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Each cycle *mcmcphase* perturbs one branch length and a topology change
is tried every ten cycles (see the Bayesian phylogenetics section).
Each cycle *PHASE*
will also try to modify the substitution model.
Let us consider the following example with the **MIXED** model
and three substitution models,

**{PERTURBATION}**

**#PERTURBATION OF THE TREE :**

**...**

**#PERTURBATION OF THE MODEL :**

**Model 1 priority = 8**

**Model 2 priority = 24**

**Model 3 priority = 7**

**Average rates, proposal priority = 1**

**Average rates, initial step = .3**

**Average rates, proposal minimum acceptance rate = .15**

**Average rates, proposal maximum acceptance rate = .20**

**{PERTURBATION1}**

**Frequencies, proposal priority = 1**

**Rate ratios, proposal priority = 2**

**Gamma parameter, proposal priority = 1**

**{PERTURBATION1}**

**{PERTURBATION2}**

**Frequencies, proposal priority = 3**

**Rate ratios, proposal priority = 4**

**Gamma parameter, proposal priority = 1**

**Invariant parameter, proposal priority = 1**

**{PERTURBATION2}**

**{PERTURBATION3}**

**Frequencies, proposal priority = 4**

**Rate ratios, proposal priority = 2**

**Gamma parameter, proposal priority = 1**

**{PERTURBATION3}**

**{PERTURBATION}**

The *mcmcphase* program will modify the average substitution rate of the second
model with probability given in 1.1a; the probability of
modifying the average substitution rate of the third model is the same.
The average substitution rate of the first model is the reference, it is
never modified and remains equal to .
With probability given in 1.1b, *mcmcphase* will modify
the parameters of the substitution model (*i.e.*,
any parameters but the
average substitution rate). The priorities inside the corresponding
*PERTURBATION**i* block are used, the figures inside
each *PERTURBATION**i* block do not have any effect outside
the block.

In our example, if the second model is selected for the next modification, we
define
:

and we modify either all the frequencies (probability 1.2a),
or one of the rate ratios (probability 1.2b each), or
the invariant parameter (probability 1.2c), or the gamma
shape parameter (probability 1.2d).

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Gowri-Shankar Vivek
2003-04-24