All software listed below may be downloaded and used free of charge by academic and other non-profit researchers.

SELEX Data Processing

• SELEXSeqParser [Download] (platform independent): A command line Java tool for extracting SELEX 'oligos' from concatenated SELEX experiment sequences given an identifying, intervening motif (i.e. a restriction site).

• DuplicateCloneFilter [Download] (platform independent): A command line Java tool for filtering duplicate clone sequences from sequence files.

• MemeR [Download] (platform independent): A command line Java wrapper for Meme.

ChIP Chip Data Processing

• TiMAT [Download] (platform independent): Tiling Microarray Analysis Tools - twenty sum odd command line Java applications for the analysis of Affymetrix tiled genomic microarrays and a variety of processed files for D. Melanogaster.

The above programs were developed by David Nix in the Eisen Lab.