This program is one of the slowest programs in this package, and can be very tedious to run. It is possible to have the program search for the maximum likelihood tree. It does not place prior probabilities on trees as they do. The present program extends their approach to multiple species by a technique which, while it does not give explicit expressions for likelihoods, does enable their computation and the iterative improvement of branch lengths. It also allows for multiple restriction enzymes.
Different lineages evolve independently.
Each site undergoes substitution at an expected rate which we specify. Substitutions consist of replacement of a nucleotide by one of the other three nucleotides, chosen at random. Users who are upset at this might ponder the fact that a version allowing different rates of transitions and transversions would run an estimated 16 times slower. The input is fairly standard, with one addition. As usual the first line of the file gives the number of species and the number of sites, but there is also a third number, which is the number of different restriction enzymes that were used to detect the restriction sites.