ARCHIVED: Using PAUP* 4.0 on Quarry at IU

This content has been archived, and is no longer maintained by Indiana University. Information here may no longer be accurate, and links may no longer be available or reliable.

Note: After seven years of production service, Indiana University's Quarry research computing cluster was decommissioned January 30, 2015. IU students, faculty, and staff can request accounts on Karst, IU's newest high-throughput computing cluster; for instructions, see ARCHIVED: Requesting an account. User data on Quarry has not be removed; you can access your old home directory data on Quarry from your account on any other IU research computing resource (see Available access to allocated and short-term storage capacity on IU's research systems). All software modules that were available on Quarry are available on Karst. If you have questions or concerns about Quarry's retirement, or need help, contact the High Performance Systems group.

Phylogenetic Analysis Using Parsimony version 4.0 (PAUP* 4.0) is a computational phylogenetic program for inferring evolutionary trees (phylogenies) using parsimony, and maximum likelihood and distance methods. For more, see the PAUP* 4.0 website.

At Indiana University, the portable beta test version (paup4b10-opt-linux-a) is available on the Quarry cluster, but it is a copyright-restricted package. To request use of PAUP* 4.0 on Quarry, IU researchers should email the National Center for Genome Analysis Support (NCGAS).

To configure your environment on Quarry to use PAUP* 4.0, load the paup module:

  module load paup

Documentation (in PDF format) is in:

  /N/soft/rhel6/paup/paup4b10-opt-linux-a/Docs

Sample files are in:

  /N/soft/rhel6/paup/paup4b10-opt-linux-a/Sample_NEXUS_data
  /N/soft/rhel6/paup/paup4b10-opt-linux-a/Sample_analysis_files
  /N/soft/rhel6/paup/paup4b10-opt-linux-a/Sample_import_data

If your run will use 20 minutes of processor time or less, you can run PAUP* 4.0 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 prepare a job script for submitting a batch job via the TORQUE resource manager. For information about using TORQUE on Quarry, see ARCHIVED: Use TORQUE to submit and manage jobs on high performance computing systems

PAUP* 4.0 produces files with filenames similar to paupjob.9999.out, where 9999 is replaced with the number of your job. PAUP* 4.0 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 will be stored in the same directory as the input file.

For more about software available on Indiana University's research supercomputers, see Software available on IU's research supercomputers.