Metaxa: A software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets
Johan Bengtsson, K. Martin Eriksson, Martin Hartmann, Zheng Wang, Belle D. Shenoy, Gwen-Aelle Grelet, Kessy Abarenkov, Anna Petri, Magnus Alm Rosenblad, R. Henrik Nilsson
Antonie van Leeuwenhoek Journal of Microbiology, 2011
(DOI: 10.1007/s10482-011-9598-6)

Important notice:
Please note that this version of Metaxa has been superseded by Metaxa2, which can be found here

Download the Metaxa package (version 1.1.2)

Read the manual (updated for version 1.1.2!)

Read the FAQ

Please e-mail me if you encounter bugs or have questions, but first check out the FAQ! If you do not find your answer there, then feel free to e-mail me. My e-mail address is firstname.lastname[a] (and my name is Johan Bengtsson).

How to guide: Using Metaxa to automatically classify SSUs to the species level

If you for some reason would like to use the old version of Metaxa, you can download that here:
Download the Metaxa package (version 1.0.2)

Version history

  • 9th January 2013 – 1.1.2 – fixed BLAST table output bug, updated manual
  • 29th June 2012 – 1.1.1 – tweaked HMM scoring system, making searches even faster, and fixed a bug causing the –heuristics T option to be ignored in certain circumstances
  • 16th December 2011 – 1.1 – new scoring system, more than 2.5x faster on large data sets, slightly better accuracy on short sequences
  • 22nd June 2011 – 1.0.2 – better Windows file handling, bug fixes.
  • 10th June 2011 – 1.0.1 – enabled options for using HMMER’s heuristic filtering, fixed a rarely occurring bug.
  • 11th May 2011 – 1.0 – public release.
  • 11th April 2011 – 1.0 rc3 – release candidate 3 (improved OS compatibility of installer).
  • 23rd March 2011 – 1.0 rc2 – release candidate 2.
  • 21st March 2011 – 1.0 rc1 – release candidate 1.
  • 19th March 2011 – 1.0 public beta – first public release.

If you for any reason would be interested in an older version of Metaxa, please e-mail me at the address below.

Contact information

Johan Bengtsson (firstname.lastname [at]
University of Gothenburg
Department of Neuroscience and Physiology
Medicinaregatan 11
Box 434
405 30 Gothenburg