The mlphase program is a maximum-likelihood phylogenetic inference program similar to dnaml in PHYLIP and baseml in PAML. The mlphase program has a broad range of functionalities and can be used with a large number of evolutionary substitution models including those which take into account the RNA secondary structure in the evolution of RNA sequences.
The mlphase program has two main modes of operation:
Constraints can be placed on the phylogenetic tree topologies that are considered during ML inference in order to reduce the search space and the computation time.
The optimise program is a simpler version of mlphase and is provided for convenience. This program returns the ML branch lengths and ML evolutionary parameters of a fixed user-defined tree topology, for instance a consensus tree found with a MCMC run. This is equivalent to the first mode of mlphase with only one tree. The optimise program requires less parameters than mlphase; it is simpler to use and allows quick experimentations with different initial parameters when an entrapment in a local maximum of the likelihood is suspected.