Next: Control file for 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
topology and branch lengths) and a substitution model for
nucleotide evolution with user-defined parameters.
To use likelihood, type at the command-line:
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
programs, likelihood does not send any results to a file.