Bioinformatics software at IU
UITS provides bioinformatics software on the the Quarry cluster.
On the research computing resources at Indiana University, the Modules environment management system provides a convenient method for dynamically customizing your software environment.
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:
module load package/version
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
For more about the Modules package, see the
module manual page
page. Additionally, see On Big Red II, Karst, Mason, 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.
This is document alei in the Knowledge Base.
Last modified on 2014-10-17.
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