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  • Description: 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.
  • Availability:



  • Description: 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.
  • Availability:


  • Description: 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.
  • Availability:


  • Description: 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.
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  • Description: RDBS (Randomness Detection in Biological Sequence) is a tool for detecting sequence randomness based on a collection of eight statistical random tests.
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