Hi all!
I ran Prottest to determine the best model for a given protein sequence alignment, so I can eventually use that model in RAxML. The output of Prottest tells me that the best model according to AIC is: WAG+I+G+F.
Now I have to set the model in RAxML command. Based on the RAxML manual I think "WAG" is the model, "I" is for invariant sites, "F" is for using empirical AA frequency, but i'm not sure what the "G" is for? This is what I have come up with, does anyone know if this is the right model based on the Prottest output?
raxmlHPC-PTHREADS-SSE3 -m PROTGAMMAIWAGF
Thanks!
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written
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yp19
2 answers
G represents a Gamma Distribution (see http://treethinkers.org/tutorials/the-gamma-distribution/ for a well detailed explanation).
Your command correctly interprets the prottest output.
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