usage: mspms [-h] [-V] [--mutation-rate theta] [--trees]
             [--recombination rho num_loci] [--structure value [value ...]]
             [--migration-matrix-entry dest source rate]
             [--migration-matrix entry [entry ...]]
             [--migration-rate-change t x]
             [--migration-matrix-entry-change time dest source rate]
             [--migration-matrix-change entry [entry ...]]
             [--growth-rate alpha]
             [--population-growth-rate population_id alpha]
             [--population-size population_id size]
             [--growth-rate-change t alpha]
             [--population-growth-rate-change t population_id alpha]
             [--size-change t x] [--population-size-change t population_id x]
             [--population-split t dest source]
             [--admixture t population_id proportion]
             [--random-seeds x1 x2 x3] [--precision PRECISION]
             sample_size num_replicates


mspms nsam nreps -t θ

nsam is the number of copies of the locus in each sample
nreps is the number of independent samples to generate. 
The third parameter here is the mutation parameter, θ = (4N 0 μ) , where N 0 is the diploid population size and where μ is the neutral mutation rate for the entire locus.

mspms 5 10 -t 0.5

mspms nsam nreps -T
mspms 5 10 -T

mspms 6 10 -t 0.5 -seeds 100 200 300

Crossing over:
mspms nsam nreps -t θ -r ρ nsites
mspms 5 10 -t 0.5 -r 0.002 5