The parsimony methods used are precisely those available in MIX, and thus the biological assumptions are the same as in that program. MIX is a general parsimony program which carries out the Wagner and Camin-Sokal parsimony methods in mixture, where each character can have its method specified. The program defaults to carrying out Wagner parsimony. Wagner parsimony allows both kinds of changes. The criterion is to find the tree which requires the minimum number of changes.
Different characters evolve independently.
Different lineages evolve independently. Both of these kinds of changes are a priori improbable over the evolutionary time spans involved in the differentiation of the group in question. Rates of evolution in different lineages are sufficiently low that two changes in a long segment of the tree are far less probable than one change in a short segment. The input for BOOT is largely identical to the standard input for discrete characters programs, described above in the documentation file for the discrete-characters programs. The program starts by asking the user to supply a random number seed.