Overview

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

Correlated allele frequency changes reveal clonal structure and selection in temporal genetic data

Yunxiao Li¹ and John P. Barton^1,2,#

¹ Department of Physics and Astronomy, University of California, Riverside
² Department of Computational and Systems Biology, University of Pittsburgh School of Medicine
^# correspondence to jpbarton@pitt.edu

Contents

Scripts for analyzing simulated data, LTEE data, and two other parallel evolution data sets investigated in the manuscript can be found in the simulation_analysis.ipynb, LTEE_data_analysis.ipynb, and parallel_evolution_data_analysis.ipynb notebooks respectively. Scripts for generating the figures included in the manuscript can be found in the figures.ipynb notebook, and references therein. Before generating files for batch jobs, please create an empty folder named jobs under the root directory.

Due to the large size and number of some files generated by the scripts, 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 into 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).