Written by Joseph Felsenstein. Permission is granted to copy this document provided that no fee is charged for it and that this copyright notice is not removed. 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 options U, J, O, T, A, and M are the usual User Tree, Jumble, Outgroup, Ancestral States, and Multiple Data Sets options, described either in the main documentation file or in the Discrete Characters Programs documentation file. The O option is acted upon only if the final tree is unrooted and is not a user-defined tree.