Skip to main content

Table 1 Runtime results comparing Hapi to other family-based haplotyping algorithms

From: Rapid haplotype inference for nuclear families

   All families ≤3 Children
Machine Program Runtime Speedup Runtime Speedup
  Hapi 3.112 s - 2.225 s -
2.30 GHz Merlin 1005 s 323× 8.662 s 3.84×
AMD Opteron Allegro v2 7661 s 2,462× 14.50 s 6.43×
  Superlink 1393 s* 448× 38.75 s 17.2×
1.40 GHz Hapi 4.732 s - 3.451 s -
Pentium M PedPhase 2.0 >21,600 s (6 h) >4,500× >21,600 s (6 h) >6,000×
  1. Runtimes for maximum likelihood haplotyping using Hapi, Merlin Allegro and Superlink of nuclear families from the Huntington's Disease Venezuela Collaborative Study [32]. We list times for haplotyping all nuclear families and for haplotyping those with three or fewer children. *Superlink failed to haplotype the family with 11 children; we therefore used only 8 of the children from the 11 child family to time it. Times are averages from running Hapi eight times and Merlin, Allegro, and Superlink three times each. Runtimes also on a different machine for minimum-recombinant haplotyping using Hapi (averaged from eight runs) and PedPhase for chromosome 1 only.