The program as presently constructed runs only once for each bootstrap data set. However each run involves global branch swapping and can find multiple, equally parsimonious trees. In the input file the user supplies a random number seed that controls the random sampling process. To take more random samples from the same data set one can simply run the program again and supply a different random number seed, combining the resulting information on frequencies of monophyletic groups by hand. Each site evolves independently.
Different lineages evolve independently.
The probability of a base substitution at a given site is small over the lengths of time involved in a branch of the phylogeny. The expected amounts of change do not vary enough among sites that two changes in one site are more probable than one change in another. Change from an occupied site to a deletion is counted as one change. Reversion from a deletion to an occupied site is allowed and is also counted as one change. The input file starts with a line containing the number of species and the number of sites.