- ParaAT (Parallel Alignment & back-Translation): a parallel tool for constructing multiple protein-coding DNA alignments.
- Reference: Zhang, Z. et al. (2012) ParaAT: A parallel tool for constructing multiple protein-coding DNA alignments, Biochem Biophys Res Commun, 419, 779-781.
- CAT (Composition Analysis Toolkit): a toolkit for estimating codon usage bias and its statistical significance.
- Reference: Zhang, Z. et al. (2012) Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance, under review.
- LOX (Level Of eXpression): a program that employs Markov Chain Monte Carlo to estimate level of expression from census sequencing data sets with multiple treatments or samples.
- Reference: Zhang, Z., Lopez-Giraldez, F. and Townsend, J.P. (2010) LOX: inferring Level Of eXpression from diverse methods of census sequencing, Bioinformatics, 26(15):1918-1919.
MACML (Model Averaging Clustering by Maximum Likelihood): a program that clusters sequences into heterogeneous regions with specific site types, without requiring any prior knowledge.
Reference: Zhang, Z. and Townsend, J.P. (2009) Maximum-likelihood model averaging to profile clustering of site types across discrete linear sequences, PLoS Computational Biology, 5(6):e1000421.
KaKs_Calculator: a program that adopts model selection and model averaging to calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates.
Reference: Zhang, Z. et al. (2006) KaKs_Calculator: calculating Ka and Ks through model selection and model averaging, Genomics Proteomics Bioinformatics, 4(4): 259-263.