Setting different mutation rates for each taxon set

[Kiran Hazra]

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]

Hi Kiran, 

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

https://github.com/4ment/flc

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. 

https://github.com/4ment/flc/blob/master/examples/Human.H3.81-98-elc-StrictClock.xml

https://github.com/4ment/flc/blob/95b7b8faf11c3ca1034704c42e20280d62eeb8e4/examples/Human.H3.81-98-elc-StrictClock.xml#L164

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