Using mlphase

The mlphase program can be used:

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

In the first mode of operation, mlphase operates like optimise but several trees can be considered at once. In the second mode of operation, when mlphase performs a branch and bound search or an exhaustive search, the ten phylogenies (and associated substitution model parameters) with the highest likelihood are returned. These two search algorithms return the best tree unless they become trapped in local minima during the optimisation process. The heuristic stepwise addition returns only one tree. It is less likely to find the optimal tree but it is computationally feasible with a larger number of taxa. Be warned that the optimiser might crash unexpectedly sometimes and you can change the initial values to overcome that (hopefully rare) problem.

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.