From merlin
Revision as of 11:22, 10 February 2021 by Admin (talk | contribs) (Downloads)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search

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.


  • Any bugs or suggestions please email us at:


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

  • merlin 4.0.7 - beta - NEW (10/02/2020)

Previous versions

  • merlin 4.0.3 - beta - (27/05/2020)
  • merlin 4.0.4 - beta - (06/07/2020)
  • merlin 4.0.5 - beta - (12/10/2020)
  • merlin 4.0.6 - beta - (03/12/2020)

Known issues

  • I updated a plugin using the merlin plugin manager and now my version is unstable with several errors, how can I fix this ?
    • Step 1 - Run and close merlin twice. This is necessary for merlin to automatically identify and remove older versions of plugins and libraries.
    • Verification - To make sure that merlin is updated and functional, open your "lib" folder within your merlin directory and search for "merlin-*.jar" files (* meaning the multiple libraries). If there are duplicate libraries (where one is the older version and the other is the most recent one) please run merlin and close it after booting to the initial menu.

  • 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),


Application icons: