NAME

       Bio::DB::Taxonomy::greengenes - Use the Greengenes taxonomy

SYNOPSIS

         use Bio::DB::Taxonomy;

         my $db = Bio::DB::Taxonomy->new(
            -source   => 'greengenes',
            -taxofile => 'taxonomy_16S_candiv_gg_2011_1.txt'
         );

DESCRIPTION

       This module is in beta. Its interface or its results may change in a future update.

       Bio::DB::Taxonomy::greengenes is an implementation of Bio::DB::Taxonomy which stores and
       accesses the Greengenes taxonomy of Bacteria and Archaea. Internally, it keeps the
       taxonomy into memory by using Bio::DB::Taxonomy::list. As a consequence, note that the IDs
       assigned to the taxonomy nodes, e.g. gg123, are arbitrary, contrary to the pre-defined IDs
       that NCBI assigns to taxons.

       The latest release of the Greengene taxonomy (2011) contains about 4,600 taxa and occupies
       about 4MB of memory once parsed into a Bio::DB::Taxonomy::greengenes object. The taxonomy
       files taxonomy_16S_all_gg_2011_1.txt and taxonomy_16S_candiv_gg_2011_1.txt that this
       module can use are available from
       <http://www.secondgenome.com/go/2011-greengenes-taxonomy/>.

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to the Bioperl mailing list.  Your participation
       is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their
       resolution. Bug reports can be submitted via the web:

         https://github.com/bioperl/bioperl-live/issues

AUTHOR - Florent Angly

       florent.angly@gmail.com

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

   new
        Title   : new
        Usage   : my $obj = Bio::DB::Taxonomy::greengenes->new();
        Function: Builds a new Bio::DB::Taxonomy::greengenes object
        Returns : an instance of Bio::DB::Taxonomy::greengenes
        Args    : -taxofile  => name of the file containing the taxonomic information,
                                typically 'taxonomy_16S_candiv_gg_2011_1.txt' (mandatory)