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Paup on Biowulf

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 can be used interactively on Helix. For multiple simultaneous Paup runs, Paup can also be used on the Biowulf cluster.

Submitting a swarm of PAUP jobs

Create a swarm command file with a single line for each run. Sample file:

----- this file is paup.swarm------------
cd /data/user/myrun1; paup analysis1.nex
cd /data/user/myrun2; paup analysis2.nex
cd /data/user/myrun3; paup analysis3.nex
[...]
If each Paup process requires less than 1 GB of memory, submit this to the batch system with the command:
swarm -f cmdfile --module paup

If each Paup process requires more than 1 GB of memory, use

swarm -g # -f cmdfile --module paup
where '#' is the number of Gigabytes of memory required by each Paup process.

See the swarm documentation for details.

Documentation

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