Using likelihood

The likelihood program is used to compute the likelihood of a model of evolution (i.e., tree + parameterised substitution model) given a set of studied sequences. To use likelihood, one has to provide a phylogeny for the taxa under investigation (i.e., topology and branch lengths) and a substitution model for nucleotide evolution with user-defined parameters. To use likelihood, type at the command-line:
likelihood likelihood-control-file
where likelihood-control-file is a valid control file for the likelihood program. For verification purposes likelihood outputs the phylogenetic tree used on the screen before the likelihood value. Unlike most other PHASE programs, likelihood does not send any results to a file.