1 # These are modules which are deprecated and later removed from the toolkit
2 # See http://www.bioperl.org/wiki/Deprecated_modules for the latest details
5 Deprecated Modules Deprecated Removed Comment
6 --------------------------------------------------------------------------------
7 Bio::Annotation 1.0 1.1 use Bio::Annotation::Collection
8 Bio::Tools::Blast 1.0 1.1 use Bio::SearchIO
9 Bio::Tools::Blast::HSP 1.0 1.1 use Bio::Search::HSP::GenericHSP
10 Bio::Tools::Blast::Sbjct 1.0 1.1 use Bio::Search::Hit::GenericHit
11 Bio::Tools::Blast::HTML 1.0 1.1 use Bio::SearchIO::Writer::HTMLWriter
12 Bio::Tools::SeqAnal 1.0 1.1 used only by deprecated Bio::Tools::Blast
13 Bio::Tools::WWW 1.1 1.1.1 Just a collection of links
14 Bio::UnivAln 1.0 1.1 use Bio::SimpleAlign
15 Bio::Tools::RestrictionEnzyme 1.5 1.6 use Bio::Restriction
16 Bio::Tools::BPlite 1.5 1.6 use Bio::SearchIO
17 Bio::Tools::BPpsilite 1.5 1.6 use Bio::SearchIO
18 Bio::Tools::BPbl2seq 1.5 1.6 use Bio::SearchIO
19 Bio::Ontology::SimpleGOEngine 1.5.1 1.6 use Bio::Ontology::OBOEngine
20 Bio::Taxonomy 1.5.1 1.7 use Bio::Taxon & Bio::Tree::Tree
21 Bio::Taxonomy::Node 1.5.1 1.7 renamed Bio::Taxon
22 Bio::Taxonomy::Taxon 1.5.1 1.7 use Bio::Taxon
23 Bio::Taxonomy::Tree 1.5.1 1.7 use Bio::Taxon & Bio::Tree::Tree
24 Bio::Taxonomy::FactoryI 1.5.1 1.7 Redundant, no implementors
25 Bio::Search::Processor 1.5.1 1.7 Superseded by Bio::SearchIO
26 Bio::Factory::ResultFactoryI 1.5.2 1.6 Superseded by Bio::Factory::ObjectFactory
27 Bio::Factory::HitFactoryI 1.5.2 1.6 Superseded by Bio::Factory::ObjectFactory
28 Bio::Root::Err 1.5.2 1.5.2 Bio::Root* redundant classes
29 Bio::Root::Global 1.5.2 1.5.2 Bio::Root* redundant classes
30 Bio::Root::IOManager 1.5.2 1.5.2 Bio::Root* redundant classes
31 Bio::Root::Object 1.5.2 1.5.2 Bio::Root* redundant classes
32 Bio::Root::Utilities 1.5.2 1.5.2 Bio::Root* redundant classes
33 Bio::Root::Vector 1.5.2 1.5.2 Bio::Root* redundant classes
34 Bio::Root::Xref 1.5.2 1.5.2 Bio::Root* redundant classes
35 Bio::Tools::WebBlat 1.5.2 1.5.3 Requested that this not be maintained