how to set up SRD06 codon substitution model in beast2?

[lwang....@gmail.com]

Hi everyone,

I am new to using BEAST2. I just wanted to use SRD06 codon susititution model for may study. However, I can not find a button which could automatically set up SRD06 (like in beast v1.10.4) in beauti v2.6.3. I just found a button named "split" in the beauti which can split the input alignment into 1+2, and 3, which I think was just like the SRD06. However, are there any other parameters I should set up using beauti? In addition, how do I set up the "unlink substitution rate parameters across codon postions" and "unlink rate heterogeneity model across codon positions", which was from BEAST v1.10.4, in BEAST2?

[Artem B]

Hello comrade!

It is pretty easy. As you can see on the partitions panel, your partitions now have different substitutional models. In other words, they are already unlinked. So if you go to the Site Model panel, you will see two partitions at the left, for each one you should set a HKY+Г model (see pic.).

Note that your molecular clock model unlinked as well, so if you want to get a classic SRD06 like in BEAST1, you should link the clocks manually. Just press a shift button and choose both partitions, then click "link clock models" button above (see pic. 2).

Best,
Artem

среда, 30 сентября 2020 г. в 11:29:11 UTC+8, lwang....@gmail.com:

[lwang....@gmail.com]

Dear Artem,

Thank you for your advice. I have now set  SRD06 substitution model in BEAST2 correctly.