Code for producing the simulations in 'Nearly Neutral Evolution Across the Drosophila melanogaster Genome'

Files containing the SLiM input files and processing code used to run SLiM and produce figures 4 and 5 in the manuscript 'Nearly Neutral Evolution Across the Drosophila melanogaster Genome'.
The full SLiM manual, and the software, are available from: https://messerlab.org/slim/

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Figure 4 notes:
Please see ‘figure4-SLiM_input_example.txt’ for reference. This is an example of an input file used for SLiM.
To produce the figure, the frequency of adaptive mutations (class ‘m1’), as a proportion of total mutations that occur, was altered by changing the initializeGenomicElementType() line. The frequencies used were as follows: 0.05%, 0.1%, 0.15%, 0.2%, 0.25%, 0.3%, 0.35%, 0.4%, 0.45% and 0.5%.
example line from script, such that m1 mutations occur as 0.05% of all mutations:initializeGenomicElementType("g1", c(m1, m2, m3, m4, m5, m6, m7, m8, m9, m10), c(0.0005, 0.11105555, 0.11105555, 0.11105555, 0.11105555, 0.11105555, 0.11105555, 0.11105555, 0.11105555, 0.11105555)).
Allowing for recombination:initializeRecombinationRate() line was changed: using parameters 0.00001 and 0.00005.
For figure 4, we calculated the nucleotide site diversity of each different class of mutation. The python code for performing the analysis is available- the code has been divided into three files, that are labelled in order in which they should be run.
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Figure 5 notes:
Please see ‘figure5-SLiM_input_example.txt’ for reference. This is an example of an input file used for SLiM.

Again, the frequency of adaptive mutations (class ‘m1’), as a proportion of total mutations that occur, was altered by changing the initializeGenomicElementType() line. The frequencies used were as follows: 0.05%, 0.1%, 0.2%, 0.3%, 0.4%, 0.5%, 0.8% and 1%.
Deleterious mutations and neutral mutations occur with equal frequency, with deleterious mutations having fitness effects draw from a gamma distribution.
The python code for performing the analysis is available, as above- the code is largely similar, however, in figure 5, rather than nucleotide site diversity, synonymous and nonsynonymous polymorphism counts are used.