * Bio::TreeIO::svggraph - SVG::Graph::Data::Tree | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Set-Scalar | * Set::Scalar - Set of scalars (inc | None | | | references) | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::Tree::Compatible - Set::Scalar | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Spreadsheet-ParseExcel | * Spreadsheet::ParseExcel - Get | None | | | information from Excel file | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::Microarray::Tools::MitoChipV2Parser - Spreadsheet::ParseExcel | | * Bio::Microarray::Tools::ReseqChip - Spreadsheet::ParseExcel | | * Bio::SeqIO::excel - Spreadsheet::ParseExcel | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Spreadsheet-WriteExcel | * Spreadsheet::WriteExcel - Write | None | | | cross-platform Excel binary file. | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::Microarray::Tools::ReseqChip - Spreadsheet::WriteExcel | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Statistics-Frequency | * Statistics::Frequency - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::Microarray::Tools::ReseqChip - Statistics::Frequency | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Storable | * Storable - Persistent data | None | | | structure mechanism | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::DB::SeqFeature::Store - Storable | | * Bio::Restriction::Enzyme - Storable | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Test-Exception | * Test::Exception - Functions for | None | | | testing exception-based code | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::Root::Test - Test::Exception | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Test-Simple | * Test::Builder - NA | None | | | * Test::More - More functions for | | | | writing tests | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::Root::Test::Warn - Test::Builder | | * Bio::Root::Test - Test::More | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Test-Warn | * Test::Warn - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::Root::Test - Test::Warn | | * Bio::Root::Test::Warn - Test::Warn | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Tie-Cacher | * Tie::Cacher - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::DB::SeqFeature::Store - Tie::Cacher | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Time-HiRes | * Time::HiRes - High resolution | None | | | time, sleep, and alarm | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::DB::SeqFeature::Store::Loader - Time::HiRes | | * Bio::DB::SeqFeature::Store::DBI::mysql - Time::HiRes | | * Bio::DB::SeqFeature::Store::DBI::Pg - Time::HiRes | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Tree-DAG_Node | * Tree::DAG_Node - base class for | None | | | trees | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::TreeIO::svggraph - Tree::DAG_Node | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | URI | * URI - NA | None | | | * URI::Escape - General URI | | | | escaping/unescaping functions | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::DB::NCBIHelper - URI | | * Bio::DB::Query::WebQuery - URI | | * Bio::Tools::EUtilities::EUtilParameters - URI | | * Bio::DB::CUTG - URI::Escape | | * Bio::DB::Biblio::eutils - URI::Escape | | * Bio::FeatureIO::gff - URI::Escape | | * Bio::FeatureIO::interpro - URI::Escape | | * Bio::SeqFeature::Annotated - URI::Escape | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | WWW-Mechanize | * WWW::Mechanize - Automates web | None | | | page form & link interaction | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::DB::MeSH - WWW::Mechanize | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | Win32 | * Win32 - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::DB::Fasta - Win32 | | * Bio::DB::GFF - Win32 | | * Bio::DB::Qual - Win32 | | * Bio::Root::IO - Win32 | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | XML-DOM | * XML::DOM - Implements Level 1 of | None | | | W3's DOM | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::FeatureIO::interpro - XML::DOM | | * Bio::SeqIO::bsml - XML::DOM | | * Bio::SeqIO::interpro - XML::DOM | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | XML-DOM-XPath | * XML::DOM::XPath - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::FeatureIO::interpro - XML::DOM::XPath | | * Bio::SeqIO::interpro - XML::DOM::XPath | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | XML-LibXML | * XML::LibXML - Interface to the | None | | | libxml library | | | | * XML::LibXML::Reader - NA | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::TreeIO::phyloxml - XML::LibXML | | * Bio::TreeIO::phyloxml - XML::LibXML::Reader | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | XML-Parser | * XML::Parser - Flexible fast | None | | | parser with plug-in styles | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::Biblio::IO::medlinexml - XML::Parser | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | XML-SAX | * XML::SAX - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::ClusterIO::dbsnp - XML::SAX | | * Bio::SearchIO::blastxml - XML::SAX | | * Bio::SeqIO::bsml_sax - XML::SAX | | * Bio::SeqIO::tigrxml - XML::SAX | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | XML-SAX-Writer | * XML::SAX::Writer - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::SeqIO::tigrxml - XML::SAX::Writer | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | XML-Simple | * XML::Simple - Easy API to | None | | | maintain XML (esp config files) | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::DB::HIV::HIVQueryHelper - XML::Simple | | * Bio::DB::Query::HIVQuery - XML::Simple | | * Bio::Tools::EUtilities - XML::Simple | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | XML-Twig | * XML::Twig - A module for easy | None | | | processing of XML | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::DB::Biblio::eutils - XML::Twig | | * Bio::DB::Taxonomy::entrez - XML::Twig | | * Bio::Variation::IO::xml - XML::Twig | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | XML-Writer | * XML::Writer - Module for writing | 0.4 | | | XML documents | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::SearchIO::Writer::BSMLResultWriter - XML::Writer | | * Bio::SeqIO::agave - XML::Writer | | * Bio::SeqIO::chadoxml - XML::Writer | | * Bio::SeqIO::tinyseq - XML::Writer | | * Bio::SeqIO::game::gameWriter - XML::Writer | | * Bio::Variation::IO::xml - XML::Writer | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | bioperl-ext | * Bio::Ext::Align - NA | None | | | * Bio::SeqIO::staden::read - NA | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::SearchDist - Bio::Ext::Align | | * Bio::Tools::AlignFactory - Bio::Ext::Align | | * Bio::Tools::dpAlign - Bio::Ext::Align | | * Bio::Tools::pSW - Bio::Ext::Align | | * Bio::SeqIO::abi - Bio::SeqIO::staden::read | | * Bio::SeqIO::alf - Bio::SeqIO::staden::read | | * Bio::SeqIO::ctf - Bio::SeqIO::staden::read | | * Bio::SeqIO::exp - Bio::SeqIO::staden::read | | * Bio::SeqIO::pln - Bio::SeqIO::staden::read | | * Bio::SeqIO::ztr - Bio::SeqIO::staden::read | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | libwww-perl | * HTTP::Request - Class | 5.64 | | | encapsulating HTTP Requests | | | | * HTTP::Request::Common - Functions | | | | that generate HTTP::Requests | | | | * HTTP::Response - Class | | | | encapsulating HTTP Responses | | | | * LWP - Libwww-perl | | | | * LWP::Simple - Simple procedural | | | | interface to libwww-perl | | | | * LWP::UserAgent - A WWW UserAgent | | | | class | | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::Tools::EUtilities::EUtilParameters - HTTP::Request | | * Bio::DB::DBFetch - HTTP::Request::Common | | * Bio::DB::HIV - HTTP::Request::Common | | * Bio::DB::NCBIHelper - HTTP::Request::Common | | * Bio::DB::SwissProt - HTTP::Request::Common | | * Bio::DB::WebDBSeqI - HTTP::Request::Common | | * Bio::DB::Query::WebQuery - HTTP::Request::Common | | * Bio::Tools::Run::RemoteBlast - HTTP::Request::Common | | * Bio::DB::WebDBSeqI - HTTP::Response | | * Bio::Tools::Protparam - LWP | | * Bio::Tools::Run::RemoteBlast - LWP | | * Bio::DB::Biblio::eutils - LWP::Simple | | * Bio::Root::IO - LWP::Simple | | * Bio::DB::GenericWebAgent - LWP::UserAgent | | * Bio::DB::MeSH - LWP::UserAgent | | * Bio::DB::WebDBSeqI - LWP::UserAgent | | * Bio::DB::Query::WebQuery - LWP::UserAgent | | * Bio::Root::Build - LWP::UserAgent | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | libxml-perl | * XML::Parser::PerlSAX - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::OntologyIO::InterProParser - XML::Parser::PerlSAX | | * Bio::SeqIO::tinyseq - XML::Parser::PerlSAX | | * Bio::SeqIO::game::gameSubs - XML::Parser::PerlSAX | ============================================================================== ============================================================================== | Distribution | Module used - Description | Min. ver. | |---------------------------+--------------------------------------+-----------| | mod_perl | * Apache2::SubProcess - NA | None | |==============================================================================| | Used by: | |------------------------------------------------------------------------------| | * Bio::DB::WebDBSeqI - Apache2::SubProcess | ==============================================================================