discoal是一个合并模拟程序，能够模拟具有重组，选择性扫描和人口变化（包括人口分裂和混合事件）的模型。

下载

wget https://github.com/kr-colab/discoal/archive/refs/heads/master.zip

安装

解压后进入软件目录

make discoal

参数详情：

$ ./discoal
usage: discoal sampleSize numReplicates nSites -ws tau
parameters:
     -t theta
     -r rho (=zero if not specified)
     -g conversionRate tractLengthMean (gene conversion)
     -gr conversionToCrossoverRatio tractLengthMean (gene conversion where initiation rate = rho*conversionToCrossoverRatio)
     -p npops sampleSize1 sampleSize2 etc.
     -en time popnID size (changes size of popID)
     -ed time popnID1 popnID2 (joins popnID1 into popnID2)
     -ea time daughterPopnID founderPopnID1 founderPopnID2 admixProp (admixture-- back in time daughterPopnID into two founders)
     -ws tau (sweep happend tau generations ago- stochastic sweep)
     -wd tau (sweep happend tau generations ago- deterministic sweep)
     -wn tau (sweep happend tau generations ago- neutral sweep)
     -ls tau leftRho (stochastic sweep some genetic distance to the left of the simulated window--specified by leftRho=4Nr)
         similarly, ld and ln simulate deterministic and neutral sweeps to the left of the window, respectively
     -f first frequency at which selection acts on allele (F0; sweep models only)
     -uA rate at which adaptive mutation recurs during the sweep phase (sweep models only)
     -N sweepEffectivePopnSize (sweep models only)
     -a alpha (=2Ns)
     -x sweepSite (0-1)
     -c partialSweepFinalFrequency (partial sweeps)
     -i dt (sweep time increment scalar; default 400 -> 1/400N)
     -M migRate (sets all rates to migRate)
     -m popnID1 popnID2 migRate (sets migRate from popnID1 to popnID2)
     -A sampleSize popnID time (ancient sample from popnID at specified time)
     -Pt low high (prior on theta)
     -Pr low high (prior on rho)
     -Pre mean upperBound (prior on rho -- exponentially distributed but truncated at an upper bound)
     -Pa low high (prior on alpha)
     -Pu low high (prior on tau; sweep models only; still must use "-ws tau" and "tau" will be ignored)
     -PuA low high (prior on uA; sweep models only)
     -Px low high (prior on sweepSite; sweep models only)
     -Pf low high (prior on F0; sweep models only)
     -Pc low high (prior on partialSweepFinalFreq; sweep models only)
     -Pe1 lowTime highTime lowSize highSize (priors on first demographic move time and size)
     -Pe2 lowTime highTime lowSize highSize (priors on second demographic move time and size)
     -R rhhRate (recurrent hitch hiking mode at the locus; rhh is rate per 2N individuals / generation)
     -L rhhRate (recurrent hitch hiking mode to the side of locus; leftRho is ~Unif(0,4Ns); rhh is rate per 2N individuals / generation)
     -h (hide selected SNP in partial sweep mode)
     -T (tree output mode)
     -d seed1 seed2 (set random number generator seeds)

参考：
https://github.com/kr-colab/discoal
https://github.com/kr-colab/discoal/blob/master/discoaldoc.pdf