Using PAUP on the Libra cluster at IU

PAUP estimates phylogenetic trees using either parsimony or maximum likelihood methods. On Libra at Indiana University, PAUP is installed in: /N/soft/aix-5/miscapps/paup

The binary is in:

Documentation (in PDF format) is in: /N/soft/aix-5/miscapps/paup/Docs

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 file taxa.nex, use:

Note: In PAUP, the -n option is not necessary for non-interactive use.

When you run paupjob, you'll receive a message about a temporary file that is built, a message when your job is submitted to the queue, and another when the job finishes. To check the status of your job, use xloadl if you can forward the display of X Windows applications on the Libra cluster to your workstation. Alternatively, you can use llq command, which lists the status of all jobs in all queues.

PAUP produces files with filenames similar to paupjob.output.9999, where 9999 is replaced with the number of your job. PAUP error messages are stored in a file with a filename similar to paupjob.error.9999, where 9999 is replaced with your job number.

For more information about the availability of software on the Indiana University shared central systems, see At IU, what software is available on the research computing systems, and how may I request that software be added?

Also see:

• Bioinformatics support