Implamenting subsitution models other then HKY GTR TN93

[JHallas]

I'm trying to partition a 3 marker data set.  I have partitions whose models are F81+G and JC+G.  How do i go about setting up these two subsitution models in BEAUti?

thanks for the help

Josh

[Krzysztof M. Kozak]

Dear Josh,

Since Beast 2 has JC69 as a default, I understand you are using 1.8. You can get creative using the base frequency settings and on/off switching operators for individual types of transitioins and transversions. Here is an older post with some examples:

"Qiyun Zhu

8/12/12

Hello all,

I think I have found ways to specify 10x4=40 nucleotide substitution models by clicking in BEAUti (not by editing xml file). I'm not sure if I understand correctly.

BEAUti already has three models: HKY, GTR, TN93 (TrN).

By setting base frequencies to all equal, one gets K2P (K80) (from HKY), SYM (from GTR), TrNef (from TrN).

By unchecking operators ac, ag, at, cg, gt, one gets F81 (from GTR) and JC69 (from SYM).

By unchecking operator ag only, one gets TVM (from GTR) and TVMef (from SYM)

There leaves K3P(ef) and TIM(ef), which have to be set by editing xml file."