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3.6 Variables

The variable file consists of lines, each of which specifies a command line option. The lines have the following format:

name commandlineoption type value

The name doesn't really matter for most options. The commandlineoption is what you would type at the commandline to invoke this option. The type is the type of the argument (see the following list for the required values). The value is the argument for the option.

The following options can be invoked from a file. The type value should be as given in this list.

--model See -model. string


--modelfile See -modelfile. string


--numpars See -numpars. string


--nomask See -nomask.


--parameterselection See -parameterselection. string


--usematrix See -usematrix. string


--justbl See -justbl. string


--mask See -mask. string


--maskfile See -maskfile. string


--mixture See -mixture. string


--mixfile See -mixfile. string


--mixstring See -mixstring. string


--empirical See -empirical. string


--fixedprobs See -fixedprobs. string


--setfixedpars See -setfixedpars. string


--treenumber See -treenumber. string


--initpars See -initpars. string


--variables See -variables. string


--parsimony See -parsimony.


--path See -path. path


-q See -q.


-i See -i. string


-D See -D. string


--showeverysite See -showeverysite. int


--printsitelikes See -printsitelikes.


--state See -state. string


--recover See -recover. string


--noautobackup See -noautobackup.


-P See -P. string


-b See -b. string


-T See -T. string


-v See -v.


--testderivs See -testderivs.

For an example, see the file .variables. This file is automatically read before any other arguments. This is important because the path variable needs to be set before other options are processed.