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Table 3 Time in seconds to generate a sample of families of identical structure. The pedigree structures are named after the number of founders (see Figure 2). Markers and trait locus are taken to be in linkage equilibrium (LE) or disequilibrium (LD). A dash indicates that the software is unable to simulate upon the pedigree structure or the model. K is the prevalence of the disease.

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

Number of markers Pedigree structure (sample size) FastSLINK/SUP SIMLA ALLEGRO
    K = 0.10 K = 0.05  
2 × 6 LE 2F (1000) 1.4 1.1 1.4 0.4
  4F (1000) 10.9 25.4 196.7 1.1
  8F (100) 12.3 - - 0.8
  16F (10) 27.3 - - -
2 × 6000 LE 2F (1000) 64.5 160.8 189.8 51.5
  4F (1000) 163.2 2494.0 18403.1 125.5
  8F (100) 44.8 - - 28.4
  16F (10) 33.6 - - -
2 × 6 LD 2F (1000) 1.3 1.1 1.3 -
  4F (1000) 11.0 26.1 197.7 -
  8F (100) 11.8 - - -
  16F (10) 27.1 - - -
2 × 6 LD multi-locus susceptibility 2F (1000) 7.5 1.1 1.4 -
  4F (1000) 50.0 25.3 197.1 -
  8F (100) 25.4 - - -
  16F (10) 53.5 - - -