|  | 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× |
- 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.