I am also having difficulties with PAUP Version 4.0beta, PC version. What specific syntax should I use to obtain a constraint tree? I have tried the solution mentioned below, but it does not work for me. Also, what is the proper syntax for ordering characters? I entered this, CType Ord:21 [,Ord:22]; after the command reference, but to no avail.
ctype ord 21 22;
...though I haven't checked.