This option causes the algorithm to give greater importance to ordering markers with smaller distances (recombination fraction) between them and lesser importance to markers with large recombination fractions. This might be a good option when there are a large number of markers in a linkage group and some might not fit very well.
Comparing the Fitted distance correlations for each linkage group on the MDS Residual Plots output result with this option unchecked and then checked can give information about whether this transformation improves the fit.
