Hello all,

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. 
Opinions differ about this, but MAFFT - or any "regular" sequence alignment program - is generally not able to align 16S sequences properly unless they are from fairly related species. It is not a matter of codon alignment - something that understands sequence co-variation is needed to align 16S sequences properly.

[**SSU-ALIGN**][1] can search for 16S sequences and automatically align them based on their phylogenetic membership.


  [1]: http://eddylab.org/software/ssu-align/