Here is what I know so far:
- Multiple copies are present in prokaryotes, but according to a paper by Lukjancenko el al. it is enough to select the most similar ones.
- There are stem regions in the S16 which I suspect are much less variable than the loops.
And here are my questions:
About 1., it is this the usual procedure?
About 2., do people use the loops or the stems to construct a phylogenetic tree? It they use stems, do they consider the coupling between stem bases? And, if they do so, where can I get a "map" of this coupling (preferably in a parseable form, not an image)?
In the other hand, is it correct to use a simpler nucleotide substitution model? which one?
Thanks in advance for any hints.