Question: PAML and WAG+gamma model
gravatar for martanit
3.9 years ago by
martanit0 wrote:

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

codeml paml gamma • 998 views
ADD COMMENTlink modified 3.9 years ago by Biostar ♦♦ 20 • written 3.9 years ago by martanit0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2136 users visited in the last hour