- to find the Maximum Likelihood Estimates for branch lengths and, optionally, evolutionary model parameters for a user-defined set of topologies.
- to find the phylogeny and, optionally, evolutionary model parameters that yield the maximum likelihood. Three algorithms are provided for topology search:
- Simple exhaustive search
- Branch-and-bound exhaustive search
- Heuristic stepwise addition

To reduce the search space and the computation time, constraints can be placed on the
phylogenetic tree topologies considered during ML inference. With a clade file one can specify invariant monophyletic clade
topologies which should be preserved during phylogenetic inference. The program will look for an
optimal topology consistent with these clade arrangements. To use
*mlphase*, type at the command-line:

**mlphase mlphase-control-file**

where *mlphase-control-file* is a valid control file for
*mlphase*. The *mlphase* program saves the results of an inference in
a single file. Results are also displayed on screen during the run.