hello,

I'm wondering how I would specify the T92 model in a batch file. (3 parameters, transition and transversion rates plus a parameter to allow GC to have a different equilibrium freq from AT). I couldn't find a version of this particular model in the batch files included with the distribution...

thanks!

Dear Weli,

The T92 model assumes that pi(A)=pi(T)=(1-theta)/2 and pi(G)=pi(C)=theta/2, where theta is the CG content. To define this matrix you would use the standard HKY85 rate matrix and a properly constrained vector of base frequencies. Here's an example Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login

Cheers,
Sergei