BUGS

You can eliminate multiple markers in the interactive loop. You should be aware that the order marker elimination is important. If all the markers to be eliminated are on separate chromosomes, the order is unimportant. If two markers from the same chromosome are to be eliminated, order should be to eliminate the highest numbered marker. The same concept holds for traits: eliminate them in the order of highest to lowest.

Do not try to eliminate any markers or traits AND do a bootstrap, permutation or simulation of missing markers in the same run.