Question: Prottest output to Raxml input
0
gravatar for yp19
16 months ago by
yp1960
yp1960 wrote:

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!

raxml prottest • 666 views
ADD COMMENTlink modified 16 months ago by Mensur Dlakic7.0k • written 16 months ago by yp1960
3
gravatar for flogin
16 months ago by
flogin250
Brazil
flogin250 wrote:

G represents a Gamma Distribution (see http://treethinkers.org/tutorials/the-gamma-distribution/ for a well detailed explanation).

ADD COMMENTlink written 16 months ago by flogin250
2
gravatar for Mensur Dlakic
16 months ago by
Mensur Dlakic7.0k
USA
Mensur Dlakic7.0k wrote:

Your command correctly interprets the prottest output.

ADD COMMENTlink written 16 months ago by Mensur Dlakic7.0k
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