ARCHIVED: Bioinformatics support
UITS supports researchers who do biological computing, particularly in the areas of genomics, cell biology, and molecular biology. Support is provided in the forms of application support, technical support, and software development. Application support includes testing and licensing of software that is broadly useful across academic departments that analyze molecular data, including biology, medicine, and anthropology. Technical support includes consulting with regard to data management and choice of algorithms and statistical methods of data analysis. Software development includes investment of time assisting researchers developing software that poses challenges for which they lack resources to complete in a timely fashion.
Software on UITS computer systems
UITS provides bioinformatics software on the the Quarry cluster and on Big Red. Quarry is 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). Big Red is configured for massively parallel computing. To request software for general use on research systems, submit a software request form.
The following bioinformatics software is available:
BLAST can be used to query hundreds to tens of
thousands of molecular sequences against sequence databases. For
details, see BLAST sequence searching on Big Red.
CAP3 is a sequence assembly program. For details,
see Using CAP3 on Big Red at IU.
ClustalW aligns multiple sequences. A parallel
version is available on Big Red; see Running ClustalW on Big Red.
EMBOSS/wEMBOSS is a set of sequence analysis
applications that use GCG libraries to extend the functionality of the
GCG Package. wEMBOSS is the web interface of the EMBOSS. EMBOSS
command line applications run on the Quarry cluster. The wEMBOSS
interface is available on the Discern server
discern.uits.iu.edu). For details, see ARCHIVED: On Quarry, what are EMBOSS and wEMBOSS, and how can I use them?
FASTA searches databases for sequences that are
similar to a set of query sequences. The parallel version of FASTA is
available on Big Red. For more, see FASTA programs on Big Red.
fastDNAml generates phylogenetic trees from
molecular data using maximum likelihood methods. The program
implements Felsenstein's likelihood methods and Olson's search
algorithm. This implementation was parallelized by the UITS Scientific
Applications and Performance Tuning team. For more, see ARCHIVED: Maximum likelihood analysis of phylogenetic data.
GARLI conducts phylogenetic searches on aligned
sequences using maximum likelihood criteria. It supports codon- and
amino-acid-based models in addition to standard nucleotide models. See
ARCHIVED: What is GARLI, and how can I use it on Quarry?
IMPUTE 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?
MEME detects patterns in nucleotide and protein
sequences and efficiently uses multiple processors. See Using MEME on Big Red 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. See What is Migrate, and how do I use it on Quarry?
MPI-HMMER creates and queries sets of hidden
Markov models that describe molecular sequences. This port of HMMER
includes parallel versions of hmmpfam and hmmsearch and is available
on Big Red. See Using MPI-HMMER on Big Red at IU.
MrBayes estimates evolutionary trees using
Bayesian methods. It has been compiled to use multiple processors. For
more, see On Big Red, how do I submit batch jobs that run MrBayes?
MULTICLUSTAL optimizes multiple sequence
alignments by searching for the best alignment parameters. See Running MULTICLUSTAL on Big Red at IU.
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.
Phrap/Cross_match/Swat is a set of programs for
DNA analysis. It is available on Big Red. Phrap assembles shotgun DNA
sequence data. Cross_match compares any two DNA sequence sets. Swat
searches DNA/protein sequences, or a query profile, against a sequence
database. For more, see Using Phrap/Cross_match/Swat on Big Red.
PLINK is a tool set for genome association study.
See What is PLINK, and how do I use it on Quarry at IU?
RepeatMasker is a program for finding and
removing repeated low-complexity regions in DNA sequences. It's
available on Big Red. For more, see Using RepeatMasker on Big Red.
structure is a program that can cluster
individuals based on their genotypes and can assign individuals to
clusters (populations) based on their genotypes. It is installed on
Quarry. For more, see ARCHIVED: What is structure, and how do I use it on Quarry?
- TREE-PUZZLE estimates phylogenetic trees from sequence data using maximum likelihood methods. A parallel version is available on Big Red. For details, see Using TREE-PUZZLE on Big Red at IU.
Consulting is available to help researchers find solutions to bioinformatics computing problems. For assistance, email RT Science Community Tools.
Last modified on March 22, 2013.