PAML and WAG+gamma model

Question

[martanit]

Hi, I'm trying to make an ancestral reconstruction of a protein using PAML under Empirical model (WAG matrices), using gamma model in codeml, that I think is controlled by "alpha" and "fix_alpha" parameters. I try with "fix_alpha=0" and various value of "alpha" (0.1, 0.5 and a meaningless 10) but I obtained same results, and it sounds strange. On the contrary, with fix_alpha=1 and alpha =0, that means constant rate, I obtain different results. Could someone help me to understand how this model works? Thanks, Martina