This repository will contain scripts to simulate demographic scenarios in msprime. The scripts are associated with Farleigh et al., 2023. See below for details on the files contained in this repository and please do not hesitate to reach out to Keaka Farleigh (farleik@miamioh.edu) if you have any questions or need any help. Please use the citation below if you use any of these scripts in your work.
This folder contains the python script (MSprime_sims.py), that was used to run the msprime simulations; a R script (Anolis_MSprime_combine.R), that processes output from the shell script, note that this script can be rund from the command line; a shell script (Run_MSprime.sh), that runs the python script however many times you want and processes the output with the R script; and a slurm batch file (Anolis_Ref_MSprime.txt) that runs everything as a batch job.
Farleigh, K., Ascanio, A., Farleigh, M. E., Schield, D. R., Card, D. C., Leal, M., Castoe, T. A., Jezkova, T., & Rodríguez-Robles, J. A. (2023). Signals of differential introgression in the genome of natural hybrids of Caribbean anoles. Molecular Ecology, 32, 6000–6017. https://doi.org/10.1111/mec.17170