@dereneaton thanks a lot for your prompt reply, and for the hint on RADami. I will contact then Andrew and perhaps I can get RADami running on my ipyard loci data. As for the ML tree that makes topologically sense (but poorly supported) that I obtained from the super matrix concatenated loci, do you know perhaps why is this happening? Again, I will be extremely grateful for any advice or piece of information you could provide on how to improve the support on my ML phylogeny (e.g. some parameters in ipyrad that could let to more optimal results). Thanks very much!