Using optimise

The program optimise is used to compute maximum-likelihood estimates (MLE) for the branch lengths and substitution model parameters of a given model of evolution (i.e., a fixed tree topology and a specified substitution model with free parameters). One can specify some initial values for branch lengths and substitution model parameters to speed-up the convergence or to detect trapping in local maxima of the likelihood function. To use optimise, type at the command-line:
optimise optimise-control-file
where optimise-control-file is a valid control file for the optimise program.

When launched, optimise displays the initial tree and the initial likelihood on the screen and begins the optimisation. Once it is finished, the ML substitution model parameters are printed on the screen and saved in the ``.output'' file with the ML tree and the value of the maximum likelihood. The ML tree is also saved in the ``.tree'' file and a ``.model'' file is created to store the MLE for the substitution model parameters.