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. KaKs_Calculator 3.0: Calculating Selective Pressure On Coding And Non Coding Sequences.
    Cite this
    Zhang Z, 2022 Jun - Genomics, Proteomics & Bioinformatics
    Cited by 90 (Google Schoolar as of February 5, 2024)
  2. KaKs_Calculator 2.0: A Toolkit Incorporating Gamma Series Methods And Sliding Window Strategies.
    Wang D, Zhang Y, Zhang Z, Zhu J, Yu J, 2010 Mar - Genomics, Proteomics & Bioinformatics
    Cited by 1267 (Google Schoolar as of February 5, 2024)
  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 997 (Google Schoolar as of February 5, 2024)

Credits

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

    National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation, China

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wan***n@big.ac.cn (January 17, 2018)
zou***d@big.ac.cn (December 8, 2021)
chu***n@big.ac.cn (December 19, 2023)
Summary
AccessionBT000001
Tool TypeApplication
CategoryNatural selection, Comparative analysis
PlatformsLinux/Unix, MAC, Windows
TechnologiesC++
User InterfaceDesktop GUI, Terminal Command Line
Latest Release3.0 (June 24, 2017)
Download Count14417
Country/RegionChina
Submitted ByZhang Zhang