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# 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Bio::Factory::ResultFactoryI 1.5.2 1.6 Superseded by Bio::Factory::ObjectFactory
Bio::Factory::HitFactoryI 1.5.2 1.6 Superseded by Bio::Factory::ObjectFactory
Bio::Graph 1.5.2 1.6 Superseded by bioperl-network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Bio::Search::Processor 1.5.1 1.7 Superseded by Bio::SearchIO
Bio::Tools::RNAMotif 1.5.2 1.7 Superseded by Bio::SearchIO::rnamotif
Bio::Tools::Infernal 1.5.2 1.7 Superseded by Bio::SearchIO::infernal
Bio::Tools::ERPIN 1.5.2 1.7 Superseded by Bio::SearchIO::erpin
Bio::Seq::SeqWithQuality 1.5.1 1.7 Superceded by Bio::Seq::Quality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