These directories contain scripts for reproducing the analysis in the paper "Genomic islands of differentiation in a rapid avian radiation have been driven by recent selective sweeps" by Hussein A. Hejase, Ayelet Salman-Minkov, Leonardo Campagna, Melissa J. Hubisz, Irby J. Lovette, Ilan Gronau, and Adam Siepel (2020).

The scripts are not published as a finished software but for informational purposes and transparency of our analysis. Most of the analysis was done on a cluster, with segments of the genome analyzed separately.

Some details, such as where data was downloaded or how filtering was done, are described in the methods section of the main text.

The scripts assume the installation of the following software:

1. ARGweaver [1]: http://github.com/CshlSiepelLab/argweaver.git
2. SLiM version 2.3 [2]

Directories:

1. Simulations/ Contains all script for simulations.
2. ML_analysis/ Contains some miscellaneous scripts.
3. ARG_analysis/ Contains ARG-related analysis

References:

[1] Rasmussen, Matthew D., et al. "Genome-wide inference of ancestral recombination graphs." PLoS Genet 10.5 (2014): e1004342.
[2] Haller, Benjamin C., and Philipp W. Messer. "SLiM 2: Flexible, interactive forward genetic simulations." Molecular biology and evolution 34.1 (2017): 230-240.