*Paup

[Dan Jacobs]

L. Chan requested distribution information on PAUP, a package for doing
phylogeny.  Well - here it is:

     1.  David Swofford (Illinois Natural  History  Survey,  Natural  Resources
Building,   607   East  Peabody  Drive,  Champaign,  Illinois   61820,  U.S.A.)
distributes PAUP (Phylogenetic Analysis Using Parsimony).
 
     Since  December,  1985,  Swofford  has  been  distributing  a  precompiled
executable object-code versions of PAUP for the IBM PC and other MSDOS systems.
As of this writing (May, 1991) he has released version  3  (PAUP/Mac)  for  the
Macintosh,  and  later  hopes  to  release  version  3  for  PCDOS  systems and
ultimately for mainframes.  Its cost is  $50.   Orders  received  for  the  Mac
version  will  be filled but the final printed documentation will arrive later,
as it is not completed yet.

     PAUP 3.0 is probably the most sophisticated parsimony program.  It  allows
multistate  characters,  user-defined  weights on individual state transitions,
Wagner,  Camin-Sokal  and  Dollo  parsimony   methods,   bootstrap   confidence
intervals,  and  finding  all  most parsimonious trees by branch-and-bound.  It
also has provision for computing Lake's linear phylogenetic invariants.


This was clipped out of Joe Felsenstein's documentation for PHYLIP - 
another package for doing all sorts of phylogeny.  You may want to
consider getting PHYLIP, it is well supported, extremely well documented,
and FREE.  You can get it by anonymous ftp at evolution.genetics.washington.edu
in the /pub directory. (Kudos to Joe)

Best of Luck,

Dan Jacobson
danj at welchgate.welch.jhu.edu