Difference between revisions of "Downloads"

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'''''merlin''''' is available for download in a single multi-platform version.
'''''merlin''''' is available for download in a single multi-platform version.
* ''merlin 4.0.3 - beta'' - ''NEW''
* ''merlin 4.0.3 - beta'' - ''NEW''
** [https://www.merlin-sysbio.org/data/releases/merlin-gui-4.0.3-RELEASE-beta.zip merlin]
** [https://www.merlin-sysbio.org/data/releases/merlin-gui-4.0.3-RELEASE-beta.zip merlin]
* Previous versions
'''Previous versions'''
* ''merlin 4.0.2 - beta''
* ''merlin 4.0.2 - beta''

Revision as of 15:46, 27 May 2020

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. http://doi.org/10.1109/TCBB.2016.2527647


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

  • merlin 4.0.3 - beta - NEW

Previous versions

Known issues

  • Plugin merlin-addons installed prior to version 4.0.2 might stop merlin's launch after an update. To solve this issue, please delete the file merlin-addons*.jar from directory [merlin_home]/plugins_bin. After completing this step, merlin should launch normally.

  • How can I recover my workspaces if merlin does not launch?
    • Step 1 - Download the latest version available in this page. Do not launch merlin until step 4.
    • Step 2 - Copy the directories [merlin_home]/h2Database and [merlin_home]/ws from your previous merlin version.
    • Step 3 - Paste both directories in merlin´s version downloaded from the website. These directories should not exist if merlin was not launched yet.
    • Step 4 - Launch merlin. All workspaces should be available now.

We are currently working hard on finding a solution for these issues and we shall release a more stable version soon. Thank you for your patience!

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)
  • Java version: above JRE 1.8
    • Discalimer: more recent versions of Java (above 10) may cause stability issues
  • OS: Windows (XP or later), Unix (Ubuntu or macOS),


  • Any bugs or suggestions please email us at:
    • support@merlin-sysbio.org
  • Changelog history

Application icons: https://www.flaticon.com