KaKs_Calculator: Calculating Ka and Ks Through Model Selection and Model Averaging
By Zhang Zhang, Jun Yu Li, Xiao-Qian Zhao, Jun Wang, Gane Ka-Shu Wong, Jun Yu. Genomics, Proteomics & Bioinformatics, 2007
1,085 citations recorded by the source corpus.
KaKs_Calculator is a software package that calculates nonsynonymous (Ka) and synonymous (Ks) substitution rates through model selection and model averaging. Since existing methods for this estimation adopt their specific mutation (substitution) models that consider different evolutionary features, leading to diverse estimates, KaKs_Calculator implements a set of candidate models in a maximum likelihood framework and adopts the Akaike information criterion to measure fitness between models and data, aiming to include as many features as needed for accurately capturing evolutionary information in protein-coding sequences. In addition, several existing methods for calculating Ka and Ks are also incorporated into this software. KaKs_Calculator, including source codes, compiled executables, and documentation, is freely available for academic use at http://evolution.genomics.org.cn/software.htm.
Subfields: Artificial Intelligence, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/c7bee0e5b417f372318e9d05fc5c0cf7f884250a
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Citations in the corpus
- ParaAT: a parallel tool for constructing multiple protein-coding DNA alignments. (2012, methodology): “In addition, ParaAT offers user-customized options to output the resulting alignments into several different formats, so as to facilitate downstream analyses-typically quantitation of selective pressure acting on genes and estimation of synonymous and nonsynonymous substitution rates [20,22].”
- γ-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates (2009, methodology): “A C++ program implementing γ -MYN method is included in the updated KaKs_Calculator [42], available upon request.”
- KaKs_Calculator 3.0: Calculating Selective Pressure on Coding and Non-coding Sequences (2021, methodology): “Compared with previous 71 versions [17, 18], we implement an algorithm in KaKs_Calculator 3.”