Provided by: libbio-perl-perl_1.7.6-3_all bug


       Bio::DB::Taxonomy::silva - Use the Silva taxonomy


         use Bio::DB::Taxonomy;

         my $db = Bio::DB::Taxonomy->new(
            -source   => 'silva',
            -taxofile => 'SSURef_108_tax_silva_trunc.fasta',


       This is an implementation of Bio::DB::Taxonomy which stores and accesses the Silva
       taxonomy. Internally, Bio::DB::Taxonomy::silva 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. sv72, are arbitrary, contrary to the pre-defined IDs that NCBI assigns to
       taxons. Note also that no rank names or common names are assigned to the taxa of

       The latest Silva taxonomy (2011) contains about 126,000 taxa and occupies about 124 MB of
       memory once parsed into a Bio::DB::Taxonomy::silva object.  Obviously, it can take a
       little while to load.

       The taxonomy file SSURef_108_tax_silva_trunc.fasta that this module uses is 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::silva->new();
        Function: Builds a new Bio::DB::Taxonomy::silva object
        Returns : an instance of Bio::DB::Taxonomy::silva
        Args    : -taxofile  => name of the FASTA file containing the taxonomic information,
                                typically 'SSURef_108_tax_silva_trunc.fasta' (mandatory)