Phage Annotation Server is a thin runner around three published, independently-developed tools.
It performs no annotation of its own, so please cite whichever tools you actually
used for your job (Pharokka always ran; Phold and Phynteny ran unless the job
failed before reaching them) in your manuscript's methods section, rather than citing this
site itself.
Protocols paper (recommended overview citation)
Bouras G, Grigson SR, Durr L, Papudeshi B, Mallawaarachchi V, Vreugde S, Edwards RA.
"Decoding Viral Dark Matter: Metagenomic Prokaryotic Virus Characterization With
Pharokka, Phold, and Phynteny." Current Protocols, Volume 6, Number 7, 6 July
2026. doi:10.1002/cpz1.70405
This is the step-by-step protocol for running pharokka → phold → phynteny
together as a pipeline (what this site automates) -- a good single citation to
accompany the individual tool citations below.
@article{bouras2026protocols,
author = {Bouras, G. and Grigson, S. R. and Durr, L. and Papudeshi, B. and Mallawaarachchi, V. and Vreugde, S. and Edwards, R. A.},
title = {Decoding Viral Dark Matter: Metagenomic Prokaryotic Virus Characterization With Pharokka, Phold, and Phynteny},
journal = {Current Protocols},
volume = {6},
number = {7},
year = {2026},
doi = {10.1002/cpz1.70405},
url = {https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpz1.70405}
}
Bouras G, Nepal R, Houtak G, Psaltis AJ, Wormald P-J, Vreugde S. "Pharokka: a fast
scalable bacteriophage annotation tool." Bioinformatics, Volume 39, Issue 1,
January 2023, btac776. doi:10.1093/bioinformatics/btac776
@article{bouras2023pharokka,
author = {Bouras, George and Nepal, Roshan and Houtak, Ghais and Psaltis, Alkis James and Wormald, Peter-John and Vreugde, Sarah},
title = {Pharokka: a fast scalable bacteriophage annotation tool},
journal = {Bioinformatics},
volume = {39},
number = {1},
pages = {btac776},
year = {2023},
doi = {10.1093/bioinformatics/btac776},
url = {https://doi.org/10.1093/bioinformatics/btac776}
}
Pharokka itself wraps several other tools (PHANOTATE, tRNAscan-SE, MMseqs2, PHROGs,
and more) -- see pharokka's own
Citation section for the full list if you want to credit those individually too.
Bouras G, Grigson SR, Mirdita M, Heinzinger M, Papudeshi B, Mallawaarachchi V, Green R,
Kim SR, Mihalia V, Psaltis AJ, Wormald P-J, Vreugde S, Steinegger M, Edwards RA.
"Protein Structure Informed Bacteriophage Genome Annotation with Phold."
Nucleic Acids Research, Volume 54, Issue 1, 13 January 2026, gkaf1448.
doi:10.1093/nar/gkaf1448
@article{bouras2026phold,
author = {Bouras, G. and Grigson, S. R. and Mirdita, M. and Heinzinger, M. and Papudeshi, B. and Mallawaarachchi, V. and Green, R. and Kim, S. R. and Mihalia, V. and Psaltis, A. J. and Wormald, P.-J. and Vreugde, S. and Steinegger, M. and Edwards, R. A.},
title = {Protein Structure Informed Bacteriophage Genome Annotation with Phold},
journal = {Nucleic Acids Research},
volume = {54},
number = {1},
pages = {gkaf1448},
year = {2026},
doi = {10.1093/nar/gkaf1448},
url = {https://doi.org/10.1093/nar/gkaf1448}
}
Phold also asks you to cite its core dependencies where relevant (Foldseek, ProstT5,
ColabFold, PHROGs, and the CARD/VFDB/DefenseFinder/acrDB/Netflax databases it searches
against) -- see phold's own
Citation section for the full list.
@article{grigson2025phynteny,
author = {Grigson, S. R. and Bouras, G. and Papudeshi, B. and Mallawaarachchi, V. and Roach, M. J. and Decewicz, P. and Edwards, R. A.},
title = {Synteny-aware functional annotation of bacteriophage genomes with Phynteny},
journal = {bioRxiv},
year = {2025},
doi = {10.1101/2025.07.28.667340},
url = {https://www.biorxiv.org/content/10.1101/2025.07.28.667340}
}
Preprint at time of writing -- check
Phynteny's repository
for an updated citation if it has since been published.
A note on accuracy
Citation text and BibTeX above are transcribed directly from each tool's own repository
(README / CITATION.cff) rather than invented. If a tool has since published
an updated citation, its own repository is the source of truth -- please check there
before submitting a manuscript.
