BioPerl
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# AcePerl support is deprecated, per LDS - cjfields - 5-5-2011
#'Ace' => [0,
# 'Access of ACeDB database/Bio::DB::Ace,Bio::DB::GFF::Adaptor::ace'],
'Algorithm::Munkres' => [ 0, 'Phylogenetic Networks/Bio::PhyloNetwork' ],
'Array::Compare' => [ 0, 'Phylogenetic Networks/Bio::PhyloNetwork' ],
# this won't actually install due to circular dep, but we have no way of
# doing a post-install the [circular dependency!] specifies it is only
# installed on explicit request for this specific module, not when simply
# choosing to install 'all' modules
#'Bio::ASN1::EntrezGene' => [0,
# 'Parsing entrezgene/Bio::SeqIO::entrezgene [circular dependency!]'],
'Bio::Phylo' => [
0,
'NeXML related modules/Bio::AlignIO::nexml,Bio::Nexml::Factory,'
. 'Bio::SeqIO::nexml,Bio::TreeIO::nexml'
],
'CGI' => [ 0, 'CGI-y things/Bio::DB::Query::HIVQuery' ],
'Clone' => [ 0, 'Cloning objects/Bio::Root::Root,Bio::Tools::Primer3' ],
'Convert::Binary::C' =>
[ 0, 'Strider functionality/Bio::SeqIO::strider' ],
'DB_File' => [ 0, 'Database functionality/Bio::Assemby,Bio::DB' ],
'Error' => [
0, 'OO-based exception handling (very optional)/Bio::Root::Exception'
],
'GD' => [ 0, 'Alignment graphic output/Bio::Align::Graphics' ],
'Graph' => [
0.50,
'Phylogenetic Networks, ontology engine implementation, contig analysis'
. '/Bio::PhyloNetwork,Bio::Ontology::SimpleGOEngine::GraphAdaptor,'
. 'Bio::Assembly::Tools::ContigSpectrum'
],
'GraphViz' => [
0, 'Phylogenetic Network Visualization/Bio::PhyloNetwork::GraphViz'
],
'HTML::Entities' =>
[ 0, 'Remote analysis POST submissions/Bio::SearchIO::blastxml' ],
'HTML::HeadParser' => [
3,
'Parsing <HEAD> section of HTML docs/Bio::Tools::Analysis::DNA::ESEfinder'
],
'HTML::TableExtract' =>
[ 0, 'Parsing HTML tables/Bio::DB::SeqVersion::gi' ],
'HTTP::Request::Common' => [
0,
'GenBank+GenPept sequence retrieval, remote http Blast jobs'
. '/Bio::DB::*,Bio::Tools::Run::RemoteBlast,'
. 'Bio::Tools::Analysis::Protein*,Bio::Tools::Analysis::DNA*'
],
'Inline::C' => [ 0.67, 'Speeding up code like Fasta Bio::DB::Fasta' ],
'IO::Scalar' => [
0, 'Deal with non-seekable filehandles/Bio::Tools::GuessSeqFormat'
],
'List::MoreUtils' => [
0,
'Back- or reverse-translation of sequences/'
. 'Bio::Tools::SeqPattern,Bio::Tools::SeqPattern::BackTranslate'
],
'LWP::UserAgent' => [
0,
'Remote access/Bio::DB::*,Bio::Tools::Run::RemoteBlast,Bio::WebAgent'
],
'PostScript::TextBlock' => [ 0, 'EPS output/Bio::Tree::Draw::Cladogram' ],
'Set::Scalar' => [ 0, 'Proper operation/Bio::Tree::Compatible' ],
'Sort::Naturally' => [
0,
'Sort lexically, but sort numeral parts numerically/'
. 'Bio::Assembly::IO::ace,Bio::Assembly::IO::tigr'
],
'Spreadsheet::ParseExcel' =>
[ 0, 'Parsing Excel files/Bio::SeqIO::excel' ],
'Storable' => [
2.05,
'Storing sequence objects in local file cache/'
. 'Bio::DB::FileCache,Bio::SeqFeature::Collection,Bio::PopGen::HtSNP,'
. 'Bio::PopGen::TagHaplotype,Bio::DB::GFF::Adaptor::berkeleydb,Bio::Root::Root'
],
'SVG' => [ 2.26, 'Creating SVG images/Bio::Draw::Pictogram' ],
'SVG::Graph' => [ 0.01, 'Creating SVG images/Bio::TreeIO::svggraph' ],
'Text::ParseWords' =>
[ 0, 'Test scripts/Bio::DB::SeqFeature::Store::FeatureFileLoader' ],
'XML::DOM' => [ 0, 'Parsing XML/Bio::SeqIO::bsml,Bio::SeqIO::interpro' ],
'XML::DOM::XPath' => [ 0, 'Parsing XML/Bio::SeqIO::interpro' ],
'XML::LibXML' =>
[ 0, 'Parsing XML/Bio::SeqIO::seqxml,Bio::TreeIO::phyloxml' ],
'XML::Parser' => [ 0, 'Parsing XML/Bio::OntologyIO::InterProParser' ],
'XML::Parser::PerlSAX' => [
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