BEAST model defaults
Prottest3 and ModelFinder gave me "WAG+F+I+G4" as the best model for my alignment. But I don't know how to specify 'F' (empirical frequencies) in BEAST. It seems that in BEAST one can specify only 'I' and 'G'. Should I find another best model without 'F' or BEAST always use empirical frequencies for analysis?
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