GTR+F+I+G4

[jj biodiversity]

Hello,

Trying BEAST for the first time, but having trouble setting the site model on Beauti.

I am trying to set GTR+F+I+G4 as recommended by IQTREE, but I'm just not sure what to to do about estimate check boxes, values for substitution rate and proportion invariant..

Help will be greatly appreciated!

[Pratanu Kayet]

Substitution rate that is kappa(k) value or you can use R-value to calculate kappa.

the alpha parameter is corresponding to your gamma value.

As per I remember, if you take a look at your IQTREE log file it will give you those parameter values.

And checkboxes are for your choices that if you want to estimate those values or if you want to fix those values in your corresponding analysis.

if you want to estimate those values then, click on the check, so BEAST will take those values as a hint and estimate it for you. 

or, if you want to use those as fix values then left uncheck so BEAST will take those values as fixed parameters throughout the analysis. 

--
You received this message because you are subscribed to the Google Groups "beast-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to beast-users...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/beast-users/02750f8f-9552-4509-9740-c7bda032fd5dn%40googlegroups.com.

[Pratanu Kayet]

I'm really very sorry for one wrong information, that kappa isn't a substitution rate, it is the Transition per transversion ratio. for substitution rate use the default parameter from BEAUTi and click on the check box, so BEAST  will give an estimated rate for you, or you can look for existing literature as per your analysis of interest, where substitution rate will be given.