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.



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: