PERTURBATION block

The PERTURBATION block contains the mixing parameters used for the proposals. The following mixing parameters are relative to the branches:

Initial branch step proposal parameter: the initial standard deviation of the normal distribution used to modify the branch lengths. This proposal parameter is modified during the ``burnin''.
Initial branch step proposal parameter = 0.1

Branch length upper bound: the upper bound used for the uniform prior distribution of branch lengths.
Branch length upper bound = 3.5

The PERTURBATION block also contains mixing parameters for the proposals of substitution model parameters. These parameters are dependant on the substitution model used. With simple substitution models, i.e., any nucleotide or base-paired model used alone, the following parameters are added in the PERTURBATION block to perturb the frequencies:

Frequencies, proposal priority: an integer value to specify how often we try to perturb the frequencies with respect to other parameters. This parameter is usually compulsory except for models with fixed frequencies (i.e., JC69 and K80). Use the value 0 to prevent the perturbation (i.e., if you want the frequencies to remain equal to the empirical frequencies or to the values provided in an initial substitution model).
Frequencies, proposal priority = 1

Frequencies, proposal minimum acceptance rate and Frequencies, proposal maximum acceptance rate: during the ``burnin'', mcmcphase will try to adapt the proposal step so as to reach an acceptance rate within the specified range. By default this range is [0.21, 0.25]. If you want to change the default values, provide the two parameters. Use the range [0.0, 1.0] to turn off the dynamic adaptation of the proposal step.
Frequencies, proposal minimum acceptance rate = 0.0
Frequencies, proposal maximum acceptance rate = 1.0

Frequencies, initial Dirichlet tuning parameter: the initial proposal parameter (the higher the Dirichlet parameter, the lower the step). This parameter is compulsory if you turned off the dynamic adaptation of the step. Allowed values are in the range [100.0, 100000.0] and the default value is 1000.0.
Frequencies, initial Dirichlet tuning parameter = 1500.0

Similar parameters are used for the rate ratios:

Rate ratios, proposal priority: an integer value to specify how often we try to perturb each rate ratio with respect to other parameters. Rate ratios are treated individually but they share the same priority. This parameter is usually compulsory except for models with fixed rates (i.e., JC69). You can use the value 0 to have constant rate ratios but you should not do that unless you provide initial parameters with a ``.model'' file.
Rate ratios, proposal priority = 2

Rate ratios, proposal minimum acceptance rate and Rate ratios, proposal maximum acceptance rate: rate ratios are treated individually but they share the same range for the acceptance rate. The default range is [0.21, 0.25] and you can turn off the dynamic modification of the step with the range [0.0, 1.0].
Rate ratios, proposal minimum acceptance rate = 0.3
Rate ratios, proposal maximum acceptance rate = 0.6

Rate Ratios, initial step: allowed initial values are in the range ]0, 5.0]. The default value (when the dynamic step option is on) is 0.2. You cannot provide a different initial step for each rate ratio at the moment.
Rate Ratios, initial step = 0.25

Similarly, you can/must use the following parameters when using a +I (invariant category) or/and a +dG (discrete gamma categories) model:

Gamma parameter, proposal priority: compulsory if a gamma model is used.

Gamma parameter, proposal minimum acceptance rate: default value = 0.21

Gamma parameter, proposal maximum acceptance rate: default value = 0.25

Gamma parameter, initial step: default value = 0.2

and,

Invariant parameter, proposal priority: compulsory if an invariant model is used.

Invariant parameter, proposal minimum acceptance rate: default value = 0.21

Invariant parameter, proposal maximum acceptance rate: default value = 0.25

Invariant parameter, initial step: default value = 0.05

The upper-bound for the uniform prior distribution of each rate ratio is $1000.0$. The upper-bound for the uniform prior distribution of the gamma parameter is $200000.0$. Be aware that there might be something wrong if you reach that upper-bound value during a MCMC inference, i.e., there may be insufficient data to properly estimate the parameter.