May 2013 Notice: The most recent Greengenes database and taxonomy updates are now found at Taxonomic information on this site is deprecated and should be used with caution.



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greengenes: 16S rDNA data and tools

The greengenes web application provides access to the 2011 version of the greengenes 16S rRNA gene sequence alignment for browsing, blasting, probing, and downloading.  The data and tools presented by greengenes can assist the researcher in choosing phylogenetically specific probes, interpreting microarray results, and aligning/annotating novel sequences.  If you are an ARB user, you can use greengenes to keep your own local database current.

The May 2013 greengenes taxonomy now available!

The trees, tables and sequence data organized as described in McDonald et al. ISME J article can all be found in one place.


  • Search is now possible using new Simrank (developed by Niels Larsen) for similarity searching against the 2011 greengenes sequences.
  • New import filter template posted for slurping greengenes exports into ARB.
  • Looking for Hugenholtz or PHPR taxonomy? It is now the greengenes taxonomy.
  • Dr. Mike Dyall-Smith has graciously made available his tutorial for installing Arb on MacOSX. Thanks Mike.
  • The greengenes taxonomy for the Cyanobacteria is now consistent with cyanoDB using cyanoDB type species as a guide to map cyanoDB taxonomy to the greengenes reference 16S tree.
  • Thanks to Greg Caporaso and Rob Knight for posting OTU reference and utility files for use with QIIME software.
  • The Wall Street Journal picks the Berkeley PhyloChip as the top advance in environmental technology of 2008 and 3rd best innovation overall.
  • Pollution Engineering Magazine selects Berkeley PhyloChip as most likely to aid pollution control and abatement in the near future.
  • The Berkeley PhyloChip wins R&D100 award as one of the 100 most significant technological advances of the year.
  • Are you the world expert on the taxonomy of a particular phylogenetic lineage? Have you checked this database and nobody has got it right? Tell us! - we will fix it.
  • We thank Jakob Fredslund for developing a tool, Gexcellent, to convert XML trees to Newick format!
  • We thank J.P. Euzéby and Hans Trüper for expert etymological advice.

Browse taxonomic tree of your choice and mark nodes.

Export sequence records of your choice.

Specify a Slice (sub-alignment) of the prokMSA to view/download.

Calculate Consensus sequences from My Interest List (soon!).

Compare my local sequences/probes against the prokMSA using BLAST or Simrank.

Search the annotations of the prokMSA.

Locate Probes and primers within the prokMSA using pattern matching.

Align a few or a few thousand 16S rDNA sequences with the NAST aligner.

Trim a batch of sequences using quality scores.

Download alignments, taxonomies, posters, protocols, etc.

More Tools are being developed and are available for preview.

Infrastructure provided by: VIMSS - CEB - JGI - LBL
  • Last Database Update: October 2, 2011 1:41PM
  • 1049116 aligned 16S rDNA records >1250nt