Recipe 18.13 - Tree-sequence recording and nucleotide-based models I.txt

// Keywords: nucleotide-based, nucleotide sequence, sequence-based mutation rate

initialize() {
	defineConstant("L", 1e5);
	initializeSLiMOptions(nucleotideBased=T);
	initializeTreeSeq();
	initializeAncestralNucleotides(randomNucleotides(L));
	initializeMutationTypeNuc("m1", 0.5, "f", 0.0);
	initializeGenomicElementType("g1", m1, 1.0, mmJukesCantor(1e-6));
	initializeGenomicElement(g1, 0, L-1);
	initializeRecombinationRate(1e-6);
}
1 early() { sim.addSubpop("p1", 1000); }
1000 late() { sim.treeSeqOutput("recipe_nucleotides.trees"); }