Categorized software tools:

Array Design |   Image Analysis |   Ratios |   Clustering |   Oligo-Design |   Miscellaneous | Function | Sequence Tools

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

• BASE:A web-based microarray database system
• Longhorn Array Database (LAD) : A Stanford Microarray Database powered microarray data warehouse
• 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: Currently being setup.
• BRB ArrayTools (Richard Simon's). Works on your computer using Microsoft Excel
• MEV: Microarray Experiment Viewer: Currently being setup
  

For image analysis and spot quantification:

• GenePix Pro: NEW! 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-overlayed 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
• ImaGene 4.2: For the extraction and quantification of gene expression data generated by most third-party array scanners. Feartures include the ablity to simultaneously load and analyse up to five images, automated spot finding, segmentation and analysis tools. Additionally, GeneSight-Lite comes bundled with ImaGene
• 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
  
• Acuity-Lite (Comes with GenePix-Pro)
• Pathway Tools: Huge package with powerful inter-relational databses. Unfortunately still has relatively poor graphic outputs
• GeneOntology Tree Machine (GOTM) from Vanderbilt University
• WebBlast and Local Blast (We maintain our own databases for more rapid blasting of whole genomes)