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.

## References

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

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