Scripts to simulate sequence data used to create null distributions in testing for incomplete lineage sorting in C. vaginalis Fast Rate CATA ./ms 53 1000 -s 15 -I 3 22 20 11 -t 3.7 -n 1 0.70 -n 2 0.87 -n 3 0.76 -ej 1.52 1 2 -en 1.52 2 0.55 -ej 2.59 2 3 -en 2.59 3 1.0 -T | tail +4 | grep -v // >cata_treefile ./seq-gen -n1 -on -s0.005 -l346 -mGTR -i0.9 -f0.3045 0.1550 0.1847 0.3558 -r1212.7146 2275.3370 1212.7146 1.0000 2275.3370 1.0 -xpaupblock_cata.txt cata_in.nex CIR ./ms 61 1000 -s 10 -I 3 24 24 13 -t 1.18 -n 1 0.70 -n 2 0.87 -n 3 0.76 -ej 1.52 1 2 -en 1.52 2 0.55 -ej 2.59 2 3 -en 2.59 3 1.0 -T | tail +4 | grep -v // >cir_treefile ./seq-gen -n1 -on -s0.0047 -l159 -mGTR -r0.00001 3.5144 0.00001 1.0000 0.00001 1.0 -xpaupblock_cir.txt cir_in.nex CPS ./ms 58 1000 -s 8 -I 3 23 22 13 -t 1.42 -n 1 0.70 -n 2 0.87 -n 3 0.76 -ej 1.52 1 2 -en 1.52 2 0.55 -ej 2.59 2 3 -en 2.59 3 1.0 -T | tail +4 | grep -v // >cps_treefile ./seq-gen -n1 -on -s0.0087 -l113 -mGTR -i0.813 -r1.0000 4.2450 1.0000 1.0000 39.2268 1.0 -xpaupblock_cps.txt cps_in.nex EF1a ./ms 56 1000 -s 7 -I 3 22 23 11 -t 2.24 -n 1 0.70 -n 2 0.87 -n 3 0.76 -ej 1.52 1 2 -en 1.52 2 0.55 -ej 2.59 2 3 -en 2.59 3 1.0 -T | tail +4 | grep -v // >ef_treefile ./seq-gen -n1 -on -s0.0051 -l161 -mhky -f0.2935 0.1598 0.1513 0.3954 -xpaupblock_ef.txt ef_in.nex FIL ./ms 61 1000 -s 11 -I 3 24 24 13 -t 4.28 -n 1 0.70 -n 2 0.87 -n 3 0.76 -ej 1.52 1 2 -en 1.52 2 0.55 -ej 2.59 2 3 -en 2.59 3 1.0 -T | tail +4 | grep -v // >fil_treefile ./seq-gen -n1 -on -s0.02 -l127 -mGTR -i0.891 -r1.0000 4780.7309 1793.0786 1793.0786 4780.7309 1.0 -xpaupblock_fil.txt fil_in.nex MEP ./ms 61 1000 -s 10 -I 3 24 24 13 -t 1.56 -n 1 0.70 -n 2 0.87 -n 3 0.76 -ej 1.52 1 2 -en 1.52 2 0.55 -ej 2.59 2 3 -en 2.59 3 1.0 -T | tail +4 | grep -v // >mep_treefile ./seq-gen -n1 -on -s0.017 -l91 -mGTR -i0.701 -r1.0000 14.0827 1.0000 1.0000 1.2761 1.0 -xpaupblock_mep.txt mep_in.nex Slow Rate CATA ./ms 53 1000 -s 15 -I 3 22 20 11 -t 3.60 -n 1 0.72 -n 2 0.90 -n 3 0.76 -ej 0.78 1 2 -en 0.78 2 0.58 -ej 1.31 2 3 -en 1.31 3 1.0 -T | tail +4 | grep -v // >cata_treefile ./seq-gen -n1 -on -s0.0047 -l346 -mGTR -i0.9 -f0.3045 0.1550 0.1847 0.3558 -r1212.7146 2275.3370 1212.7146 1.0000 2275.3370 1.0 -xpaupblock_cata.txt cata_in.nex CIR ./ms 61 1000 -s 10 -I 3 24 24 13 -t 1.16 -n 1 0.72 -n 2 0.90 -n 3 0.76 -ej 0.78 1 2 -en 0.78 2 0.58 -ej 1.31 2 3 -en 1.31 3 1.0 -T | tail +4 | grep -v // >cir_treefile ./seq-gen -n1 -on -s0.0047 -l159 -mGTR -r0.00001 3.5144 0.00001 1.0000 0.00001 1.0 -xpaupblock_cir.txt cir_in.nex CPS ./ms 58 1000 -s 8 -I 3 23 22 13 -t 1.38 -n 1 0.72 -n 2 0.90 -n 3 0.76 -ej 0.78 1 2 -en 0.78 2 0.58 -ej 1.31 2 3 -en 1.31 3 1.0 -T | tail +4 | grep -v // >cps_treefile ./seq-gen -n1 -on -s0.0087 -l113 -mGTR -i0.813 -r1.0000 4.2450 1.0000 1.0000 39.2268 1.0 -xpaupblock_cps.txt cps_in.nex EF1a ./ms 56 1000 -s 7 -I 3 22 23 11 -t 2.18 -n 1 0.72 -n 2 0.90 -n 3 0.76 -ej 0.78 1 2 -en 0.78 2 0.58 -ej 1.31 2 3 -en 1.31 3 1.0 -T | tail +4 | grep -v // >ef_treefile ./seq-gen -n1 -on -s0.0051 -l161 -mhky -f0.2935 0.1598 0.1513 0.3954 -xpaupblock_ef.txt ef_in.nex FIL ./ms 61 1000 -s 11 -I 3 24 24 13 -t 4.16 -n 1 0.72 -n 2 0.90 -n 3 0.76 -ej 0.78 1 2 -en 0.78 2 0.58 -ej 1.31 2 3 -en 1.31 3 1.0 -T | tail +4 | grep -v // >fil_treefile ./seq-gen -n1 -on -s0.02 -l127 -mGTR -i0.891 -r1.0000 4780.7309 1793.0786 1793.0786 4780.7309 1.0 -xpaupblock_fil.txt fil_in.nex MEP ./ms 61 1000 -s 10 -I 3 24 24 13 -t 1.50 -n 1 0.72 -n 2 0.90 -n 3 0.76 -ej 0.78 1 2 -en 0.78 2 0.58 -ej 1.31 2 3 -en 1.31 3 1.0 -T | tail +4 | grep -v // >mep_treefile ./seq-gen -n1 -on -s0.017 -l91 -mGTR -i0.701 -r1.0000 14.0827 1.0000 1.0000 1.2761 1.0 -xpaupblock_mep.txt mep_in.nex