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## Introduction

BEAST offers a wide range of prior distributions that can be used for the parameters used in its models. This page provides a description of and the rationale behind the default priors on each parameter of those standard models in BEAUti, with the goal of providing every parameter with a proper and reasonable prior.

Complementing the parameter priors described here, we also provide a page on coalescent priors, which offers possible choices to put a prior on the underlying tree and its branch lengths.

### Relative rate parameters in BEAST v1.10

As of version 1.10, BEAST makes use of a re-parameterisation of the between partition relative rates parameter.
The old parameterisation - default in versions before 1.10 - is called `mu`

, the new parameterisation is called ```nu``.

The reason for this change is to allow the use of a Dirichlet prior on the relative rates.
This, in turn, is to provide a proper prior so that the marginal likelihood estimation (MLE) can work on these models (previously, with `mu`

, an improper uniform prior [0,Inf[ was used).

The difference between `mu`

and `nu`

is that `mu`

is weighted by partition size so it is a per-site relative rate and if multiplied by the clock rate, will give the absolute rate of a site in that partition.
`nu`

is a per-partition rate; this allows the delta exchange transition kernel to maintain a mean of 1 and thus be suitable for the Dirichlet prior.

As of BEAST 1.10, the `nu`

parameters are what are operated on and they have the Dirichlet prior in the priors table in BEAUti.
To make things more comparable with older versions of BEAST, the `mu`

values are also calculated and logged.
In future versions we will keep logging both `nu`

and `mu`

for completeness.

You can switch this to the old formulation (i.e. BEAST v1.8.4 and older) by checking the “Use classic priors/operators” at the top of the Priors table in BEAUti.