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PAUP

Introduction

PAUP is a leading program for performing phylogenetic analysis for bioinformatics sequences.

Version

Version 4 Beta 10 is currently available at OSC.

Availability

PAUP is available on the Glenn Cluster.

Usage

PAUP may be used by all licensed users of OSC

Execution:

PAUP is accessed after loading the module for paup.

module load paup
paup nexus_file > nexus_file.out

Batch file example:

The following batch job will execute PAUP program for the file nexus_file and create a file called nexus_file.out containing the output results.

#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 * $PBS_O_WORKDIR

Optimal Performance:

PAUP currently runs as a single processor program. No further enhancements are suggested.

Bugs:

No known bugs

Documentation

PDF forms of the documentation are located at /usr/local/paup/paup4b10-opt-linux-a/Docs/.
Cmd_ref_v2.pdf – command reference manual
Quick_start_v1.pdf – quick start guide for the command line version