flip option in trim.flows

Dear mothur team,

first I would like to thank you for actively developing and maintaining mothur. It has been a great help for my analyses.
I am now (re-)analysing an old dataset which was obatined by a previous phd student in the lab. I decided to follow the 454 SOP as usual but I recognized that one run is not denoisable. In order to find out what the problem is I played arround with trim.seqs and finally managed to get the sequences for all barcoded samples. So far so good. Almost all (>90%) of the sequences have been flipped in the fasta/qual file which I extracted from the sff. I strongly suspect that the trim.flows command has problems of finding those flipped sequences because the resulting (and trimmed files) are almost empty.
Is it possible to integrate the flip option also in trim.flows? Or am I missunderstanding the way trim.flows works in contrast to trim.seqs?

Best Wishes,

You should be able to run trim.flows as long as all of the sequences are in the correct orientation. Then you can use flip=T in trim.seqs