Finding phylogenetic distance between sequences?
No, because it is really not a binary decision. There are attempts to associate percent pairwise difference with taxonomic ranks (particularly species), but this is problematic because every independent lineage can vary according to its own rate. You could use sequences from different families, or orders, or even phyla, but these two can depend on whether specialists in the field are lumpers, or splitters. For example, all ants are in the same family, and Formicidae is over 100 million years old, while birds that may have diverged from a common ancestor within the last 10 million years are in a different family. You can use pairwise distance OR higher-level taxonomy as a proxy. But it would be crude. Why not program your software to make hard decisions about homology, and then find the closest most distant homologue in terms of pairwise differences?