The file used for IMa2 analyses contains 100 RAD sequence loci of length 75bp, sequenced for 20 nune vs 20 non-dune sunflowers from Great Sand Dunes National Park and Preserve. This is a sample of 100 of the acceptable loci and was analysed using the following commands. M mode Burnin run example: IMa2 -o gsd75_sample100_3_300med_burn_a.out -i ../gsd75_sample100_3.txt -b 6.0 -l 6.0 -hfg -hn300 -ha0.99 -hb0.75 -t 0.01 -q 2 -m 1000 -p257 -r25 Sampling run example (using .mcf file from burnin run): nohup IMa2 -o gsd75_sample100_3_300med_a_01.out -i ../gsd75_sample100_3.txt -f gsd75_sample100_3_300med_burn_4a.out.mcf1 -b 3.0 -l 12.0 -hfg -hn300 -ha0.99 -hb0.75 -t 0.01 -q 2 -m 1000 -p257 -r3 -s 796205 L mode IMa2 -b300000 -c12 -i ../gsd75_sample100_3.txt -j1 -l300000 -m1 -o gsd75_sample100_3_300med.out -p57 -q2 -t0.01 -m 1000 -r0 -v gsd75_sample100_3_300med_ -w ima2_all_nested_models_2_pops.txt