What are topological constraints?
Topological constraints are unresolved trees used to filter out trees discovered during the search that do not match a particular topological criterion. One possible use of a topological constraint is to force a particular group to be convex (i.e., monophyletic if the tree is rooted outside the group). This type of topological constraint is referred to as a monophyly constraint. Monophyly constraint trees contain all the taxa but are unresolved to some degree. A second type of constraint is called a backbone constraint. Backbone constraint trees are normally fully resolved, but are missing one or more taxa. A tree encountered during a search is consistent with a backbone constraint tree so long as pruning all taxa not in the constraint tree yields the constraint tree topology. One may wish to compare the support of the data for the best tree obtained under the constraint to the best tree without the constraint. Note that PAUP* offers much more flexibility in terms of topological constr
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