Provided by: libbio-perl-perl_1.7.2-2_all bug


       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'


       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


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AUTHOR - Florent Angly


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

        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)