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Revision as of 16:00, 11 May 2018 by Admin (talk | contribs) (Changelog)
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Please cite using

Dias, O., Rocha, M., Ferreira, E.C. and Rocha, I. (2015) Reconstructing genome-scale metabolic models with merlin. Nucleic Acids Res., 10.1093/nar/gkv294.

Dias, O., Gomes, D., Vilaca, P., Cardoso, J., Rocha, M., Ferreira, E., & Rocha, I. (2016). Genome-wide Semi-automated Annotation of Transporter Systems. IEEE/ACM Transactions on Computational Biology and Bioinformatics / IEEE, ACM, (1), 1–1.


merlin is available for download in a single multi-platform version.

  • merlin 3.6.2 beta is now available for download.

System requirements

The current version of merlin requires:

  • Processor: Reasonably powerful x64 hardware. Any recent Intel or AMD processor should do.
  • Memory: 1GB memory (most operations use less than 1GB, however the local alignments may take up to 3GB)
  • OS: Windows (XP or later), Linux (Tested on Ubuntu Precise Pangolin)
  • Database:
    • H2: embedded database available
    • MySQL: alternatively a MySQL Server can be used
  • If you want to upload your previous workspace to the new version of merlin, please contact us at:


  • Any bugs or suggestions please email us at:
  • Latest update: 2018-05-11 NEW RELEASE 3.6.2
    • New features:
      • SBML level 3 writer included
    • Debuging:
      • Bug in SBML level 2 writer fixed
      • Drains removal,creation and others debugged
      • Decimal boundaries insertion correction
  • Changelog history

Application icons: