OMArk is a software to assess the quality of gene repertoire annotated from a genomic sequence—also called proteome. It relies on comparisons to the predicted ancestral gene repertoire of the target species and to the extant gene repertoire of close species to:

  • Estimate the completeness of the gene-repertoire by comparison to conserved orthologous groups.
  • Estimate the proportion of accurate and erroneous gene models in the proteome.
  • Detect possible contamination from other species in the proteome.

The software is available as a command-line tool on GitHub or can be executed from this webserver. Submit genomes

Using OMArk in your research? Please cite:
Nevers, Y., Warwick Vesztrocy, A., Rossier, V. et al. Quality assessment of gene repertoire annotations with OMArk. Nat Biotechnol 43, 124–133 (2025). https://doi.org/10.1038/s41587-024-02147-w