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:
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
After loading the PAUP module, PAUP can be run with commands similar to the following:
paup nexus_file > nexus_file.out
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 cd $PBS_O_WORKDIR cp ./nexus_file $TMPDIR cd $TMPDIR module load paup paup nexus_file > nexus_file.out cp nexus_file.out $PBS_O_WORKDIR
- 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