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SLiM simulation generalizing Min et al.

  • Run conda env create -f environment.yml first to make a conda environment.
  • Set L1 or L2 to 1 to make it into 1D.
  • Run simulation on terminal not SLiMgui if you want to run a bigger simulation. For instance, you would type slim -d L1=500 -d L2=500 2d_spatial_sweep.slim to run the simulation overwriting the default width and height of deme grid, increasing each of them by 2 orders of magnitude.
  • You might need to increase the runtime (currently 10k gen) depending on how large the population is to make sure the final frequency is close to or equal to 1.
  • post_slim_process.py (incomplete) use pyslim to recapitate and add neutral mutations, and tskit for further analyses. It will also continue neutral simulation post fixation, using pyslim.

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Simulating 2d sweep in SLiM

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