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RE: MacClade vs. PAUP

> From: owner-dinosaur@usc.edu [mailto:owner-dinosaur@usc.edu]On Behalf Of
> David Peters
> Sent: Friday, March 11, 2005 8:01 AM
> To: dinosaur list
> Subject: MacClade vs. PAUP
> What does it mean when MacClade (through human manipulation) comes up
> with a tree that is two steps shorter than the best one PAUP can
> produce?
> Same data matrix.
> Just scratching my head.

You'll need to check that all the options are set the same. For example, how 
are they counting multistate characters? Are the
polytomies considered hard polytomies or soft ones? Is it counting 
unique/"uniformative" characters or not? And so on.

                Thomas R. Holtz, Jr.
                Vertebrate Paleontologist
Department of Geology           Director, Earth, Life & Time Program
University of Maryland          College Park Scholars
        Mailing Address:
                Building 237, Room 1117
                College Park, MD  20742

Phone:  301-405-4084    Email:  tholtz@geol.umd.edu
Fax (Geol):  301-314-9661       Fax (CPS-ELT): 301-405-0796