Hi,
if it is not too much of a hassle then it would be nice if you could Include a pdiffs option in pcr.seqs command like it is available in trim.seqs. I used the pcr.seqs command to remove reverse primers from my sequences because those were only occuring in some of my sequences and I needed the nomatch=keep option to retain those data were the reverse primers were not present. The pcr.seqs command though failed to remove primers that had a mismatch or were truncated and I had to go through the alignment and manually delete the remaining primers. While a pdiffs option would not solve this problem completely of course, it would still reduce the amount of manual labor in such a case.
Cheers,
René
P.S.: The wiki entry for the pcr.seqs command says the option for “nomatch” is “true” when the correct one is “keep” instead.