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I have my DNA and my mom's DNA on Ancestry and Gedmatch. My mom was adopted.

I got her original birth certificate from Kansas and found her birth mom's family (birth mom was deceased) but the man identified as her father on the birth certificate apparently is not.

I found one of his sons, and he did the DNA test. His results came back that he and my mom are not related.

Mom was born in Topeka, Kansas, in Dec 1926.

If it is possible to use AncestryDNA or GEDmatch to find her paternal side, then how do I do that?

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As Jamie Cox commented, you would do best to work to categorize your mother's matches. Working with her matches is better than working with yours for the purpose of identifying her father because a) she will have more matches among the relevant people, and b) for some of them, they will be stronger because she is one generation closer to them.

So, categorize her matches as those you are sure are from her mother's side and the others. Her mother's side matches you exclude from further consideration, even though there is a small possibility that she might be related to a match via both sides.

The "others" category will include essentially all from her father's side, but it will also include some from her maternal side. Absence of a match is not proof of an absence of a particular relationship (other than for very close relatives like a parent), and additionally there are matches which are maternal but not in a way you have knowledge of.

Look at the strongest of the "others" matches. You will need tree information for those people. You may want to research your mother's maternal side in more depth to see if the remaining matches actually belong to that side. Collect the ones still potentially paternal and try to find where they're related. If you're persistent and lucky you may eventually perceive two groups of related matches, and find from the tree information or further research, that the two groups are related to a male who could be your mother's father.

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AncestryDNA has new color-coding tools. You can color all of your mom's relatives as a pink dot & then concentrate on your dad's. Start with the highest match that isn't coded pink. Mark that match with a new color (blue) & click "shared matches." Mark every one of those matches blue. Follow the same procedure - new color & mark the shared matches. Look for common surnames among matches marked a certain color & look for common ancestors.

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