Domain set enrichment. code by Diego Martinez used in this paper https://mbio.asm.org/content/3/5/e00259-12
Comparative Genome Analysis of Trichophyton rubrum and Related Dermatophytes Reveals Candidate Genes Involved in Infection Diego A. Martinez, Brian G. Oliver, Yvonne Gräser, Jonathan M. Goldberg, Wenjun Li, Nilce M. Martinez-Rossi, Michel Monod, Ekaterina Shelest, Richard C. Barton, Elizabeth Birch, Axel A. Brakhage, Zehua Chen, Sarah J. Gurr, David Heiman, Joseph Heitman, Idit Kosti, Antonio Rossi, Sakina Saif, Marketa Samalova, Charles W. Saunders, Terrance Shea, Richard C. Summerbell, Jun Xu, Sarah Young, Qiandong Zeng, Bruce W. Birren, Christina A. Cuomo, Theodore C. White mBio Sep 2012, 3 (5) e00259-12; DOI: 10.1128/mBio.00259-12
Diego's instructions Lump multiple species together when comparing a set - I just added them as if they were a psuedo genome.
I think this is commented for use but let me know if it doesnt make sense.