BEAST model defaults

Question

[Vasiliy Krestov]

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?

Answer 1

[Mensur Dlakic]

Should I find another best model without 'F' or BEAST always use empirical frequencies for analysis?

Don't forget that there is also an option of using a different program that can set empirical frequencies.

This post explains how to do it using BEAUti. Also see here.