1.3 Starting Options:

--initpars list gives a list of initial parameter values.

--initparsfile filename gives a file containing a list of initial parameter values.

--initprobs list gives a list of initial mixing probabilities.

-m filename Matrix file (see Matrices) - the program will base its initial estimate of the parameters on the Q matrix read from this file. It chooses the parameters that best approximate the Q matrix loaded from this file, as its starting value.

--variables filename reads additional commandline arguments from the specified file. See Variables. By default the file .variables is read for extra commandline arguments. Editing this file can be used to change the default values of variables, or in environments without a command line, to give the commandline arguments.

--parsimony Determines whether parsimony methods are used to find initial parameter estimates and branchlengths. The options are:

1	PARAMETERS	Use parsimony to estimate initial parameters, but use the branchlengths specified in the tree.
2	BRANCHES	Use parsimony to estimate branch lengths, but use other methods to estimate initial parameters.
3	BOTH	Use parsimony to estimate both initial parameters and initial branch lengths.
0	NONE	Do not use parsimony (Default).