tskit-dev - Software

tskit-dev projects

Ecosystem projects

SLiM SLiM

Website Documentation Publication MesserLab/SLiM

SLiM is a genetically explicit forward simulation software package for population genetics and evolutionary biology. It is highly flexible, with a built-in scripting language, and has a cross-platform graphical modeling environment called SLiMgui.

initialize() {
    initializeTreeSeq();
    initializeMutationRate(1e-8);
    initializeMutationType(
        "m1", 0.5, "e", 0.001
    );
    initializeGenomicElementType(
        "g1", m1, 1.0
    );
    initializeGenomicElement(
        g1, 0, 999999
    );
    initializeRecombinationRate(1e-8);
}
1 early() { sim.addSubpop("p1", 500); }
2000 late() { 
    sim.treeSeqOutput("out.trees");
}

fwdpy11

Documentation molpopgen/fwdpy11

Forward-time simulation in Python using fwdpp

pop = fwdpy11.DiploidPopulation(
  100, 1000.0
)
p = {
  "nregions": [],
  "rates": (0.0, 1e-3, None),
  "prune_selected": False,
  "demography": 
    fwdpy11.DiscreteDemography(),
  "simlen": 10 * pop.N + 200,
  ...
}
params = fwdpy11.ModelParams(**p)
fwdpy11.evolvets(rng, pop, params)