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3.8 Models

The model file consists of a number of models. Each model consists of the model name, then any parameters as a comma separated list between parantheses e.g. ‘(a,b,c)’, then the model specification enclosed between braces ‘{’ and ‘}’. [Currently, if there are no parameters, there needs to be a space between the model name and the opening brace. Hopefully this bug will be sorted out soon.]

The model specification consists of a collection of assignments of the form


then a closing brace. The parameters are substituted directly into the VALUE part when they occur (separated by spaces). For example, if there is a parameter called "a", whose value is "testparameters", then a line of the form

PARAMETERS=myparamfile. a

would set the parameter file to

myparamfile. testparameters

If you want to avoid the space, you can replace the line in the model file by:


Currently, arithmetic expressions are not available in the model file. I plan to add support for them in a later version. They will start with the <#> character. If you want to avoid a character having it's normal meaning, you can either precede it with a backslash, or place the text in quotation marks.

The model file simply substitutes the values of the fieldname into commandline arguments. It can therefore do anything that the commandline options can do.

The following aspects of the model can be set in the model file: (given with the equivalent commandline options, which can be looked up in see Invoking Cold).

MIXTURE--mixture See -mixture. the number of sets of parameters in the mixture model.

MIXFILE--mixfile See -mixfile. a file that describes how the parameters vary (see above).

MIXSTRING--mixstring See -mixstring. like mixfile, but gives the mixture as a string, rather than loading it from a separate file.

PARAMETERS-p See -p. the file from which parameters are read

PARAMETERSELECTION--parameterselection See -parameterselection. the parameters from this file to be used in the model.

INITIALMATRIX-m See -m. the matrix used to choose the initial parameters.

NUMPARS--numpars See -numpars. the number of parameters to be read from the parameter file.

MASKFILE--maskfile See -maskfile. the file containing the mask to be used.

MASK--mask See -mask. the mask to be used (if more than one is available)

USEMATRIX--usematrix See -usematrix. use a constant matrix for the Q matrix, instead of optimising parameters.

INITIALPARS--initpars See -initpars. the initial values for parameters.

JUSTBRANCHLENGTHS--justbl See -justbl. only optimise the branch lengths. [Doesn't yet work with mixed models]

EMPIRICAL--empirical See -empirical. sets empirical pi values.

FIXEDPROBS--fixedprobs See -fixedprobs. fixes mixing probabilities as the given values.

FIXEDPARS--setfixedpars See -setfixedpars. sets the values of fixed parameters

See the file models for examples.