Description

PAUP (Phylogenetic Analysis Using Parsimony) v 4.0 is a major upgrade and new release of the software package for inference of evolutionary trees. With the inclusion of maximum likelihood and distance methods in PAUP* 4.0, the new version represents a great improvement over its predecessors. In addition, the speed of the branch-and-bound algorithm has been enhanced and a number of new features have been added, from agreement subtrees to tests for combinability of data and permutation tests for nonrandomness of data structure.

Paup was developed by David Swofford's group at the Smithsonian/FSU. PAUP website.

PAUP is intended to be used on the Helix platform of the Helix Systems. To run a PAUP job, log on to helix.nih.gov using ssh, and type 'paup'. You will get the Paup prompt, and can then type commands as desired. It is also possible to enter PAUP commands in a batch file. Sample batch files are in the directory /usr/local/paup/Sample_analysis_files

If you expect to run more than 1 or 2 simultaneous PAUP jobs, you should run PAUP on the Biowulf cluster.

Version

Type paup on command line

Sample session

% paup MP_analysis.nex
P A U P *
Portable version 4.0b10 for Unix
Mon May 15 12:38:24 2006

      -----------------------------NOTICE-----------------------------
        This is a beta-test version.  Please report any crashes,
        apparent calculation errors, or other anomalous results.
        There are no restrictions on publication of results obtained
        with this version, but you should check the WWW site
        frequently for bug announcements and/or updated versions.  
        See the README file on the distribution media for details.
      ----------------------------------------------------------------

Processing of file "~/paup/MP_analysis.nex" begins...

Data read in DNA format

Data matrix has 8 taxa, 1200 characters
Valid character-state symbols: ACGT
Missing data identified by '?'
"Equate" macros in effect:
   R,r ==> {AG}
   Y,y ==> {CT}
   M,m ==> {AC}
   K,k ==> {GT}
   S,s ==> {CG}
   W,w ==> {AT}
[...]
Tree number 1 (rooted using default outgroup)

/---------------------------------------------------------------------------------- A
|
|---------------------------------------------------------------------------------- B
|
|          /----------------------------------------------------------------------- C
|          |
|          |                     /------------------------------------------------- D
\----------+                     |
           |                     |                                /---------------- E
           \---------------------+               /----------------+
                                 |               |                \---------------- F
                                 \---------------+
                                                 |                /---------------- G
                                                 \----------------+
                                                                  \---------------- H

Processing of file "~/paup/MP_analysis.nex" completed.

paup> quit 

Documentation

PAUP Quick Start (PDF)
PAUP Command Reference (PDF)