Introductory walkthrough of SLiM
SLiM is a newer, powerful piece of population genetic simulation software that is well documented, user-friendly, flexible, and has a pretty sweet GUI interface (plus command-line capability). The following script represents an initial dummy simulation situation I created as I got my feet wet with SLiM, and I added many commented notes to make it clear what each command was doing.
// in SLiM context are comments.
// set up a simple neutral simulation
initialize() {
initializeMutationRate(1e-7);
// m1 mutation type: neutral
// arguments: arbitrary id
// dominance coefficient (0-1, no dominance)
// mutation distribution (f=fixed)
// mutation distribution argument (sel. coefficient)
initializeMutationType("m1", 0.5, "f", 0.0);
// g1 genomic element type: uses m1 for all mutations
// arguments: arbitrary id
// mutation type to use (from mutation type specified above)
// proportion mutations drawn from this mutation type
initializeGenomicElementType("g1", m1, 1.0);
// uniform chromosome of length 100 kb with uniform recombination
// arguments: genomic element type to use
// first base position
// last base position (=1kb length)
initializeGenomicElement(g1, 0, 1000);
// recombination rate across simulated chromosomes
// arguments: recombination rate per base
initializeRecombinationRate(1e-8);
}
// perform action at generation 1
1 {
// create a population of 500 individuals
// arguments: arbitrary id
// population size
sim.addSubpop("p1", 500);
}
// run for burn-in number of generations to have population reach equilibrium
1000000 late() {
p1.outputSample(100);
}
// output samples of 10 genomes periodically, all fixed mutations at end
// at generation N (= 1001, here)
// late() = at end of generation (after offspring)
1000001 late() {
// output sample of 100 genomes (haploid) = 2N
// from population 1 that was initialized above
// p1.outputSample(100);
sim.outputFull();
}
/// DESCRIPTION OF FULL OUTPUT (/// = description)
// #OUT: 2 A
/// #output prefix: generation type of output
//
// Populations:
/// Population-level output
// p1 500 H
/// subpopulation size reproduction_type (H=hermaphroditic)
//
// Mutations:
/// Mutation-level output: 1 mutation per line
// 13 4 m1 89111 0 0.5 p1 1 2
/// temp_id permanent_id mutation_type bp_position sel_coeff dominance_coeff
/// pop_id generation_mutation_arose prevalence_num_genomes_possess
//
// Individuals:
/// Individual-level ouptput: 1 individual per line, starting at 0
// p1:i0 H p1:0 p1:1
/// pop_id:ind_id reproduction_type pop_id:genome1_id pop_id:genome2_id
//
// Genomes:
/// Genome-level output: 1 genome per line, starting at 0
// p1:0 A
/// pop_id:genome_num autosome(A)/sex-linked <1+ mutations ordered sequentially)