Control file for optimise

An example of a valid control file for optimise can be found in appendix A.2. The control file of the optimise program must/may provide:

a DATAFILE block: see the data file block section.

a MODEL block: see the model block section.

Tree file: the name of the file containing the phylogeny, i.e., a tree in the Newick format (see section 2.1.2) with optional initial branch lengths values.
Tree file = mammals69-mix-consensus.tree

Random seed: the integer value provided with this field is used to initialise the random number generator (used to draw random initial branch lengths if they are not provided).
Random seed = 1

Starting model parameters file: the name of a file containing initial values for the parameters of the substitution model used. If this field is not provided, the analysed sequences are used to initialise the model.
Starting model parameters file = data/hiv.model

Output file: the basename for the three files basename.tree, basename.model and basename.output. They contain the results generated by optimise.
Output file = mammals69-mix-optimise