Hello all, I have the following problem: I have an analysis with some DNA partitions, some indel partitons and 2 partitions of protein coding DNA regions. Now I wanted to test BEFORE I run the final calculation with all partitions (in MrBayes) if it is better to use a site specific rate model (SSR) or a codon model (Goldman and Yang or Muse and Gaut). So I wanted to test it by run 2 analysises with the protein coding MSAs ONLY, first with the SSR, and then with the codon model and test which one is better (Likelihood or BF). So far so good - note it is not the question how to do that. Now the question is: Is it true, that if the model which win the test will also be the better one for the protein coding MSAs when they are a part of the complete analysis - Or, must I always test this within the complete partition analysis? All the best Dieter
