How to get PAUP (Phylogenetic Analysis Using Parsimony):
The only up-to-date version of PAUP presently available is version 3.0s for
the Mac (dated Dec. 1991). I understand that David Swofford is also
working on an updated version for PC-DOS machines (under Windows?) as well
as on a universal graphical interface which will first be implemented in a
Unix version.
Version 3.0s of PAUP for the Mac can be obtained from:
David L. Swofford
c/o Mary Lou Williamson
Illinois Natural History Survey
607 E. Peabody Drive
Champaign, ILL 61820, USA
Phone: 217-333-6846
Send to Mary Lou Williamson at the address above: (1) a check for $50.00
($60 outside North America) drawn on a U.S. bank and made out to the
University of Illinois/IHNS, or an International Money Order, (2) a note
stating that you understand that the present version of the User's Manual
is a draft that is incomplete in many parts, and that this is acceptable to
you. You will receive the program with manual within 2-3 weeks. A final
version of the manual will be sent to you once it is finished.
PAUP is an excellent program that is quite usable even with the present
incomplete manual. It runs even on classic Macs. For $50, it is a
bargain. If you're in the habit of ripping off software companies by using
illegal copies of their products, DON'T do this with PAUP! David Swofford
provides a tremendous service to molecular phylogenists with this program,
and the amount he charges goes into a Univ. of Ill. account and is used
only to cover costs and pay for some upgrades in hardware and software that
make his life as a program developer easier. You wouldn't want the man to
get disgruntled and stop improving his program, an activity to which he
devotes a good amount of his time (undoubtedly too much, from his
perspective). The PAUP production is a one-man operation, and the reason
why it is somewhat inconvenient to obtain the program is simply because
David's use of a simple "cash sales" account keeps the price of the program
to a minimum. Overseas users are probably best off sending in an
International Money Order.
I have been using public domain (or minimal cost) software for multiple
sequence alignment and phylogeny reconstruction for the past 6 months, and
this is a good occasion for me to express my gratitude to all those who put
out a great deal of effort to make this software available to the rest of
us. My thanks specifically go to Joe Felsenstein (Phylip), David Swofford
(PAUP), Jotun Hein (Treealign), Don Gilbert (Readseq), Steve Clark
(Maligned), Des Higgins (ClustalV), and to the administrators of various
Internet-accessible ftp archives, in particular Don Gilbert
(ftp.bio.indiana.edu) and Dan Davison (ftp.bchs.uh.edu).
Jochen Kleinschmidt
NYU Medical Center
