Setting different mutation rates for each taxon set

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Kiran Hazra

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Sep 3, 2025, 3:32:04 PMSep 3
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I already know the approximate mutation rates of the two clades that make up my study species; the rate is much higher in one clade than in the other. Is there any way to have BEAST2 use a different substitution rate as a prior for each clade?

Kylie

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Sep 5, 2025, 10:21:07 PMSep 5
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Hi Kiran, 

You can use the FLC package (Flexible local clock) to set up two different clock priors on your two clades. 

For example, you could use a strict clock with a log normal prior on clade 1, and another strict clock with a different log normal prior on the remaining clade. 

There are also local relaxed clocks available in FLC, but this setting currently only works for trees with highly certain topologies. 

Hope that helps, 

Kylie

Kiran Hazra

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Sep 9, 2025, 11:33:51 PMSep 9
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Thank you, I really appreciate your help.

- Kiran
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