** Next:** Proposals for the parameters
** Up:** Priors and proposals
** Previous:** Priors and proposals
** Contents**

We have no strong evidence for any particular prior and we
therefore choose a simple factorized prior
. We assume a uniform prior on all
trees
, we use a flat Dirichlet distribution
prior for frequency parameters (*i.e.*,
all sets of
frequencies are equally likely as long as they sum to one) and we
choose a uniform positive prior for substitution rate parameters,
gamma distribution parameter and branch lengths. Consequently,
for all pairs of possible states , the priors are equal.
One should set upper limits in the case of uniform priors but since these
parameters usually remain between reasonable limits during simulations
these boundaries should not have any effect on experimental results unless
unreasonable values are chosen. It is good practice to check whether
these upper boudaries are reached while monitoring the parameters
convergence.

Gowri-Shankar Vivek
2003-04-24