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