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BMT_rate.XYZ6 in Tracer #4

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THccaa opened this issue Feb 9, 2021 · 1 comment
Open

BMT_rate.XYZ6 in Tracer #4

THccaa opened this issue Feb 9, 2021 · 1 comment

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@THccaa
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THccaa commented Feb 9, 2021

I am wondering what the 'sixth rate' described in the troubleshooting section is (Low ESSs for BMT_rate.XYZ6)? I do not see anything matching this pattern in Tracer.

I ran BEAST with bModelTest as the site model and checked the log file in Tracer. The traces look well and all ESS are in the ten thousands except for one paramter: BMT_gammaShape (ESS: 37).
I am wondering whether this is the above mentioned 'sixth rate', because I do have a very low model support for GTR (0.36), and, hence, the explanation given in the section 'Low ESSs for BMT_rate.XYZ6' would fit to my situation. I just want to make sure I am not mixing something up here.

@rbouckaert
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@Th-al this is indeed the sixth rate, and given the low support for GTR, you should not worry about it mixing badly. This low ESS rate is rarely used in the model in your analysis, and there is no need to run the analysis longer in order to obtain an ESS over 200.

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