KaKs_Calculator calculating selective pressure on coding and non-coding sequences

Introduction

KaKs_Calculator is capable for calculating selective pressure on both coding and non-coding sequences. For coding sequences, it integrates several methods to calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates; particularly, it adopts model selection and model averaging to include as many features as needed for accurately capturing evolutionary information in protein-coding sequences. Similar to the Ka/Ks ratio for coding sequences, selection on non-coding sequences can be quantified as non-coding nucleotide substitution rate (Kn) normalized by synonymous substitution rate of adjacent coding sequences.

Publications

  1. Ka Ks Calculator 3.0: Calculating Selective Pressure On Coding And Non Coding Sequences.
    Cite this
    Zhang Z, 2022 Jan 3 - Genomics, Proteomics & Bioinformatics
    Cited by 3 (Google Schoolar as of August 5, 2022)
  2. KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies
    Dapeng Wang, Yubin Zhang, Zhang Zhang, Jiang Zhu, Jun Yu, 2010/5/6 - Genomics, Proteomics & Bioinformatics
    Cited by 753 (Google Schoolar as of August 5, 2022)
  3. KaKs_Calculator: Calculating Ka and Ks Through Model Selection And Model Averaging
    Zhang Z, Li J, Zhao XQ, Wang J, Wong GK, Yu J, 2006 Nov - Genomics, Proteomics & Bioinformatics
    Cited by 821 (Google Schoolar as of August 5, 2022)

Credits

  1. Zhang Zhang zhangzhang@big.ac.cn
    InvestigatorDeveloper

    National Genomics Data Center, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, China

Community Ratings

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zha***g@big.ac.cn (June 28, 2017)
dot***g@gmail.com (June 29, 2017)
wan***n@big.ac.cn (January 17, 2018)
zou***d@big.ac.cn (December 8, 2021)
Summary
AccessionBT000001
Tool TypeApplication
CategoryNatural selection, Comparative analysis
PlatformsLinux/Unix, MAC OS X, Windows
TechnologiesC++
User InterfaceDesktop GUI, Terminal Command Line
Latest Release3.0 (June 24, 2017)
Download Count5662
Country/RegionChina
Submitted ByZhang Zhang