[Bioperl-l] BioPerl 1.6.1 released

[Scott Cain]

Chris,

Congratulations and thanks so much for the time and effort that went into this.

Scott


On Tue, Sep 29, 2009 at 2:01 PM, Chris Fields <cjfields at illinois.edu> wrote:
> We are pleased to announce the availability of BioPerl 1.6.1, the latest
> release of BioPerl core code.  You can grab it here:
>
> Via CPAN:
>
> http://search.cpan.org/~cjfields/BioPerl-1.6.1/
>
> Via the BioPerl website:
>
> http://bioperl.org/DIST/BioPerl-1.6.1.tar.bz2
> http://bioperl.org/DIST/BioPerl-1.6.1.tar.gz
> http://bioperl.org/DIST/BioPerl-1.6.1.zip
>
> The PPM for Windows should also finally be available this week, ActivePerl
> problems permitting (we will post more information when it becomes
> available).
>
> Tons of bug fixes and changes have been incorporated into this release.  For
> a more complete change list please see the 'Changes' file included with the
> distribution.
>
> A few highlights:
>
> * FASTQ parsing and interconversion of the three FASTQ variants (Sanger,
> Illumina, Solexa) now works (a concerted OBF effort!)
> * Significant refactoring of Bio::Restriction methods
> * Complete refactoring of Bio::Search-related tiling code, including HOWTO
> documentation
> * GBrowse-related fixes
>   - berkeleydb database now autoindexes wig files and locks correctly
>   - add Pg, SQLite, and faster BerkeleyDB implementations
> * Infernal 1.0 output is now parsed
> * New SearchIO-based parser for gmap -f9 output
> * BLAST XML parsing essentially complete
> * Installation via CPANPLUS should now work
> * For those using Strawberry Perl on Windows, the latest build is expected
> to pass all tests.
> * 'raw' sequence format now parsed by line or optionally as a single
> sequence
> * SCF parsing/writing now round-trips
> * Demo code for using RPS-BLAST and Bio::Tools::Run::RemoteBlast
> * Bio::Tools::SeqPattern now has a backtranslate() method
> * Bio::Tree::Statistics now has methods to calculate Fitch-based score,
> internal trait values, statratio(), sum of leaf distances [heikki]
> * scripts
>   - update to bp_seqfeature_load for SQLite [lstein]
>   - hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
>   - fastam9_to_table - fix for MPI output [jason]
>   - gccalc - total stats [jason]
>   - einfo  - simple script to find up-to-date NCBI database list, list field
> and link values for a specific database
>
> We will shortly release updates for BioPerl-db, BioPerl-run, and
> BioPerl-network.  Enjoy!
>
> chris
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>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research