Bio::DB::Taxonomy::silva(3) 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 Bio::DB::Taxonomy::silva.

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

[email protected]


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)