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.
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 [...]
swarm -f cmdfile --module paup
If each Paup process requires more than 1 GB of memory, use
swarm -g # -f cmdfile --module paupwhere '#' is the number of Gigabytes of memory required by each Paup process.
See the swarm documentation for details.