Licences
Phage Annotation Server performs no annotation of its own -- it runs pharokka, phold and phynteny, which in turn use a number of separately-licensed tools, databases and models. Those licences are set by their maintainers, not by us, and your use of the results is subject to them. See the terms of use.
Two databases restrict commercial use. Antimicrobial-resistance
hits come from CARD and virulence-factor hits from
VFDB; neither is fully open source. If your use is commercial,
obtain the necessary licence directly from those providers. If you would rather
avoid them entirely, --skip_extra_annotations under Advanced options
runs the pipeline without the CARD and VFDB searches.
The three pipeline tools
| Tool | Version | Licence | Source |
|---|---|---|---|
| pharokka | 1.10.1 | MIT | github.com/gbouras13/pharokka |
| phold | 1.3.0 | MIT | github.com/gbouras13/phold |
| phynteny_transformer | 0.1.3 | MIT | github.com/susiegriggo/Phynteny_transformer |
Executables and libraries
Licences below are read from the conda package metadata of the exact build this server runs, not from documentation -- so they reflect what is actually installed.
| Component | Version | Licence |
|---|---|---|
| PHANOTATE | 1.6.7 | GPL-3.0-only |
| pyrodigal | 3.7.1 | GPL-3.0-or-later |
| pyrodigal-gv | 0.3.2 | GPL-3.0-or-later |
| tRNAscan-SE | 2.0.13 | GPL-3.0-or-later |
| Aragorn | 1.2.41 | GPLv3 |
| MinCED | 0.4.2 | GPL-3.0 |
| MMseqs2 | 18.8cc5c | MIT |
| Foldseek | 10.941cd33 | GPL-3 |
| PyHMMER | 0.12.1 | MIT |
| Mash | 2.3 | BSD-3-Clause |
| PyTorch | 2.13.0 | BSD-3-Clause |
| Transformers | 5.14.1 | Apache-2.0 |
| Biopython | 1.87 | Biopython Licence |
Several of these are GPL-licensed. That is a disclosure and attribution matter rather than a restriction on you: running software server-side is not distribution, and GPL-3.0 has no network-copyleft clause. It does not impose any obligation on your use of the results.
Reference databases and models
Verify before relying on this table. Unlike the software above, these are downloaded datasets whose terms are not carried in machine-readable package metadata. Each row links to the provider -- their page is the licence of record, it can change, and it takes precedence over anything summarised here.
| Database / model | Used for | Terms |
|---|---|---|
| CARD | Antimicrobial-resistance hits | Restricts commercial use — card.mcmaster.ca/about |
| VFDB | Virulence-factor hits | Restricts commercial use — mgc.ac.cn/VFs |
| PHROGs | Functional categories (the colours in the genome browser) | phrogs.lmge.uca.fr |
| DefenseFinder | Anti-phage defence systems | defensefinder.mdmlab.fr |
| acrDB | Anti-CRISPR proteins | bcb.unl.edu/AcrDB |
| Netflax | Toxin-antitoxin systems | server.atkinson-lab.com/netflax |
| INPHARED | Closest-relative search (Mash) | github.com/RyanCook94/inphared |
| ProstT5 | Protein → 3Di translation (phold) | huggingface.co/Rostlab/ProstT5 |
| ESM2-650M | Protein embeddings (phynteny) | huggingface.co/facebook/esm2 |
This service
The web application itself is a thin runner around the tools above. It is offered under the terms of use, with no warranty. It grants you no rights to any of the third-party data listed on this page.
Citing
Licensing and citation are different obligations -- complying with a licence does not discharge the expectation to cite. Please cite the tools and databases you actually used: see the citations page.
Something wrong here?
If you maintain one of these projects and this page misstates your licence, please tell us and we will correct it promptly: (email address).