ModelFinder help

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Volodymyr Dvornyk

May 27, 2020, 10:49:58 AM5/27/20

I found the description of the ModelFinder results quite confusing. For example, the following one:

Another example is for model TIM2 that has the 6-digit code 010232. Thus, TIM2{4.39,5.30,12.1} means that A-C=A-T=4.39 (coded 1), A-G=5.30 (coded 2), C-T=12.1 (coded 3) and C-G=G-T=1.0 (coded 0). This is, in turn, equivalent to specifying GTR{4.39,5.30,4.39,1.0,12.1}.

According to the 6-digit model code, A-C=A-T is coded 0, not  C-G=G-T (which are coded 2). Therefore, I am totally confused what the values in the result correspond to.

Rob Lanfear

May 27, 2020, 4:32:31 PM5/27/20
Hi Volodymyr,

The codes simply specify how the six possible parameters should be grouped together. Any parameter with the same integer is set to be equal to other parameters which share that integer.

Maybe it would help to look at the 'phyml commandline' column of this file:

It specifies the six-digit codes for a whole heap of models.

One thing to note though, is that you should rarely if ever really need to use these codes. Simply running ModelFinder with the default settings will test all of the most commonly-used models for you.


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Rob Lanfear
Division of Ecology and Evolution,
Research School of Biology,
The Australian National University,
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