This repository has all the scripts used to generate results for the manuscript - "Revisiting the notion of deleterious sweeps" by Johri,Charlesworth et al.
The scripts are arranged in folders based on the specific analysis or question investigated. Following are the folders and a summary of the analysis:
-> sweeps_without_interference : investigation of probability, time and effect of sweeps at a single selected site.
-> sweeps_with_interference : investigation of probability, time and effect of sweeps at selected sites in the presence of interfernece amongst deleterious mutations. Selected sites were part of exons, spaced out by introns and intergenic regions (for Drosophila and Human-like parameters and genome architecture).
-> RecurrentSweeps : Effects of recurrent sweeps on linked neutral diversity.
-> FST : investigation of how the presence of deleterious mutations will affect detection of outlier loci when using FST to identify candidates of positive selection.
-> AMOVA : investigation of how the presence of deleterious mutations will affect detection of outlier loci when using AMOVA to identify candidates of positive selection.
The specific command lines used for all scripts are provided in README.sh files in each folder.