Bioperl is set of Perl Modules for bioinformatics. It contains objects for Sequences, features on Sequences, and other important bioinformatics attributes.
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Over 3000 file changes have gone into this release
since the 1.2 development tree was branched off
from the main. Several new HOWTOs are available at
http://bioperl.org/HOWTOs/. SimpleWebAnalysis,
Trees, Feature Annotation, OBDA Access, and Flat
Databases were added. This release is also paired
with releases of bioperl-ext (C-extensions) and
bioperl-run (Perl module wrappers around many
common compbio applications).
This release fixes several bugs in Bio::SearchIO,
Bio::TreeIO, Bio::SeqIO genbank parsing, several
memory leaks with Features and Tree/Node objects,
and several more important bugs listed in the
Changes file. It also adds support for GFF3 in
Bio::DB::GFF, and the tutorial for Bio::Graphics
has be updated to reflect the most current API.
Numerous small bugs have been fixed, making this a necessary update to
1.2.1. The OBDA Registry code has been brought up to spec, numerous
OntologyIO dagflat parsers have been brought up to snuff, a
SearchIO::blast bug which missed last reports has been fixed, support
has been added for NCBI eutils changes, Bio::TreeIO::newick can now
parse labeled internal nodes, several Bio::DB::GFF fixes and new
Bio::Graphics glyphs have been added, and fixes have been made to
several parsers detailed in the Changes file.
WrapperBase is now included, making StandAloneBlast work from the release. Bio::Coordinate was fixed and cleaned up. Bio::Index::EMBL and bpindex were fixed.
This release represents improvements to various parsers (Bio::SearchIO, Bio::SeqIO), a simplified function based interface to the toolkit (Bio::Perl), and improvements to the documentation. Several new modules including Unigene, LocusLink, OMIM parsers, and Bio::Assembly for assembly data. There are fixes to allow Bio::DB::GenBank/GenPept to use the new NCBI Eutils interface; old versions of Bioperl and these modules will break when NCBI disables the old Web CGI interface.
