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)