/
DEPENDENCIES
576 lines (571 loc) · 44.8 KB
/
DEPENDENCIES
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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 |
==============================================================================