A repository for our paper on SLiM 5.0.
This repository is associated with the publication:
XXXXX
It contains scripts and data used in that publication:
SimpleExample.slim : a simple SLiM model that shows how to set up more than one diploid autosome. In the manuscript, this is Code Sample 1.
DroMelFullGenome.slim : a more complex SLiM simulation that models the complete Drosophila melanogaster genome. In the manuscript, this is Code Sample 2 and 3.
Comeron_tables : this directory contains the original recombination rate maps from:
Comeron, J.M., Ratnappan, R., and Bailin, S. (2012). The many landscapes of recombination in Drosophila melanogaster. PLoS Genetics 8(10): e1002905. doi:10.1371/journal.pgen.1002905
They are copied here because they are the basis of our second SLiM model, and furthermore, because they are somewhat difficult to find now; two links are given in the "Data availability" section of the original Comeron et al. (2012) paper, but neither of those links works.
recmaps : this directory contains a script, TweakMaps.R, that reads rate maps from Comeron_tables, tweaks them, and writes them out again. See TweakMaps.R for discussion of exactly what tweaking is done.
It also contains the results from that process: the files chr2.csv, chr3.csv, and chrX.csv that provide the tweaked rate maps used in the SLiM model DroMelFullGenome.slim.
LICENSE : The license under which these files are released. (The files under Comeron_tables are not covered by this license, since they are simply copies of their data.)
README.md : This README file.
-- Ben Haller, 10 June 2025