Does sepp somehow reformat the seqIDs? it is surprising that there is not at least partial overlap! Could you share a sampling of IDs from the seqs and tree?
The ideal of course would be something we've discussed in the past ā adding a method to build a sepp reference tree in fragment insertion or elsewhere... then rescript could be used to get/format seqs/ref trees, and plug directly into fragment-insertion. Some relevant discussion here and here:
