Option to estimate site-wise amino acid profiles, without conditions
I would find it very useful if Pelican could estimate a site-wise amino acid profile (i.e., H0), without fitting the alternative model. The use case I have in mind is to estimate site-wise amino-acid frequencies to characterize selective pressures operating in a branch-homogeneous manner on an alignment. After such an analysis, one would probably want to be able to retrieve sequence logos per site.