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helminth_models.txt
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helminth_models.txt
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Figures
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# Fig1 A. Selection strength and starting allele freq for different times of selection; freq vs SAA
## ./msms -N 1000000 -ms 20 10000 -s 50 -r 15 -Sp 0.5 -Smu 0.01 -SAA $selp -SAa $selp -Saa 0 -SF 0 0.3 -oOC -Smark -oTrace -SFC
# Fig1 B. Facet Pi plots in multi population model; sel vs Nm
## ./msms -N 1000000 -ms 100 10000 -s 50 -r 15 -I 5 20 20 20 20 20 $Nmp -Sp 0.5 -Smu 0.01 -SAA $selp -SAa $selp -Saa 0 -SI 0.00024 5 0 0 0 0 0 -oOC -Smark
# Fig1 C. Fluctuating selection where this is treatment every 5 years and selection lasts for 5 years
## ./msms -N 1000000 -ms 20 10000 -s 50 -r 15 -SI 0.00012 1 0 -Smu 0.01 -SAA 10000 -SAa 0 -Saa 0 -Sp 0.5 -SFC -oOC -oTrace -Smark
*-Sc .000105 -1 0 0 0 -Sc .00009 -1 2*N*s 0 0 -Sc .000075 -1 0 0 0 -Sc .00006 -1 2*N*s 0 0*
# Fig1 D. Gene flow from population under selection to a population that is not under selection condition on final freq in pop1
## ./msms -N 1000000 -ms 100 10000 -s 50 -r 15 -I 5 20 20 20 20 20 $Nmp -Sp 0.5 -Smu 0.01 -SAA 10000 -SAa 10000 -SF 0 1 0.3 -oOC -Smark -oTrace
*examine the freq of resistant allele in the 5th column in the trace*
# Fig1 E. Gene flow from a population under selection to a population that is also under selection
## ./msms -N 1000000 -ms 100 10000 -s 50 -r 15 -I 2 20 20 $Nmp -Sp 0.5 -SAA 10000 -SAa 10000 -SI 0.00024 2 1E-6 0 -oOC -Smark -oTrace
*examine the freq of resistant allele in the 5th column in the trace, can also add -Smu 0.01 de novo in both pops*
Origins
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# DN1 no recombination
## ./msms -N 1000000 -ms 20 10000 -s 50 -Sp 0.5 -Smu 0.01 -SAA 10000 -SAa 10000 -SI 0.00024 1 0 -oOC -Smark
# DN1 with recombination
## ./msms -N 1000000 -ms 20 10000 -s 50 -r 15 -Sp 0.5 -Smu .01 -SAA 10000 -SAa 10000 -SI 0.00024 1 0 -oOC -Smark ###recomb
# SGV1_f01 starting allele freq 0.01
## ./msms -N 1000000 -ms 100 10000 -s 50 -r 15 -Sp 0.5 -Smu .01 -SAA 10000 -SI 0.00024 1 0.01 -oOC -Smark
# SGV1_f05 starting allele freq 0.05
## ./msms -N 1000000 -ms 100 10000 -s 50 -r 15 -Sp 0.5 -Smu .01 -SAA 10000 -SI 0.00024 1 0.05 -oOC -Smark
Table
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# FST with no migration
## ./msms -N 1000000 -ms 100 1 -s 50 -r 15 -I 5 20 20 20 20 20 0 -ej 0.00060 2 1 -ej 0.00060 3 1 -ej 0.00060 4 1 -ej 0.00060 5 1
Notes
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*0.00012: 40yrs,gens 12*
*0.00024: 80yrs, gen 12; 40yrs gens 24*
*0.00048: 80yrs, gen 24*
*grep "Origin" DN1r.${thetap}-${selp}.msms | cut -d":" -f2 | awk '$1 > 1 { count ++ } END { print count / 10000 }' >> probRorigin.out*
*grep -B1 "segsites" DN1r.${thetap}-${selp}.msms | cut -f 3 | awk '{ sum += $1 } END { print sum / 10000 } >> freqRallele.out*