I was wondering what the consensus feeling is in this group for using secondary
structure as a guide for aligning rRNA gene sequences. I personally feel it is
necessary in order to insure comparison of homologous sites, but I have met
many people that do not believe in secondary structures and therefore, align
their sequences randomly (i.e., by base letter). I would especially appreciate
responses from people that design phylogenetic software or people that work on
the development of secondary structure models.