The software tools here were developed in the Zhang lab over many years by grant support from NSF, NIH, The Alzheimer's Association and Monsanto Corporation.

Computational Biology:

• WordSpy: A steganalysis-based, genome scale motif finding method (webserver)

• Rearrangement clustering of gene expression data using the Traveling Saleman Problem (software)

• CAGER: Classification analysis for gene expression regression (webserver)

• Iterated loop matching for RNA folding with pseudonots (software and webserver)

• Selecting degenerate multiple PCR primers (software)

Optimization and Search:

• Cut-and-solve for the ATSP (software)

• MaxSolver: An exact max-SAT solver (software)

• Backbone guided WalkSAT with dynamic noise strategy for SAT and Max-SAT (software)