Parameters | Predictive Modeling | Perform recoding with respect to:

Perform recoding with respect to:
Use the radio buttons to specify which allele to recode the genotypic data by.
This option is used only when Single-Character Homozygous Genotypes is selected as the Format of Marker Alleles.
Note: If an Annotation major allele is specified, then the recoding is done in terms of the opposite (minor) allele and this option is ignored.