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Table 1 Characteristics of three software that simulate marker data under non-null genetic models.

From: SUP: an extension to SLINK to allow a larger number of marker loci to be simulated in pedigrees conditional on trait values

  SLINK/SUP SIMLA ALLEGRO
Simulates on pedigrees as they have been collected Yes No Yes
Simulates marker data conditional on    
   1) observed affection status Yes Yes Yes
   2) observed affection status and observed exposure/liability class Yes No No
   3) observed quantitative trait values Yes No No
Simulates LD between    
   1) marker loci Yes Yes No
   2) marker and trait loci Yes Yes No
Simulates values for    
   1) affection status Yes Yes No
   2) environmental exposure No Yes No
   3) quantitative trait Yes Yes No
   4) covariates No Yes No
Simulates multi-locus susceptibility between    
   1) unlinked loci Yes (indirectly) Yes No
   2) linked loci No/Future Yes No
Simulates under sex-specific maps Yes No Yes
Simulates X-linked genetic data Yes/Future No Yes
Simulates upon pedigrees with loops Few No Yes
Pedigree restrictions 16 founders 4 founders < 31 bits
  1. Some features are planned future extensions of SUP. The number of bits is defined as twice the number of non-founders minus the number of founders.