--model modelname loads the arguments from the chosen model, which must be described in the model file. The model file models is provided with the package, and contains details for various standard models. If these are not sufficient, the user can supply their own model file for describing their own models.
--modelfile filename instructs the program to use the specified model file instead of the default one.
--numpars number tells the program to only read the first number parameter matrices (thereby selecting a submodel of the model described in the parameter file).
--mask number selects a mask to use from the maskfile. (This allows the user to specify no multiple-nucleotide changes for example). The input is the number of the chosen mask within the file. The default mask file "masks" supplied with the package only contains one mask at present, so this value should always be 1 unless using a user-supplied mask file.
--maskfile filename instructs the program to use the file specified when reading masks, instead of the default mask file.
--nomask tells the program to ignore the mask matrix (which determines which codon changes are possible in a single step - e.g. only single nucleotide change, ...)
-p filename Parameter file - the program loads the parameters from the given text file. The files parametermatrices and standardmodelmatrices are provided with the package. Alternatively, the user can write their own parameter files
allows a selected subset of the parameters to be used. The format is
fairly obvious, it should accept a comma-separated list of ranges, for
1,3-7,9-11,36. If you want to include spaces in the list,
you will probably have to enclose the list in quotes.
--usematrix filename specifies that parameters don't vary, and that the specified transition matrix should be used.
--justbl instructs the program to fix the parameter values, and only optimise the branch lengths.
--mixture number Tells the program to use a mixed model, and indicates the number of separate distributions to be mixed. Parameters can be further controlled by the option --mixfile See -mixfile, or --mixstring See -mixstring.
--mixfile filename Defines the parameters in a mixed model (some parameters may be estimated for each component of the mixture; others may be the same for all component; while others may be fixed in certain components). See Mixture, for details of the format of this file.
--mixstring string Like mixfile, except that the information is input on the command line as a string instead of being read from a file. The format is the same as for the mixture file.
--empirical style Instructs the program to estimate the Pi parameters empirically in the manner described. There are currently four options:
--fixedprobs values Instructs the program to use the given values for mixing probabilities, rather than estimating them. This can be useful for discrete approximations to fixed distributions.
--equalprobs Instructs the program to use an equal mixing probability for each class.
--varprobs number Indicates the number of mixing probabilities which are allowed to vary independantly.
--setfixedpars values Sets the values of fixed parameters.