arg-needle
This repository contains arg-needle, which implements the ARG inference algorithms ARG-Needle and ASMC-clust. Prebuilt CPython wheels are available for Linux (compatible with glibc ≥ 2.28) and macOS (built on macOS 15 for x86_64 and macOS 14 for arm64).
| Platform \ CPython | ≤3.8 | 3.9 | 3.10 | 3.11 | 3.12 | 3.13 | 3.14 |
|---|---|---|---|---|---|---|---|
| Linux x86_64 | ❌ | ✅ | ✅ | ✅ | ✅ | ✅ | ✅ |
| Linux aarch64 | ❌ | ✅ | ✅ | ✅ | ✅ | ✅ | ✅ |
| macOS Intel (x86_64) | ❌ | ✅ | ✅ | ✅ | ✅ | ✅ | ✅ |
| macOS Apple Silicon (arm64) | ❌ | ✅ | ✅ | ✅ | ✅ | ✅ | ✅ |
Quickstart
Install the Python module from PyPI
The Python module can be installed with:
pip install arg-needle
Documentation
Please see the ARG-Needle manual for all usage instructions and documentation.
License
arg-needle is distributed under the GNU General Public License v3.0 (GPLv3). For any questions or comments on arg-needle, please contact Pier Palamara using <lastname>@stats.ox.ac.uk.
Acknowledgements
arg-needle has been developed by Brian C. Zhang with support from Fergus Cooper, Árni Freyr Gunnarsson, and Pier Francesco Palamara.
Reference
If you use this software, please cite:
B. C. Zhang, A. Biddanda, Á. F. Gunnarsson, F. Cooper, P. F. Palamara, Biobank-scale inference of ancestral recombination graphs enables genealogical analysis of complex traits. Nature Genetics, 2023.
arg-needle Release Notes
v1.1.0 (2025-12-18)
- Public source code release: https://github.com/PalamaraLab/arg-needle
- Python wheels are now available for Linux and macOS on both x86_64 and arm64/AArch64 architectures, for CPython versions 3.9 to 3.14 inclusive.
v1.0.3 (2023-08-30)
- ASMC decoders can now take a genetic map file with a specified non-default location.
- ASMC decoders no longer require genetic positions to be strictly increasing: adjacent identical positions are now acceptable.
v1.0.2 (2023-05-25)
Fix default values for sequencing in arg_needle script.
v1.0.1 (2023-03-17)
Bug fix for running build_arg_simulation with ASMC-clust.
v1.0.0 (2023-03-10)
Initial PyPI release of arg-needle.
3 maintainers
Metadata
3 maintainers
Release files for arg-needle 1.1.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Built distributions (wheels)
Total release size: 803.9 MB
Release files / arg_needle-1.1.0-cp314-cp314-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl
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