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
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| --empirical | See -empirical. | string
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| --fixedprobs | See -fixedprobs. | string
|
| --setfixedpars | See -setfixedpars. | string
|
| --treenumber | See -treenumber. | string
|
| --initpars | See -initpars. | string
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| --variables | See -variables. | string
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| --parsimony | See -parsimony. |
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| --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
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| --noautobackup | See -noautobackup. |
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| -P | See -P. | string
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| -b | See -b. | string
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| -T | See -T. | string
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| -v | See -v. |
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| --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.