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)

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]microbiology.se (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 2012 – 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] microbiology.se)
University of Gothenburg
Department of Neuroscience and Physiology
Medicinaregatan 11
Box 434
405 30 Gothenburg