Overview

This repository contains data and scripts for reproducing the results accompanying the manuscript

Estimating linkage disequilibrium and selection from allele frequency trajectories

Yunxiao Li^1, and John P. Barton^1,2,#

¹ Department of Physics and Astronomy, University of California, Riverside, Riverside, CA 92521, USA.

² Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.

^# correspondence to 830 Murdoch Building, 3420 Forbes Ave, Pittsburgh, PA 15260, USA. Email: jpbarton@pitt.edu

Contents

Scripts for generating and analyzing the simulation data can be found in the simulation-analysis.ipynb notebook, and references therein. Before generating files for batch jobs, please create an empty folder named jobs under the root directory. Scripts for generating figures contained in the manuscript are located in the figures.ipynb notebook.

Due to the large size and number of some files generated by simulations, some data has been stored in a compressed format using Zenodo. To access the full set of data, navigate to the Zenodo record. Then download and extract the contents of the archive data.zip as the folder /data.

License

This repository is dual licensed as GPL-3.0 (source code) and CC0 1.0 (figures, documentation, and our presentation of the data).