TIM2 and TPM2uf substitution models in Beauti 1.8.3

[felixvaux...@gmail.com]

Hi All,

I was wondering if it is possible to use the TIM2 and TPM2uf substitution models in Beauti 1.8.3? I had these models selected for some of my alignments using jModelTest2.

I read a previous discussion here:
https://groups.google.com/forum/#!topic/beast-users/_zCoCTSkWRs

And at the time with Beauti 1.7 it seemed like changing sites and operator settings it was fairly straight forward to implement substitution models other than HKY, TRN93, GTR and JC.

I've checked the jModelTest2 manual (page 20) and I think that I should be able to get my desired models by doing the following:

TrN -> TIM2
Change base frequency to unequal.
Change free parameters from 5 to 3.

HKY -> TPM2uf
Change free parameters from 5 to 4.

Does anyone know if this is possible to accomplish, and if so how?

Cheers,
Felix

[Simon Ho]

Hi Felix,

I don't think it's possible to implement these substitution models in BEAUti. In terms of the pairwise substitution rates, TIM2 has {a=c, d=f, b, e} and TPM2uf has {a=c, d=f, b=e}. These particular combinations are not achievable by switching off some of the operators for the parameters of the 4 substitution models available in BEAUti.

To implement the TIM2 and TPM2uf models, you would need to edit the XML file directly. If you run into problems, let me know and I can help with this.

Cheers,
Simon

[cmil...@gmail.com]

Hi All,

I have a similar question, I would like to implement the TPM2uf substitution model in my analysis, can anyone advise on how to edit the XML file to do this?

Best wishes,
Caroline

[Santiago Sánchez]

Hi Caroline,

I know this is not the answer you are looking for, but I would recommend you to try bModelTest in BEAST 2. It will essentially estimate de best substitution while your analysis is running, averaging parameters from the MCMC. It is really easy to set up and I haven't notice any slowdowns in run times.

You can check the log file in tracer to see if this is in fact the best model. I think it would be model 6  or 121323.

You can read the publication here and a good tutorial can be found here.

Hope this helps!

Cheers,

Santiago

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==========================

Santiago Sanchez-Ramirez, PhD

Postdoctoral Associate

Ecology and Evolutionary Biology

University of Toronto

https://sites.google.com/view/sanchez-ramirez-s/home

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