Available Options

List of available options

--help (-h) print help message
--seed (-s) <int> random seed
--length (-L) <genome_length> genome length, base pairs
--popSize (-N) [P <p>] <N> population size
--theta (-t) [P <p>] <theta> mutation rate per site
--rho (-r) [P <p>] <rho> recombination rate per site
--migMat (-m) <m> migration rate from Population 2 to Population 1
--selectionCoeff <s> selection coefficient for the selected locus
--dominance <h> sets heterozygous fitness to 1 + hs
--dominanceBackground <h> sets heterozygous fitness to 1 + hs in neighboring regions
--selectionStartSite <s1> start of the region under selection
--selectionEndSite <s2> end of the region under selection
--selectionRegionDensity (-SRD) <d> density of loci under selection in the region
--fitnessBoolOR fitness is 1 + s if we have any of the alleles in the selected region
--fitnessTS fitness for truncation selection; fitness is 0 if number of mutations is greater than threshold
--tThresh <t> threshold parameter for truncation selection
--fitnessSE fitness corresponding to synergistic epistasis
--SEa <double> first parameter for synergistic epistasis
--SEb <double> second parameter for synergistic epistasis
--BURN (-B) <burn> burnin time in units of 2N generations
--tSpeciation (-TS) <tau> run duration until speciation in units of 2N generations
--tSweepStart (-TW) <tau> run duration until start of sweep in units of 2N generations
-Tg P <p> <tau> <alpha> P <p> <tau> <alpha> population growth start time and rate
--tTotal (-TE) <tau> total run duration after burnin in units of 2N generations
--sampSize (-n) <SS1> [<SS2>] sample size for output
--outputTime <tau1> [<tau2>...<taun>] output times after burnin in units of 2N generations
--outfile (-o) <file> output file prefix