A Python package implementing ARG-Needle and ASMC-clust genealogical inference.

Use

pip install arg_needle

to install from PyPI, and

pip install .

to install from a local clone.

Please see the ARG-Needle manual for all usage instructions and documentation.

• Bump the version number in setup.py and CMakeLists.txt
• Update RELEASE_NOTES.md
• Push changes and check that all GitHub workflows pass
• Tag the commit in Git using syntax vX.Y.Z
• Make a release on GitHub, which should trigger a new build that will upload Python wheels to PyPI

arg-needle has been developed by Brian C. Zhang with support from Fergus Cooper, Árni Freyr Gunnarsson, and Pier Francesco Palamara.

The files src/hashing/FileUtils.cpp and src/hashing/FileUtils.hpp are adapted from analogous files in the Eagle software, which can be found at https://github.com/poruloh/Eagle/tree/master/src. Eagle was developed by Po-Ru Loh and released under the GNU General Public License v3.0 (GPLv3). Its license can be found under the 3rd_party/ directory.

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.