PAUP is a leading program for performing phylogenetic analysis for bioinformatics sequences. PAUP currently runs as a single processor program. No further enhancements are suggested.

Availability and Restrictions


The following versions of PAUP are available on OSC systems:

Version Oakley
4b10 X*
* Current default version

You can use module spider paup to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.


PAUP is available to all OSC users without restriction.

Publisher/Vendor/Repository and License Type

Dave Swofford, Freeware



To configure your environment for using PAUP, run the following command:

module load paup

Using PAUP

After loading the PAUP module, PAUP can be run with commands similar to the following:

paup nexus_file > nexus_file.out

Batch Usage

PAUP is best run via the batch processing system. The following example batch script file will use the input file nexus_file and the output file nexus_file.out

#PBS -l walltime=10:00:00
#PBS -l nodes=1:ppn=1
#PBS -N paup
#PBS -j oe

cp ./nexus_file $TMPDIR

module load paup
paup nexus_file > nexus_file.out
cp nexus_file.out $PBS_O_WORKDIR

Further Reading

  • The PAUP home page
  • PDF forms of the documentation are located at /usr/local/paup/4b10/Docs/ on Oakley
    • Cmd_ref_v2.pdf – command reference manual
    • Quick_start_v1.pdf – quick start guide for the command line version

See Also

  • Mrbayes
Fields of Science: