# These are modules which are deprecated and later removed from the toolkit # See http://www.bioperl.org/wiki/Deprecated_modules for the latest details Version Version Deprecated Modules Deprecated Removed Comment -------------------------------------------------------------------------------- Bio::Annotation 1.0 1.1 use Bio::Annotation::Collection Bio::Tools::Blast 1.0 1.1 use Bio::SearchIO Bio::Tools::Blast::HSP 1.0 1.1 use Bio::Search::HSP::GenericHSP Bio::Tools::Blast::Sbjct 1.0 1.1 use Bio::Search::Hit::GenericHit Bio::Tools::Blast::HTML 1.0 1.1 use Bio::SearchIO::Writer::HTMLWriter Bio::Tools::SeqAnal 1.0 1.1 used only by deprecated Bio::Tools::Blast Bio::UnivAln 1.0 1.1 use Bio::SimpleAlign Bio::Tools::WWW 1.1 1.1.1 Just a collection of links Bio::Root::Err 1.5.2 1.5.2 Bio::Root* redundant classes Bio::Root::Global 1.5.2 1.5.2 Bio::Root* redundant classes Bio::Root::IOManager 1.5.2 1.5.2 Bio::Root* redundant classes Bio::Root::Object 1.5.2 1.5.2 Bio::Root* redundant classes Bio::Root::Vector 1.5.2 1.5.2 Bio::Root* redundant classes Bio::Root::Xref 1.5.2 1.5.2 Bio::Root* redundant classes Bio::Tools::RestrictionEnzyme 1.5 1.6 use Bio::Restriction Bio::Tools::BPlite 1.5 1.6 use Bio::SearchIO Bio::Tools::BPpsilite 1.5 1.6 use Bio::SearchIO Bio::Tools::BPbl2seq 1.5 1.6 use Bio::SearchIO Bio::Ontology::SimpleGOEngine 1.5.1 1.6 use Bio::Ontology::OBOEngine Bio::Factory::ResultFactoryI 1.5.2 1.6 Superseded by Bio::Factory::ObjectFactory Bio::Factory::HitFactoryI 1.5.2 1.6 Superseded by Bio::Factory::ObjectFactory Bio::Graph 1.5.2 1.6 Superseded by bioperl-network Bio::Tools::WebBlat 1.5.2 1.6 Requested that this not be maintained Bio::DB::XEMBL 1.5.2 1.6 Service no longer available; use DBFetch Bio::DB::XEMBLService 1.5.2 1.6 Service no longer available; use DBFetch Bio::Taxonomy 1.5.1 1.7 use Bio::Taxon & Bio::Tree::Tree Bio::Taxonomy::Node 1.5.1 1.7 renamed Bio::Taxon Bio::Taxonomy::Taxon 1.5.1 1.7 use Bio::Taxon Bio::Taxonomy::Tree 1.5.1 1.7 use Bio::Taxon & Bio::Tree::Tree Bio::Taxonomy::FactoryI 1.5.1 1.7 Redundant, no implementors Bio::Search::Processor 1.5.1 1.7 Superseded by Bio::SearchIO Bio::Tools::RNAMotif 1.5.2 1.7 Superseded by Bio::SearchIO::rnamotif Bio::Tools::Infernal 1.5.2 1.7 Superseded by Bio::SearchIO::infernal Bio::Tools::ERPIN 1.5.2 1.7 Superseded by Bio::SearchIO::erpin Bio::Seq::SeqWithQuality 1.5.1 1.7 Superceded by Bio::Seq::Quality Bio::DB::GDB 1.6 1.6 Service no longer available Bio::Expression - - Moved to inactive bioperl-microarray