---
name: "Bio::DB::Taxonomy::silva"
section: "3pm"
platform: "linux"
package: "libbio-perl-perl"
version: "1.7.8-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::DB::Taxonomy::silva"
---

# Bio::DB::Taxonomy::silva(3pm)

Use the Silva taxonomy

## NAME

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

## SYNOPSIS

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

## DESCRIPTION

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 \<http://www.arb-silva.de/no\_cache/download/archive/release\_108/Exports/\>.

## FEEDBACK

### 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.

```
  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
```

### Support

Please direct usage questions or support issues to the mailing list:

*bioperl-l@bioperl.org*

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.

### 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:

```
  https://github.com/bioperl/bioperl-live/issues
```

## AUTHOR - Florent Angly

florent.angly@gmail.com

## APPENDIX

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

### new

```
 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)
```