substitution rate/ clock.rate...

Vano

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Jun 14, 2022, 2:13:45 PM6/14/22

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Hi everyone, I literally broke my brain trying to find out this case. This blog BEAST and the BEAST basics: molecular clocks and how to input rates into BEAST - blog (rbind.io) says that in the most article pairwise rates of evolution are commonly reported, so we need to divide it on two to get per-lineage rate to input it in the clock.rate window in the beast. So, posterior distribution of the clock.rate must be per-lineage too? In none of article which reported substitution rate I've seen was not any mentions about is their estimation pairwise or per-lineage, so how to understand it?

Pavel Rinkman

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Jun 14, 2022, 2:45:03 PM6/14/22

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If I am not mistaken, they are just addends (as logarithms) both in likelihood & prior.

вторник, 14 июня 2022 г. в 21:13:45 UTC+3, Vano:

nate...@gmail.com

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Jul 27, 2022, 2:16:36 PM7/27/22

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Hi Vano! Did you figure it out? I found this blog, but I could not find a reference to confirm if this approach (dividing per two) is appropriated.