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

Warning: to avoid errors merlin should be executed with administrator privileges.

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.

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)

-> MySQL: MySQL Server (for Windows a merlin version with MySQL embedded is available)

--- Latest update: 2016-04-10 NEW RELEASE 3.0.3! merlin 3.0.3 beta is now available for download. Any bugs or suggestions please email


   Transporters annotation panel view with buttons for adding triage information to transport proteins, transport reactions generation and model integration. 
   Also, metabolites included in reactions are searchable.
   Loaders for BLAST reports (example of a report in merlin's webpage when the update is online)
   Support to Phobius
   Support to InterPro analysis (for helping in the genome annotation)
   GFF and GBK files loading (for loading genome annotations)

Known bugs:

   Compartmentation reports parsing
   Compartments integration 

Previous update: 2016-10-19 NEW RELEASE 3.0! merlin 3.0 beta is now available for download. Any bugs or suggestions please email

Previous update: 2016-09-26 NEW RELEASE 3.0! We are wrapping up, finishing genome-scale tests and merlin will be available for download this week!

Previous update: 2016-06-15 'NEW RELEASE 3.0! merlin is undergoing a major redesign due to major changes in NCBI, UniProt and other web services. It seems that the older versions are broken, thus they will be taken down. We expect to have a fully stable version in July. Please return periodically to the website to check if the updated version with several new features (such as GFF annotation files uploading, a new database repository (H2), integration with InterProScan and several others) is online. We apologize for the inconvenience.'

Previous update: 2015-10-15 'NEW RELEASE 2.7.2! New NCBI REST API AND New UniProtJAPI version 1.0.0.'

Previous update: 2015-10-01 'Due to some recent changes in the NCBI web servers we are currently updating merlin. We apologise for any inconvenience. Please return to this page as the new version will be available as soon as possible.'

Previous update: 2015-07-24 'NEW RELEASE 2.7.1! New HMMER server links! Bug fixes. Stability improvements.'

Previous update: 2015-05-13 'NEW RELEASE 2.7! New logo! Bug fixes. Stability improvements.'

Previous update: 2015-04-20 'NEW RELEASE 2.6! Stability improvements.'

Previous update: 2014-08-01 'NEW MAJOR RELEASE 2.5.1! EBI Blast server available (Except for the metagenomics version).'

Version merlin (All platforms) triage metabolites database (over 7000 entries) Toy genome for tests
Download metabolites backup Toy genome