Hi guys, I used modeltest-ng to find the best fitting evolutionary model for my data and I want to use Mr. bayes to infer the tree. But modeltest-ng output shows matrix+I+G4, which is a problem since Mr. Bayes (as far as I know) don't have G4. Well, what is better then? is G4 replaceable for G? I actually dind't find any reference for G4 parameter, is it somehow similar to LG4M-LG4X matrices?
1 answer
My memory is fuzzy (I have used MrBayes a long time ago), and I never used ModelTest-NG, but I guess MrBayes G is the same as ModelTest-NG G4.
By default, MrBayes (and many other phylogeny estimation software) approximates the gamma distribution using four discrete rate categories, I am inferring ModelTest-NG's G4 means the same, just explicitly stating it is using four categories.
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