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.\" ========================================================================
.\"
.IX Title "Bio::DB::Taxonomy::greengenes 3pm"
.TH Bio::DB::Taxonomy::greengenes 3pm "2021-08-15" "perl v5.32.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::DB::Taxonomy::greengenes \- Use the Greengenes taxonomy
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  use Bio::DB::Taxonomy;
\&
\&  my $db = Bio::DB::Taxonomy\->new(
\&     \-source   => \*(Aqgreengenes\*(Aq,
\&     \-taxofile => \*(Aqtaxonomy_16S_candiv_gg_2011_1.txt\*(Aq
\&  );
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
\&\fIThis module is in beta. Its interface or its results may change in a future update.\fR
.PP
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 \s-1NCBI\s0 assigns to taxons.
.PP
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/>.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Florent Angly"
.IX Header "AUTHOR - Florent Angly"
florent.angly@gmail.com
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 6
\& 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 \*(Aqtaxonomy_16S_candiv_gg_2011_1.txt\*(Aq (mandatory)
.Ve