Recipe 17.1 - A minimal tree-seq model.txt

// Keywords: tree-sequence recording, tree sequence recording

initialize() {
	initializeTreeSeq();
	initializeMutationRate(0);
	initializeMutationType("m1", 0.5, "f", 0.0);
	initializeGenomicElementType("g1", m1, 1.0);
	initializeGenomicElement(g1, 0, 1e8-1);
	initializeRecombinationRate(1e-8);
}
1 early() {
	sim.addSubpop("p1", 500);
}
5000 late() {
	sim.treeSeqOutput("./recipe_17.1.trees");
}

// Section 17.2's recipe, which is a Python script that overlays
// neutral mutations onto the .trees file saved here, may be found in
// the Recipes archive downloadable at https://messerlab.org/slim/