Use of secondary structure in alignments

[Marcos de la Pena]

Hi Diane:

 Secondary structure studies on single stranded RNA phages is one of the 
most powerful techniques in resolving phylogenies of these viruses (or 
at least I believe that).

 I would recommend you a nice paper about that:

 Beekwilder M.J. et al, Journal of Molecular Biology, 1995, 247: 903-917 
  

I hope this helps you,


Marcos.