Jan 272013



SIMULATE is a program to simulate genotypes in family members for a map of linked markers unlinked to a given affection status locus. the output is ready for analysis with UNKNOWN, ISIM, LSIM, or MSIM of the SLINK package.

(1) SIMULATE is essentially the original version, in which all marker genotypes are generated based on population marker characteristics (allele frequencies, etc.) and recombination fractions between them.

(2) SIMULATE2 assumes that for founder individuals with known genotypes (i.e., they are “typed”) the original (observed) genotypes are provided. These genotypes will not be modified (generated) in the course of the simulations. For founders with unknown genotypes (“untyped”), marker genotypes will be generated as in the SIMULATE program. However, prior to running SIMULATE2, users may want to impute such genotypes from the original data so that few founders have unknown genotypes. The two program versions have somewhat different input requirements. For example, the random number generator is different –SIMULATE requires 3 seeds and SIMULATE2 requires only one.

(3) SIMULATE3 is an extension of SIMULATE in that markers must be SNPs (have only two alleles) and may be correlated (in linkage disequilibrium) with each other (see below how these correlations are generated). Also, this program version incorporates an updated random number generator, ran (int64) .


Joe Terwilliger &  Jurg Ott, Ph.D.


  • Linux / Windows


 simulatesimulate2, and simulate3.



Terwilliger JD, Speer M, Ott J:
Chromosome-based method for rapid computer simulation in human genetic linkage analysis.
Genet Epidemiol 1993;10:217-224.


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