Using an evolutionary algorithm and parallel computing for haplotyping in a general complex pedigree with multiple marker loci.

ABSTRACT:

Background

Haplotype reconstruction is important in linkage mapping and association mapping of quantitative trait loci (QTL). One widely used statistical approach for haplotype reconstruction is simulated annealing (SA), implemented in SimWalk2. However, the algorithm needs a very large number of sequential iterations, and it does not clearly show if convergence of the likelihood is obtained.

Results

An evolutionary algorithm (EA) is a good alternative whose convergence can be easily assessed during the process. It is feasible to use a powerful parallel-computing strategy with the EA, increasing the computational efficiency. It is shown that the EA can be approximately 4 times faster and gives more reliable estimates than SimWalk2 when using 4 processors. In addition, jointl

SUBMITTER: Lee SH 

PROVIDER: S-EPMC2375132 | biostudies-literature | 2008 Apr

REPOSITORIES: biostudies-literature