Interactive Clustering Model (ICM): a software for discovering the gene regulation pattern. ICM performed sequence clustering analysis. Joinly developed with Susan M. Bridges and Joyle A. Boyle.

CodonO: a software for calculating synonymous codon usage orderliness (SCUO). codonO performs codon usage bias analysis within and across genomes. Joinly developed with Dong Xu, Andris Kleinhofs, and Jizhong Zhou.

Rnall: a software for predicting local RNA secondary structures. Rnall performs local RNA secondary structure prediction in genome scale in a linear time complexity. Joinly developed with Dong Xu.

BioAnalyzer: a software with user-friendly interface for predicting and visualizing local RNA local secondary structure in genomic sequence. Joinly developed with Peter Dempsey and Dong Xu.