Parameters | Genetics | QTL Mapping Model Algorithm

The EM Algorithm^{1}computes LOD scores from maximum likelihood estimates for model parameters that are generated based on modeling the conditional phenotype as a mixture of normal distributions derived from the QTL genotypes probabilities at each testing location. The Haley-Knott algorithm^{2}regresses the genotype probabilities at QTL testing points directly on the trait instead of via a mixture model.LOD scores are estimated via maximum likelihood method.Note: This method is a simpler alternative to EM, but should return similar results.

Lander, E.S. and Botstein, D.(1989) Mapping Mendelian Factors Underlying Quantitative Traits Using RFLP Linkage Maps. Genetics 121: 185-199.

Haley, C.S. and Knott, S.A. (1992) A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69: 315–324.