I'm curious about the phylogenetic results in particular. It is such a fascinating, ancient group of organisms that reconstructing their phylogeny could be quite challenging. You acknowledge the low confidence for many of the relationships, along with the intriguing Bayesian non-convergence. With contigs drawn from 5 marker sequences, you may have a great deal of noise, which is what the Bayesian models may have been informing you. There are ways to test for saturation but I don't see anything in the paper or attachments. The choice of root can make or break phylogenetic proposals. Did you try others, or partition analysis within the major clades using other Cnidarians as root to examine saturation effects or test branch stability? You indicate use of CIPRES ML, but not how you decided upon GTR? How many bootstrap cycles? Did you try other ML systems? Details are requested. I would be interested in working with your sequence dataset.
