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

       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)

perl v5.32.1                                       2021-08-15                 Bio::DB::Taxonomy::greengenes(3pm)

florent.angly@gmail.com

Thismoduleisinbeta.Itsinterfaceoritsresultsmaychangeinafutureupdate.

       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/>.

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

         use Bio::DB::Taxonomy;

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