Bioperl: Bioperl 0.6 Released

Ewan Birney
Tue, 4 Apr 2000 10:44:36 +0000 (GMT)

   Announcing bioperl 0.6 release

The bioperl developers are delighted to announce the bioperl 0.6
release. The 0.6 release is the latest stable release, replacing the
old 0.05.1 release. Bioperl is coordinated from
Please visit the web site for more details about the project

The release is available from

as a set of CPAN modules (bioperl-0.6.tar.gz and bioperl-ext-0.6.tar.gz)

The releases are also available from CPAN. Please check out your
nearest CPAN mirror site ( for the top level).

The bioperl-0.6 is the main distribution. The bioperl-ext is an
additional distribution with compiled C extensions. bioperl-ext is not
needed for the majority of the functionality of bioperl-0.6.

The installation process is a standard CPAN module, requiring the commands

  perl Makefile.PL 
  (make test - optional)
  make install

The README has more details on this.

The 0.6 release as the following new or improved functionality:

   o Sequences can have Sequence Features attached to them
        - The sequence features can be read from or written to
          EMBL and GenBank style flat files

   o Objects for Annotation, including References (but not
     full medline abstracts), Database links and Comments are

   o A Species object to represent nodes on a taxonomy tree
     is provided

   o The ability to parse HMMER and Sim4 output has been added

   o The Blast parsing has been improved.

   o Flat file indexed databases provide both random access 
     and sequential access to their component sequences.

   o A CodonTable object has been written with all known 
     CodonTables accessible.

   o A number of new lightweight analysis tools have been
     added, such as molecular weight determination.

The 0.6 release also has improved software engineering

   o The sequence objects have been rewritten, providing more
     maintainable and easier to implement objects. These
     objects are backwardly compatible with the 0.05.1 objects

   o Many objects are defined in terms of interfaces and then  
     a Perl implementation has been provided. The interfaces
     are found in the 'I' files (module names ending in 'I').

     This means that it is possible to wrap C/CORBA/SQL access
     as true "bioperl" objects, compatible with the rest of

   o The SeqIO system has been overhauled to provide better
     processing and perl-like automatic interpretation of <>
     over arguments.

   o Many more tests have been added (a total of 172 automatic
     tests are now run before release).

Comments, praise or annoyances should be directed to the 
bioperl-guts list (

Bugs should be entered through the bug tracking interface
found at

Ewan Birney (on behalf of the bioperl developers).

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