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.
PAUP is available to all OSC users without restriction.
The following versions of PAUP are available on OSC systems:
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 * $PBS_O_WORKDIR