Oklahoma State University
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Categorized software tools: (this page is being updated and links will be restored ASAP. Click on one of the menu links for more information)







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
  • TIGR Madam:  Microarray Data Manager  (http://www.tm4.org/madam.html)
  • BioConductor: R-based software package for microarrays, sequence data, HTP-assays, and Annotation. Over 400 packages. Open source with many contributors
  • BRB ArrayTools (Richard Simon's). Works embedded into Microsoft Excel
  • TMEV/MEV4: Microarray Experiment Viewer: Software originally from the Quackenbush Lab, used for microarrays, and RNAseq. A great statistical package.


For image analysis and spot quantification:

  • GenePix Pro: Version 7 now available on 64-bit system. 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

For Functional annotation including Gene Ontology and Pathway Analysis;

  • Trinity: Annotation of RNA-seq
  • 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
  • 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: The world-wide format consensus for analyzing microarray datafiles.
  • BRB Array Tools: Microarray data management and analysis. Installs into MS Excel

For Oligos and PCRs :

  • Primer Express: A resource for anyone using the Applied Biosystems TaqMan RT-PCR system
  • PDRAW32: A nice free software package that does an excellent job of helping you design primers for your sequences. A good package for producing publication and presentation-quality images of your plasmids and gene sequence elements. Available from www.acaclone.com

For clustering:

  • Genesis: For generating hierarchical clustering, self-organizing maps (SOMs) and k-means clustering from files containing normalized and filtered expression values
  • TMeV, mentioned above, hierarchical clustering, self-organizing maps (SOMs) and k-means clustering
  • 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


For genome alignments and structure:

  • IGV the Integrative Genomics Viewer from the Broad Institute.
  • ClustalW: Classic alignment software.
  • BioEdit: An older but very fast 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-Fold: One of the most well-accepted RNA-folding software.
  • 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 "batch" command line multi-threaded software that is frequently updated.
  • MAUVE: Very powerful alignment tool capable of aligning entire genomes or large datasets.
  • MEGAN: Comparisons of large metagenomic datasets. Contig-to-contigs and generates taxonomic statistics. Also capable of comparative genomics, and automated GO-annotation.
  • 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.



  • Cn3D v4.1: A structure and sequence alignment viewer for NCBI databases
  • Glimmer:  A microbial gene-finding system http://cbcb.umd.edu/software/glimmer/
  • R:  A statistical computing and graphics package http://www.r-project.org/
  • 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


*Original coding by Ms. Hua Weng, and Dr. Patricia Canaan