test.slim

//This is a sample SLiM program that you can use to test to see if SLiM is running properly. 
//There is no need to change anything in this file to make it run.

// set up a simple neutral simulation
initialize() {
	initializeMutationRate(1e-7);
	
	// m1 mutation type: neutral
	initializeMutationType("m1", 0.5, "f", 0.0);
	
	// g1 genomic element type: uses m1 for all mutations
	initializeGenomicElementType("g1", m1, 1.0);
	
	// uniform chromosome of length 100 kb with uniform recombination
	initializeGenomicElement(g1, 0, 99999);
	initializeRecombinationRate(1e-8);
}

// create a population of 500 individuals
1 {
	sim.addSubpop("p1", 500);
}

// output samples of 10 genomes periodically, all fixed mutations at end
1000 late() { p1.outputSample(10); }
2000 late() { p1.outputSample(10); }
2000 late() { sim.outputFixedMutations(); }