[Biopython-announce] Biopython 1.51 released

Brad Chapman chapmanb at 50mail.com
Mon Aug 17 12:11:56 UTC 2009

We're pleased to announce the release of Biopython 1.51. This new stable
release enhances version 1.50 (released in April) by extending the
functionality of existing modules, adding a set of application
wrappers for popular alignment programs and fixing a number of minor
bugs. Sources and Windows Installer are available from the 
downloads page:


In particular, the SeqIO module can now write Genbank files that
include features, and deal with FASTQ files created by Illumina
1.3+. Support for this format allows interconversion between FASTQ
files using Solexa, Sanger and Ilumina variants using conventions
agreed upon with the BioPerl and EMBOSS projects.

Biopython 1.51 is the first stable release to include the
Align.Applications module which allows users to define command line
wrappers for popular alignment programs including ClustalW, Muscle
and T-Coffee.

Bio.Fasta and the application tools ApplicationResult and
generic_run() have been marked as deprecated - Bio.Fasta has been
superseded by SeqIO's support for the Fasta format and we provide
ducumentation for using the subprocess module from the Python
Standard Library as a more flexible approach to calling 

As always, the Tutorial and Cookbook has been updated to document all
the changes:


Thank you to everyone who tested our 1.51 beta or submitted bugs
since out last stable release and to all our contributors.


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