Ancestral recombination graph (ARG)

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Project description

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.

Project details

These details have not been verified by PyPI

Release history Release notifications | RSS feed

This version

1.1.0

Dec 18, 2025

1.0.3

Aug 30, 2023

1.0.2

May 25, 2023

1.0.1

Mar 17, 2023

1.0.0

Mar 10, 2023

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Uploaded Dec 18, 2025 CPython 3.14manylinux: glibc 2.27+ x86-64manylinux: glibc 2.28+ x86-64

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arg_needle-1.1.0-cp314-cp314-macosx_14_0_arm64.whl (34.5 MB view details)

Uploaded Dec 18, 2025 CPython 3.14macOS 14.0+ ARM64

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Uploaded Dec 18, 2025 CPython 3.13manylinux: glibc 2.27+ x86-64manylinux: glibc 2.28+ x86-64

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Uploaded Dec 18, 2025 CPython 3.11manylinux: glibc 2.27+ x86-64manylinux: glibc 2.28+ x86-64

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Uploaded Dec 18, 2025 CPython 3.10manylinux: glibc 2.27+ x86-64manylinux: glibc 2.28+ x86-64

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arg-needle 1.1.0

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arg-needle

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Install the Python module from PyPI

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Acknowledgements

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arg-needle Release Notes

v1.1.0 (2025-12-18)

v1.0.3 (2023-08-30)

v1.0.2 (2023-05-25)

v1.0.1 (2023-03-17)

v1.0.0 (2023-03-10)

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