I came here with a similar scenario...
I'm administering my father's DNA
But what I want to know is... Does ancestry.com have a way to search and exclude from one DNA result to another?
For example My father and I share the Same DNA, my father & mother do not. I'm not able to obtain a DNA sample from my mother.
I would like to exclude my fathers results from mine. This would then point me to be able to concentrate on my mothers side of my tree. And also be able to point my research to my fathers side for match's in common.