I manage several family members DNA - my two daughters are linked to a public direct ancestors tree but my Dad and I are linked to my sprawling public family tree of his family. As I have other public and private trees, I think that ThruLines will pick up any matches.
I also have a private, but searchable tree of bits and pieces of trees from DNA matches. I usually take one couple in their tree, and try to expand and work back to find the common ancestor. Sometimes the clues are just not enough, but I hope someday a new DNA match, or the original one, will put in more info and then find a common ancestor.
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