this is a strange question perhaps, but it's brought on by a reviewer to one of my papers. We have used
mafft to generate multiple sequence alignment for a simple phylogenetic analysis. However, the reviewer suggested we use "method that takes secondary structure of 16S" into account. I take it they meant something like
prank aligner that uses codon information to generate a more accurate multiple sequence alignment. However, I don't know of any such tool for 16S.
Can you recommend anything relevant? Would be grateful for any suggestions.