Phylogenetic trees - PHYLIP & PAUP

kleinschmidt at mcclb0.med.nyu.edu kleinschmidt at mcclb0.med.nyu.edu
Wed Jun 17 23:07:27 EST 1992

Harald Steen from the University of Oslo asked about programs that build 
phylogenetic trees from DNA sequence data.

Two good packages I know of that can construct phylogenetic trees from 
nucleotide sequence data, are PHYLIP and PAUP.  There are other programs that 
can do it from protein data, e.g. ClustalV, TreeAlign, the dendrogram one gets 
from the PileUp program in the GCG package etc, etc.  PHYLIP v.3.4 (Phylogeny 
Inference Package) is a set of some 20-30 programs written over the years by 
Joe Felsenstein of the Univ. of Washington.  You can get it by anonymous ftp 
from ftp.bio.indiana.edu (directory molbio/evolve; IP address 
as well as from evolution.genetics.washington.edu.  These programs were 
written in Pascal and come compiled in versions for VAX/VMS, Unix, MS-DOS etc.  
I have installed the package on three systems, VAX-4000, SGI Iris, and a 25 
MHz 386 MS-DOS machine.  The main program I've been using from this package 
(protpars = protein parsimony analysis) runs slow on the VAX and on the Iris 
and ultraslow on the PC; in fact, I would say that the PC version cannot be 
used for anything more than half a dozen sequences of 300 AA's each.  So these 
programs are rather slow, but they do a great deal of analysis and are well 
documented.  There is probably nothing else available that is as full-featured 
and well-rounded as this package is.  Felsenstein has also written a very good 
review article on this whole field (Annu.Rev.Genetics 22:521-565 (1988).

I had also heard very good things about PAUP (Phylogenetic Analysis Using 
Parsimony), written by David Swofford of the Illinois Natural History Survey.  
So I ordered it (U.S.$ 50) and just received it last week (after a two week 
wait).  The most up-to-date and more or less finished version available right 
now is for the Macintosh, even though the manual is still an incomplete draft.  
Swofford is also working on a version for the IBM-PC but that one isn't 
finished yet.  There also seem to be command-line driven versions available 
for Unix systems and mainframes but those may be obsolete and unsupported by 
now.  The point is, right now you can only get the Mac version.

My impression, from going through the 180 page (incomplete) manual and seeing 
the program run on a colleague's Mac, is that PAUP is an excellent program, 
well worth the few bucks you spend on it.  The manual alone is a mini course 
in molecular phylogeny and on the different methods used for inferring 
phylogenetic relationships many of which are supported by the program.  It 
seems that PAUP offers more algorithms for doing this kind of analysis than 
PHYLIP, and it is much faster and easier to use.  I don't think it runs on any 
garden variety Mac; you have to have one of the more souped-up Macs (obviously 
I'm not a Mac user).  The program is distributed on a single 3.5 in. floppy 

To get PAUP, you have to send a check drawn on a U.S. bank or an International 
Money Order for U.S.$ 50 (or for U.S.$ 60 for orders from abroad) made out to 
"University of Illinois/INHS" to Mary Lou Williamson, Illinois Natural History 
Survey, 607 East Peabody Drive, Champaign, Illinois 61820.  The phone number 
is 217-333-6846.  If you need more information, call that number and they will 
fax you an order form and a form letter explaining the current status of the 
program.  Since you're in Norway, you can save yourself an overseas call; 
e-mail me a message giving a fax number, and I will fax you a copy of the form 
letter.  When you order, they ask you to include a statement that you agree to 
receiving an incomplete draft version of the manual, with the understanding 
that the final manual will be shipped whenever it is completed.

If you have any questions, send me a message.  I will be away from 6-21 to 
6-26 though.

Jochen Kleinschmidt
NYU Medical Center
New York, NY 10016

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