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. Every job searches both databases (pharokka and phold each do), and there is no option here to turn them off. If you can't use them, run the tools locally without those databases instead.
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 |
In-browser assembly
The read assembler works differently from everything above: Flye and SPAdes run in your browser, so this site distributes them to you, as WebAssembly. They are built from github.com/gbouras13/asm-wasm (GPL-2.0), which holds their complete corresponding source: the Flye fork, the SPAdes patches and the build scripts. The licence texts are served next to the modules (LICENSE.txt, THIRD_PARTY.txt, SOURCE.txt).
| Component | Version | Licence | Source |
|---|---|---|---|
| Flye (with a single-process pipeline) | 2.9.6 | BSD-3-Clause | github.com/gbouras13/Flye (fork of mikolmogorov/Flye) |
| minimap2 (inside Flye) | 2.24 | MIT | github.com/lh3/minimap2 |
SPAdes (spades-core, --isolate) | 4.2.0 | GPL-2.0 | github.com/ablab/spades + the patches in asm-wasm |
| The browser runtime (worker, SPAdes driver) | GPL-2.0 | github.com/gbouras13/asm-wasm | |
| Emscripten runtime and system libraries, musl, libc++, mimalloc, LLVM OpenMP | Emscripten 6.0.11 | MIT, NCSA, Apache-2.0 WITH LLVM-exception | emscripten.org |
This service
Phage Annotation Server is free to use. No account, no fee, no registration — for academic and commercial users alike.
The web application's own source code is released under the
MIT Licence, the same licence as pharokka, phold and
phynteny. You are free to use, modify, self-host and redistribute it,
including commercially. The exception is the in-browser assembler in
web/static/asm/, which is GPL-2.0 (see above).
Two things that licence does not cover, and cannot:
- The third-party data above. Running a job here grants you no rights to CARD, VFDB or any other database listed on this page — those remain governed by their own licences, and CARD and VFDB restrict commercial use. See the terms of use.
- Any warranty. The service is provided as is, with no uptime guarantee, and results are predictions rather than validated findings.
In short: the software is permissively licensed and the service is free to everyone, but the reference data carries its own terms that you are responsible for meeting.
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).