Metaxa2: Improved Identification and Taxonomic Classification of Small and Large Subunit rRNA in Metagenomic Data
Johan Bengtsson-Palme, Martin Hartmann, K. Martin Eriksson, Chandan Pal,
Kaisa Thorell, D.G. Joakim Larsson, R. Henrik Nilsson
Molecular Ecology Resources (2015). doi: 10.1111/1755-0998.12399

Download the Metaxa2 package (version 2.1.3)

Read the Metaxa2 manual

Read the FAQ

Looking for the previous version of Metaxa? It is still available, here.

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]microbiology.se (and my name is Johan Bengtsson-Palme).

Version history

  • 21st January 2013 – 2.0 beta – first public release.
  • 4th March 2013 – 2.0 beta 2 – support for blast+ and paired-end reads in FASTA format.
  • 9th April 2013 – 2.0 beta 3 – LSU support, rewritten classifier with improved taxonomic prediction.
  • 22nd July 2013 – 2.0 beta 4 – cleaner database with less bad sequences, HMMER 3.1 compatibility, 12S
    support reintroduced.
  • 10th November 2013 – 2.0 beta 5 – taxonomic classifier much improved, minor bug fixes.
  • 26th November 2013 – 2.0 release candidate – software taken out of beta.
  • 28th January 2014 – 2.0 release candidate 3 – cosmetic fixes.
  • 5th November 2014 – 2.0.1 – stable released with slightly improved classifier.
  • 7th April 2015 – 2.0.2 – slight improvements to the classifier, minor bug fixes.
  • 2nd October 2015 – 2.1 – introduced Metaxa2 Diversity Tools, added the genome and reference modes, minor bug fixes.
  • 9th October 2015 – 2.1.1 – fixed a bug in metaxa2_uc.
  • 15th January 2016 – 2.1.2 – enhanced memory efficiency.
  • 7th April 2016 – 2.1.3 – features added to the metaxa2_uc and metaxa2_rf tools.

If you for any reason would be interested in an older version of Metaxa or Metaxa2, please e-mail me at the address below.

If you use Metaxa2 in your research, please cite it as:

Bengtsson-Palme J, Hartmann M, Eriksson KM, Pal C, Thorell K, Larsson DGJ, Nilsson RH: Metaxa2: Improved Identification and Taxonomic Classification of Small and Large Subunit rRNA in Metagenomic Data. Molecular Ecology Resources (2015). doi: 10.1111/1755-0998.12399

Contact information

Johan Bengtsson-Palme (firstname.lastname [at] microbiology.se)
University of Gothenburg
Department of Infectious Diseases
Guldhedsgatan 10
413 46 Göteborg