Entering edit mode
6.3 years ago
Is it appropriate to test for multiple hypotheses with PAML or HyPhy? Like, for example, would it be statistically valid to test two of the hypotheses listed at the bottom of this page on one alignment/phylogeny?
Sure, why not? - that's how research is conducted, is it not? Provided your input data suits the conditions of each analysis protocol, there should be no issue testing different hypotheses.