Table 1

Runtime results comparing Hapi to other family-based haplotyping algorithms

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.

Williams et al. Genome Biology 2010 11:R108   doi:10.1186/gb-2010-11-10-r108

Open Data