Oklahoma State University
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Categorized software tools: (this page is being updated and links will be restored ASAP (but hardware is priority)







For array design, fabrication and maintaining a database of clones and arrays

  • OmniGrid Gridder: Microarray design and fabrication software for the OmniGrid 100. This software also assists in coordination of spots-to-probes
  • CloneTracker CE: CloneTracker CE data management software is available to assist researchers in the design and fabrication of high-density microarrays by assisting in automated generation of AxSys-specific printing scripts and maintaining the coordination of spots-to-libraries
  • TIGR Madam:  Microarray Data Manager  (http://www.tm4.org/madam.html)
  • BioConductor: R-based software package for microarrays, sequence data, HTP-assays, and Annotation. Has over 400 packages!!! Open source with many contributors
  • BRB ArrayTools (Richard Simon's). Works on your computer embedded into Microsoft Excel
  • TMEV: Microarray Experiment Viewer: Awesome software from the Quackenbush Lab we use everyday!
  • AMANDA: Clustering and gene expression analysis embedded into MS Excel
  • AMIADA: Excel look-alike for microarray data


For image analysis and spot quantification:

  • GenePix Pro: Version 7 now available on 64-bit system! This software package is designed for array image analysis and quantification and provides highly desired processing features such as auto-adjustment of spots within grids, alignment of non-overlaid images, import of clone layout within the array in addition to extraction and quantification of gene expression data and can import third-party images generated from microarrays or macroarrays
  • ScanArray: The ScanArray software is used to control the ScanArray Express (PerkinElmer) confocal laser scanning device. This software generates tiff images for further analysis and quantification
  • ScanAlyze: Processes TIFF images of microarrays with pixel and spot analyses and outputs as tab-delimited text files for transfer to any database.

For Functional annotation including Gene Ontology and Pathway Analysis;

  • Genesis: Clustering, statistics, and the most up-to-date and complete Gene Ontology available. Originally by Alexander Sturn from the Quackenbush Lab, now wonderfully maintained by Rene Snajder. One of our favorites because of the graphics and ability to import genomes for mapping data
  • Pathway Tools: Huge package with powerful inter-relational databases. The graphic outputs are getting better, and it has become a very frequently used software, that interfaces with the suite of ICR Workspace software that we are looking closely at for future usage with experiments having clinical implications
  • WebGestault
  • WebBlast and Local Blast (We can create our own databases for more rapid blasting of whole genomes)
  • Cytoscape: Network software for representing protein interactions, gene expression/ontology, or all together in three-dimensional space. Now incorporates BingGO and PingGO as well as other annotation plugins that can be displayed as networks.
  • BLAST2GO: Blast outputs can be automatically directed toward Gene Ontology databases for functional annotation. Java based, memory and graphics memory intensive.
  • GenomeWorkbench: NCBI-based powerful software JAVA-based for arranging data results and linking to annotation data. Memory intensive.



For Ratio Analysis:

  • GenePix Auto-Processor (GPAP): This is our OSU-written package for pre-processing and statistical analysis of raw microarray data. Useful for producing normalized and filtered expression values and diagnosis of hybridization quality. Limited to 6 .GPR files
  • GenePix Pro: Versions 4, 6,and now the 64-bit version 7 are available. Virtually the world-wide format consensus for analyzing microarray datafiles.
  • GeneSpring: For expression data analysis and exploration
  • BRB Array Tools: Microarray data management and analysis. Installs into MS Excel
  • BioConductor: Microarray Data Management and analysis
  • TMEV4: Excellent microarray data analysis software from John Quackenbush. If you have large microarray data sets (lots of arrays) this is for you.

For Oligos and PCRs :

  • Primer Express: A resource for anyone using the Applied Biosystems TaqMan RT-PCR system
  • FastPCR:  A software for the design of PCR primers for standard and long PCRs, inverse PCR, direct amino acid sequence degenerate PCR, multiplex PCR and in-silico PCR; for sequence alignments, clustering and any kind repeat sequence searching(http://www.biocenter.helsinki.fi/bi/Programs/fastpcr.htm
  • PDRAW32: A nice free software package that does an excellent job of helping you design primers for your sequences. It is lots more than that, and is a terrific package for producing publication and presentation-quality images of your plasmids and gene sequence elements. Check it out at (www.acaclone.com)
  • Primer 3.0:  A program to pick primers from a DNA sequence http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi
  • EC_Oligo: Designs primers and also designs oligo probes for entire genomes

For clustering:

  • Genesis: For generating hierarchical clustering, self-organizing maps (SOMs) and k-means clustering from files containing normalized and filtered expression values
  • PHYLIP: For Phylogenetic Tree generation using a variety of algorithms, and has a impressive set of publication-quality output options
  • TMeV, mentioned above, is great at hierarchical clustering, self-organizing maps (SOMs) and k-means clustering from files containing normalized and filtered expression values
  • Cluster and TreeView: For generating hierarchical clustering, self-organizing maps (SOMs) and k-means clustering
  • GeneSight-Lite: Included with ImaGene (above), this is a basic expression data analysis module for producing ratios and plotting of up to three separate experiments
  • Clench v2: A program for cluster enrichment analysis and integrated visualization of expression, annotation and transcription factor binding site
  • J-Express: J-Express is a Java application that allows the user to analyze gene expression (microarray) data in a flexible way giving access to multidimensional scaling, clustering, and visualization methods in an integrated manner. Specifically,  J-Express contains implementations of hierarchical clustering, k-means partitional clustering, principal component analysis, self-organizing maps and profile similarity search
  • GeneSpring: For expression data analysis and exploration


For genome alignments and structure:

  • IGV the Integrative Genomics Viewer from the Broad Institute. Very clear and simple way to display your genomes (big and little)
  • ClustalW: State-of-the-art alignment software. Can be run stand-alone, or from within a few "shells" like BioEdit
  • BioEdit: An amazing program "shell" that can run dozens of command-line based software packages, including ClustalW, Treeview, and PHYLIP. Does its own alignments, automated searches and annotations. Great for manipulating protein or DNA files and does file conversions.
  • RNA structure 4.5: Very impressive RNA-folding program for Windows
  • RNA-Fold: One of the most well-accepted RNA-folding software. Available by contacting our services only.
  • Construct: A tool for prediction of conserved secondary structure of a set of homologous single-stranded RNA. http://www.biophys.uni-duesseldorf.de/local/ConStruct/ConStruct.html
  • CAP3 handles nex-gen sequence data and generates alignments, trees, and assemblies
  • Mothur: Excellent software for phylogenetic and biodiversity studies based on next-generation software reads. VERY powerful command line multi-threaded software that is frequently updated.
  • MAUVE: Very powerful alignment tool capable of aligning entire genomes or huge datasets... even miRNAs. Memory intensive!
  • VectorStrip: Combined with a Web-Blast can remove vector sequences from your sequences. Not high-throughput and not as good as our in-house scripts
  • MEGAN: Comparisons of large metagenomic datasets. Contig-to-contigs and generates taxonomic statistics. Also capable of comparative genomics, and automated GO-annotation. Memory intensive. Powerful.
  • BowTie: For mapping and grouping SNPs, can be used for phylogenetic determinations based on mismatches
  • MIRA. Genome Assembler for Solexa and 454 (and more).
  • Roche Genome Assembler which is Newbler-based. Very automated if you can get your data into an SFF file. Otherwise a FASTA file can be used. Request a copy.



  • Cn3D v4.1: A structure and sequence alignment viewer for NCBI databases (http://pubmedexpress.nih.gov/Structure/CN3D/cn3d.shtml )
  • RBS finder:  A perl script the implements an algorithm to find ribosome binding sites for genes in bacterial and archaeal genomes. Run as a post-processor to the Glimmer gene finder or to other prokaryotic gene finders http://www.tigr.org/software/genefinding.shtml
  • Glimmer:  A microbial gene-finding system http://cbcb.umd.edu/software/glimmer/
  • Vega:  A molecular modeling software  http://users.unimi.it/~ddl/vega/index2.htm
  • CNS solve:  A Crystallography and NMR system http://rcc.psc.sc.edu/cns.html
  • Xplor:  A system for X-ray Crystallography and NMR  http://www.ocms.ox.ac.uk/mirrored/xplor/manual/htmlman/htmlman.html
  • R:  A statistical computing and graphics package http://www.r-project.org/
  • FungOntology: A tool providing Gene Ontology for Filamentous Fungi with tools for automatic annotation of novel sequences
  • Fasta2tab: A simple tool to convert a collection of FASTA formatted sequences to tab delimited format
  • MiamExpress: A web based tool for gene expression data submissions to ArrayExpress
  • Local MS-FIT: Custom databases from UniGenes and ESTs to provide improved peptide-mass fingerprinting
  • Phred/Phrap/Consed:  DNA sequence base-caller/assembler/contig editor