perl 5.14.0 not pending anymore

BioPerl core 1.6.9 release

* Refactored Bio::Species/Bio::Tree
* New SeqIO parsers (gbxml, msout, mbsout)
* Updates for perl 5.12
* Bio::Assembly support for SAM/BAM, Newbler, ace output
* Bio::DB::SeqFeature updates
* PAML updated to work with v. 4.4d
* lots of bug fixes

* bump point version

* sync minor doc changes

svn path=/bioperl-live/branches/branch-1-6/; revision=16197

bump alpha to test ODBA-related bug fix

svn path=/bioperl-live/branches/branch-1-6/; revision=16191

* merge changes from main trunk

* bump alpha to 5 (final one, mainly for Strawberry Perl tests)

svn path=/bioperl-live/branches/branch-1-6/; revision=16186

bump alpha

svn path=/bioperl-live/branches/branch-1-6/; revision=16169

remove odd miscommit from tag

svn path=/bioperl-live/tags/bioperl-1-6-0_003/; revision=16172

sync with main trunk

svn path=/bioperl-live/branches/branch-1-6/; revision=16147

sync last bits with main trunk

svn path=/bioperl-live/branches/branch-1-6/; revision=16123