================= 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. Clocks ------ 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.