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Unit tests: Ubuntu Unit tests: macOS Python 3.8 3.11 Regression test Ubuntu asan Ubuntu no sse/avx codecov

ASMC and FastSMC

This repository provides ASMC and its extension FastSMC, implemented in C++ with Python bindings. 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

Most functionality is available through a Python module which can be installed with:

pip install asmc-asmc

Documentation

The following pages of documentation contains specific information:

This Python module is currently available on Linux and macOS.

Example Jupyter notebooks showcasing basic functionality can be found here:

License

ASMC and FastSMC are distributed under the GNU General Public License v3.0 (GPLv3). For any questions or comments on ASMC, please contact Pier Palamara using <lastname>@stats.ox.ac.uk.

Reference

If you use this software, please cite the appropriate reference(s) below.

The ASMC algorithm and software were developed in

  • P. Palamara, J. Terhorst, Y. Song, A. Price. High-throughput inference of pairwise coalescence times identifies signals of selection and enriched disease heritability. Nature Genetics, 2018.

The FastSMC algorithm and software were developed in

  • J. Nait Saada, G. Kalantzis, D. Shyr, F. Cooper, M. Robinson, A. Gusev, P. F. Palamara. Identity-by-descent detection across 487,409 British samples reveals fine-scale evolutionary history and trait associations. Nature Communications, 2020.