Hi All,
I generate my trees for codeml analysis using RAXML and used lineage-specific and site-specific models. I never changed my trees to unrooted trees and used the default output of RAXML with clock=0. Can anyone suggest if my analysis will be valid or I should redo it using unrooted trees?
From PAML documentation: For most models, the likelihood values are still correct even if you use a rooted tree, but the lengths of the two branches around the root are not stable, as only their sum is estimable. For other models, neither the likelihood nor the parameter estimates are correct. So really you should heed the message and use an unrooted tree in the analysis. If the model you use in baseml or codeml does not distinguish between rooted trees, but you use a rooted tree, the programs will issue a warning message "This is a rooted tree. Please check!" in the output.
What is the meaning of 'For most models'? P.S. I never got any warning "This is a rooted tree. Please check!" while running my data on codeml.
