Here are all the scripts and code used to perform analyses in the manuscript entitled "Genetic diversity during selective sweeps in non-recombining populations" by Sachin Kaushik, Kavita Jain, and Parul Johri.

#The manuscript can be accessed here - https://www.biorxiv.org/content/10.1101/2024.09.12.612756v1.abstract

#Below is the description of all files present here:

CI.slim file is the simulation script to obtain an SFS post-fixation of a beneficial mutation when there is clonal interference.

Diffusion_theory_sfs.nb is the mathematica file where the diffusion equations framework is provided to obtain the SFS. Further details are present in each folder in the respective mathematica file.

Ns_100_post_fixation_recombination.slim is the SLiM script to simulate a selective sweep conditional on fixation in a recombining population.

post_fix.slim is the SLiM script to simulate a selective sweep conditional on fixation in a nonrecombining population. More specific details are within the each folder where simulations are done for each figure.

post_fix_python.py is a python script that was used to obtain the SFS from SLiM's output, where particularly all 10^6 simulation replicates (txt files) are processed.

python_CI.py script generate the SFS for clonal interference case.

For all cases, the following set of steps are followed:

Step 1: Run the bash file for SLiM The bash script will run replicates of the SLiM script, and store the information in a 1000 folders with 1000 replicates each, with a total of 10^6 independent replicates.

Step 2: Run the bash file written using python to generate the population SFS for each replicate.

Step 3: Average the SFS (generated in the previous step) over all replicates using this python script.

Note that all folders here contain the specific scripts used to generate a particular figure (as indicated in the folder name).