Bioinformatics software at IU
UITS provides bioinformatics software on the the Quarry cluster.
Research computing resources at Indiana University (Big Red II, Quarry, Mason, and Rockhopper) use the Modules environment management package, which allows you to dynamically customize your software environment on each system.
To determine which bioinformatics packages (and which versions) are
available on Quarry, from the command line, enter
avail and examine the list under
To add a
package (and, optionally, a specified
version) to your user environment on Quarry, from the
command line enter:
To make permanent changes to your environment, edit your
~/.modules file. For more, see In Modules, how do I save my environment with a .modules file?
For more about the Modules package, see the
module manual page
page. Additionally, see On Big Red II, Mason, Quarry, and Rockhopper at IU, how do I use Modules to manage my software environment?
To request software for general use on Quarry, submit the Software Request Form.
Note: Quarry is designed for long-running single-processor programs, programs that require large amounts of memory, and parallel programs that require memory that is shared by many processors (SMP). For more, see Quarry at Indiana University.
Following is support information for some of bioinformatics packages available on Quarry:
IMPUTE2 is a program for predicting unobserved
genotypes based upon observed/known haplotypes in genome-wide
case-control studies. See What is IMPUTE2, and how do I use it on Quarry at IU?
MACH is a Markov-chain-based haplotyper. See What is MACH, and how do I use it on Quarry at IU?
MIGRATE uses genotypes of individuals to form
clusters that represent populations, assign individuals to
populations, and describe genotypes of individuals in terms of
populations from which they were derived. It applies maximum
likelihood and Bayesian analysis, and is available on Quarry in serial
and parallel versions. See What is Migrate, and how do I use it on Quarry?
PAUP estimates evolutionary trees and is
available on the Quarry cluster. For details, see Using PAUP* 4.0 on Quarry at IU.
PHYLIP is a well known package for phylogenetic
inferences. It is available on the Quarry cluster. For help, see the program
documentation and Using PHYLIP on Quarry at IU.
- PLINK is a tool set for genome association study. See What is PLINK, and how do I use it on Quarry at IU?
If you need help or have questions about software on Quarry, email the UITS Scientific Applications and Performance Tuning (SciAPT) team.
Last modified on November 04, 2013.