Successive Weighting and Polymorphic Terminals—A Warning to PAUP Users
Knut Rognes · Cladistics · 1999
The naïve user of PAUP 3.1.1 (and earlier versions) is warned about a shortcoming in the program's successive weighting facility. With matrices containing multistate terminals, PAUP, under the “polymorphism” interpretation, will assign higher weight to characters with more within‐terminal steps, other things being equal, i.e. to characters with the largest amount of homoplasy. The shortcoming has been corrected in PAUP* version 4.0.