AutoAB itself is copyright Jo Teichmann and licensed under AGPL-3.0, with a commercial licence available separately. See LICENSE and COMMERCIAL-LICENSE.md.
This file records the third-party components AutoAB depends on, which carry their own terms.
These are not vendored here. They are installed separately (the conda environment brings them in) and executed as external processes. AutoAB calls them as command-line programs and does not link against them.
| Tool | Licence | Role |
|---|---|---|
| IgBLAST 1.22.0 (NCBI) | Public domain (US Government work) | V/D/J germline assignment |
| Change-O | AGPL-3.0 | Clone assignment, germline reconstruction |
| pRESTO | AGPL-3.0 | Sequence preprocessing |
| Alakazam | AGPL-3.0 | Diversity, lineage, repertoire metrics |
| Shazam | AGPL-3.0 | SHM analysis, distance-to-nearest thresholds |
| ape | GPL-2/3 | Phylogenetic tree construction |
| IQ-TREE | GPL-2 | Optional maximum-likelihood trees |
| Biopython | Biopython licence (BSD-like) | Sequence I/O |
The Immcantation components (Change-O, pRESTO, Alakazam, Shazam) are AGPL-3.0, which is one reason AutoAB is released under the same licence: the combination raises no compatibility question.
| Data | Source | Terms |
|---|---|---|
geneGUI/data/IMGT_Human_Database/, IMGT_Mouse_Database/ |
IMGT/GENE-DB | IMGT requires citation and restricts redistribution. See their terms of use |
geneGUI/data/internal_data/, optional_data/ |
Ships with NCBI IgBLAST | Public domain |
geneGUI/data/internal_data/CoV-AbDab_080224.csv |
CoV-AbDab, OPIG Oxford | Free for academic use. Cite Raybould et al. |
IMGT germline sets are redistributed here for reproducibility. Now that the
repository is public, confirm this remains compatible with IMGT's terms. The
alternative is to fetch them at install time, as
backend/scripts/download_mouse_imgt.sh already does for mouse.
BCR_Deep_Clustering-main/, a third-party DNABERT-based clustering module (MIT, copyright 2024 Kerwin) that was vendored but never wired into the running tool, along with roughly 50 MB of model weights. Dropped.- Vendored IgBLAST binaries (about 110 MB), now installed by conda or fetched
by
scripts/install.sh. - Study data, collaborator result files, and journal PDFs, which never belong in a source repository.
If you use AutoAB in published work, please cite the underlying tools as well: IgBLAST, Change-O/pRESTO, Alakazam/Shazam, IMGT, and CoV-AbDab where applicable.