matsen/pplacer — comment on commit f159ac21cd13f78d66feff7b75a2ae65cf93042c
File:  line 0
By matsen:

?!??! Aaron, this is brilliant. Next, I would like to just refine the model if the reference sequences come from a "mixed" alignment, i.e. not from the reference package. If they do come from a reference package, we use the site_categories from the phylo_model.json.