Given that different groups are coming up with their own UCEs and reusing numbers that other probesets use, and given that studies might need to differentiate UCE names that thereby clash, it would be good to allow the probeset fasta file used as a reference to have UCE names that include some extra specifier, e.g. a probeset name. Thus, instead of just ">uce-2627..." it could allow something like ">uce$arachnid-2627" (or whatever format of your choosing). The extra specifier would be carried through the processing and end up in the names of contigs and alignments.
Given that different groups are coming up with their own UCEs and reusing numbers that other probesets use, and given that studies might need to differentiate UCE names that thereby clash, it would be good to allow the probeset fasta file used as a reference to have UCE names that include some extra specifier, e.g. a probeset name. Thus, instead of just ">uce-2627..." it could allow something like ">uce$arachnid-2627" (or whatever format of your choosing). The extra specifier would be carried through the processing and end up in the names of contigs and alignments.