XSim is a fast and user-friendly software tool to simulate sequence data and complicated pedigree structures
> using XSim > XSim.init(numChr,numLoci,chrLength,geneFreq,mapPos,qtlMarker,qtlEffects,mutRate) > popSizeFounder = 2 > sires = sampleFounders(popSizeFounder) > sires1,dams1,gen1 = sampleRan(popSize, ngen, sires, dams);
- An efficient Crossover Position and Origin Simulation (CPOS) method
- Using ancestors with any density of variant information up to and including sequence data, which can be obtained for founders by sequencing or simulation
- Complicated pedigree structures among descendants
- User-defined parameters including allele frequencies, map positions, number of loci, chromosome lengths, numbers of chromosomes and mutation rates.
- Both C++ and Julia versions are available
A CPOS strategy is implemented to efficiently simulate sequence data and complicated pedigree structures.
Hao Cheng, Rohan Fernando and Dorian Garrick
To use all features, please check the documents. Having trouble with XSim? Contact firstname.lastname@example.org.
Cheng H, Garrick D, and Fernando R (2015) XSim: Simulation of descendants from ancestors with sequence data. G3: Genes-Genomes-Genetics, 5(7):1415-1417.