Indiana University
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Using PAUP on Quarry at IU

PAUP estimates phylogenetic trees using either parsimony or maximum likelihood methods. PAUP*4.0-beta is the current version installed on Quarry. It is a copyright-restricted package. If you are at IU and want to use this package, email Bioinformatics Support requesting the use of the PAUP package on Quarry.

On Quarry at Indiana University, PAUP is installed in:

/N/soft/linux-rhel4-x86_64/paup

The binary is in:

/N/soft/linux-rhel4-x86_64/paup/bin/paup4b10-opt-linux-a

Documentation (in PDF format) is in:

/N/soft/linux-rhel4-x86_64/paup/Docs

Sample files are in:

/N/soft/linux-rhel4-x86_64/paup/Sample_NEXUS_data /N/soft/linux-rhel4-x86_64/paup/Sample_analysis_files /N/soft/linux-rhel4-x86_64/paup/Sample_import_data

If your run will use 20 minutes of processor time or less, you can run PAUP interactively or in non-interactive mode without using the queuing system.

If your run will use more than 20 minutes of processor time, you must use the queuing facility. To run PAUP as a batch job, use the paupjob script with the command-line options you would use with PAUP. For example, to run PAUP using the file taxa.nex, in the directory where the file is located, enter:

paupjob taxa.nex

Note: When using the paupjob script to run PAUP, the -n option is not necessary for non-interactive use.

When you run paupjob, you'll receive a $JOBID assigned to your job. To check the status of your job, you can use checkjob $JOBID on Quarry. Alternatively, you can use the showq command, which lists the status of all jobs in all queues.

PAUP produces files with filenames similar to paupjob.9999.out, where 9999 is replaced with the number of your job. PAUP error messages are stored in a file with a filename similar to paupjob.9999.err, where 9999 is replaced with your job number. Both files are in the directory where you submitted your job and where the input file is.

For more information about the availability of software on the Indiana University shared central systems, see Software on IU's research systems