When citing PyHMMER, please additionally cite HMMER, which developed the actual method and is wrapped with PyHMMER. You can for instance cite both papers as: PyHMMER (Larralde et al., 2022), a Python library binding to HMMER (Eddy, 2011).

Sean Eddy states in the HMMER manual that you should cite the HMMER website if possible, and only resort to the 2011 publication (doi:10.1371/journal.pcbi.1002195) for journals that cause problems. You can grab a BibTex file with the different publications.


PyHMMER has been used in the following research works:

  • Carroll, L.M., M. Larralde, J.S. Fleck, R. Ponnudurai, A. Milanese, E. Cappio, G. Zeller, 2021. Accurate de novo identification of biosynthetic gene clusters with GECCO (preprint). bioRxiv. doi:10.1101/2021.05.03.442509.

  • Ducarmon, Q.R., N. Karcher, H.L.P. Tytgat, O. Delannoy-Bruno, S. Pekel, F. Springer, C. Schudoma, G. Zeller. Large-scale computational analyses of gut microbial CAZyme repertoires enabled by Cayman (preprint). bioRxiv. doi:10.1101/2024.01.08.574624.

  • Jamali, K., L. Käll, R. Zhang, A. Brown, D. Kimanius, S.H.W. Scheres, 2023. Automated model building and protein identification in cryo-EM maps (preprint). bioRxiv. doi:10.1101/2023.05.16.541002.

  • Kautsar, S.A., J.J.J van der Hooft, D. de Ridder, M.H. Medema, 2021. BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters. GigaScience 10, giaa154. doi:10.1093/gigascience/giaa154.

  • Komp, E., Alanzi, H. N., Francis, R., Vuong, C., Roberts, L., Mosallanejad, A., Beck, D. A. C. Homologous Pairs of Low and High Temperature Originating Proteins Spanning the Known Prokaryotic Universe. Sci Data 2023, 10 (1), 682. doi:10.1038/s41597-023-02553-w.

  • Konstantinidis, K., C. Ruiz-Perez, K. Gerhardt, L. Rodriguez-R, C. Jain, J. Tiedje, J. Cole, 2022. FastAAI: Efficient Estimation of Genome Average Amino Acid Identity and Phylum-level relationships using Tetramers of Universal Protein (preprint). ResearchSquare. doi:10.21203/

  • Lienhard, M., T. van den Beucken, B. Timmermann, M. Hochradel, S. Boerno, F. Caiment, M. Vingron, R. Herwig, 2021. Long-read transcriptome sequencing analysis with IsoTools (preprint). Genetics. doi:10.1101/2021.07.13.452091.

  • Reynolds, R., Hyun, S., Tully, B., Bien, J., Levine, N. M. Identification of microbial metabolic functional guilds from large genomic datasets. Front Microbiol. 2023 Jun 30;14:1197329. doi:10.3389/fmicb.2023.1197329 PMID:37455725.