Ancestry-stratified allele frequency trajectories

This repository contains code for the ancestry stratified selection analyses from The Selection Landscape and Genetic Legacy of Ancient Eurasians.

If you reuse any of this code then please cite the paper:

Irving-Pease, E.K.*, Refoyo-Martínez, A.*, Barrie, W.* et al. The selection landscape and genetic legacy of ancient Eurasians. Nature 625, 312–320 (2024). https://doi.org/10.1038/s41586-023-06705-1

Installation

Download the code:

git clone [email protected]:ekirving/mesoneo_paper.git && cd mesoneo_paper/

The easiest way to install all the dependencies is with the conda package manager.

conda env create --name mesoneo --file environment.yaml

Then activate the environment:

conda activate mesoneo

Running the code

This project contains rules for running tens-of-thousands of selection tests.

# run all the selection tests using 1000G data  
./run_modern.sh

# run all the selection tests using aDNA time-series
./run_ancient.sh

# run all the selection tests using the ancestry-stratified aDNA time-series
./run_ancestries.sh

Author

Evan K. Irving-Pease, GLOBE Institute, University of Copenhagen

License

This project is licensed under the MIT License - see the LICENSE file for details