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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.

Gowri-Shankar Vivek
2003-04-24