[Bioperl-l] BioPerl 1.6.1 released

[Mark A. Jensen]

Gnarly, dude.
MAJ
----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "BioPerl List" <bioperl-l at lists.open-bio.org>
Sent: Tuesday, September 29, 2009 2:01 PM
Subject: [Bioperl-l] BioPerl 1.6.1 released


> 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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