Modelling details

It is important to understand the modelling assumptions made by BEASTling which underly all analyses generated by it. Substitution models in particular are discussed separately in the next section.

Tree prior

BEASTling defaults to using a Yule pure-birth prior for phylogenetic trees. The birthrate is fixed everywhere on the tree, and is estimated during the analysis. The prior over birthrates is a uniform prior from zero to infinity. This model is not particularly suitable for linguistic analyses, but it is arguably the simplest tree prior in BEAST which is not totally inappropriate.

A slightly more complicated but more appropriate tree prior is the BirthDeath prior, which can be specified in place of the Yule.

Branch lengths

If no calibration points have been provided in the configuration, then the trees logged from a BEASTling analysis will have units of “expected number of mutations for a feature with rate 1.0”.

If calibration points have been provided, then branch lengths will be in the same units as the calibrations.


BEASTling supports three different clock models. These are: strict clocks, where the mutation rate of any particular feature is the same at all points across the tree; relaxed clocks, where the mutation rate of every branch on the tree is tree is sampled individually; and random local clocks, which can be thought of as an interpolation between these two extremes.