I'm reposting this because I want to make a correction. In the thread below I mention using the -mset flag for testing site profile mixture models. But in fact you should use -madd flag. I'm sorry for this mistake.
Andrew Roger
So you are using IQ-TREE to estimate a tree for "deep time" phylogenetics using amino acid alignments. There is a lot of confusion about how to test model fit. Here are some suggestions.
