TreeRot aids in the determination of decay or Bremer support indices (Bremer 1988) by generating a command file for PAUP or PAUP* (Swofford 1993, 1999). The command file includes 1) a constraint statement for each node in a given shortest or strict consensus tree and 2) commands to search for trees inconsistent with each of these constraint statements in turn. Compared to the shortest unconstrained tree, the number of additional steps required in the shortest tree(s) that is inconsistent with a given node is the decay index or Bremer support index for that node. For nodes with decay indices of more than 2 or 3, the constraint statement approach is much more effective than simply finding all trees 1, 2, 3, etc. steps longer than the shortest tree and then examining their strict consensus for which nodes are lost. Note also that a similar approach can be taken in analyses using other optimality criteria - see Lee & Hugall (2003) for an example involving maximum likelihood
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