GemHaps takes a genome sequence, and an input command specifying haplotype frequencies and the number of SNPs in each haplotype (here, haplotypes are defined as a group of related nucleotide sequences, each differing by at least one SNP). The positions of mutations are randomly determined, and haplotypes are written to a file for input into GemReads. Alternatively, users may create their own tab-delimited haplotype file (for instance, describing SNPs generated according to an evolutionary model).
