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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.