BEAST 2 Help Me Choose

BEAST 2 Help Me Choose Random local clock -- rate change prior

Random local clock – rate change prior

This prior is over the number of internal nodes where a rate change takes place in the random local clock (Drummond & Suchard, 2010). When this is 0, the model behaves like the strict clock, and when it is the number of internal nodes it behaves like a relaxed clock (uncorrelated if ratesAreMultipliers=false and correlated if ratesAreMultipliers=true).

Usually, you want to encourage a low number of rate changes, so for example a Possion distribution with a low mean as prior would be appropriate. If the data indicates there are many rate changes, the random local clock will accomodate this if the prior is not too strong.


Drummond AJ, Suchard MA. Bayesian random local clocks, or one rate to rule them all. BMC biology. 2010 Dec;8(1):1-2. doi:10.1186/s12862-020-01609-4.

Bayesian evolutionary analysis by sampling trees

Disclaimer: The above is the opinion of the author RB. If you do not agree, or spot a mistake, contact the author, or discuss this in the issues area or raise a new issue. A link will be added from this page to make sure others can find it.

Served through Jekyll, customised theme based on the twentyfourteen wordpress theme.