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PERTURBATION Block for MIXED models
When a mixed model is used, the previous proposal parameters are required for
each model and must be enclosed in separate blocks. You must complete a
PERTURBATIONi block for each model in the PERTURBATION block
with the previously described parameters (see
appendix A.8).
Parameters which are specific to the MIXED model appear in the
PERTURBATION block.

Model i priority: specify a priority for each model with respect
to the other models and the priority used for the average rates.
Model 1 priority = 8
Model 2 priority = 24

Average rates, proposal priority: specify a priority for the perturbation
of the model average substitution rate.
Average rates, proposal priority = 1

Average rates, proposal minimum acceptance rate and
Average rates, proposal maximum acceptance rate: the acceptance range
mcmcphase aims for, [0.21, 0.25] by default.
Average rates, proposal minimum acceptance rate = 0.15
Average rates, proposal maximum acceptance rate = 0.25

Average rates, initial step: allowed initial values are in the range ]0, 1.0].
The default value (when the dynamic step option is on) is 0.2. You
cannot provide a specific initial step for each average substitution rate at
the moment.
Average rates, initial step = 0.14
The upperbound for the uniform prior distribution of the average substitution
rate ratios is .
Next: Proposals priority
Up: mcmcphase
Previous: PERTURBATION block
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GowriShankar Vivek
20030424