The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
KaKs_Calculator: Calculating Ka and Ks Through Model Selection and Model Averaging
Open accessAbstract
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.
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Cites
A new look at the statistical model identification
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Cited by
Shen, Z., Xiao, Y., Kang, L., Ma, W., Shi, L., Zhang, L., Zhou, Z., Yang, J., Zhong, J., Yang, D., et al. (2020) · Clinical Infectious Diseases · doi:10.1093/cid/ciaa203 · Cited by 513
“0 (MS model)[37], an asterisk is added if Ka/Ks is significantly different from 1 (p < 0.”
BackgroundSelf-citationDowning, T., Imamura, H., Decuypere, S., Clark, T. G., Coombs, G. H., Cotton, J. A., Hilley, J. D., de Doncker, S., Maes, I., Mottram, J. C., et al. (2011) · Genome Research · doi:10.1101/gr.123430.111 · Cited by 423
Cheng, F., Sun, R., Hou, X., Zheng, H., Zhang, F., Zhang, Y., Liu, B., Liang, J., Zhuang, M., Liu, Y., et al. (2016) · Nature Genetics · doi:10.1038/ng.3634 · Cited by 382
Deciphering the Diploid Ancestral Genome of the Mesohexaploid Brassica rapa
Cheng, F., Mandáková, T., Wu, J., Xie, Q., Lysak, M. A., & Wang, X. (2013) · The Plant Cell · doi:10.1105/tpc.113.110486 · Cited by 353
Kim, S., Park, J., Yeom, S.-I., Kim, Y.-M., Seo, E., Kim, K.-T., Kim, M.-S., Lee, J. M., Cheong, K., Shin, H.-S., et al. (2017) · Genome Biology · doi:10.1186/s13059-017-1341-9 · Cited by 312
Metadata
- Authors
- Zhang, Z., Li, J., Zhao, X.-Q., Wang, J., Wong, G. K.-S., & Yu, J.
- Venue
- Genomics, Proteomics & Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2006-12-01
- Volume
- 4
- Issue
- 4
- Pages
- 259-263
- ISSN
- 1672-0229 (ISSN-L)
- 2210-3244
- OpenAlex
- W2003062832
- Cited by
- 1,231
- References
- 7
- FWCI
- 2.09
- Type
- journal article
- Language
- en
- Open access
- gold
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- Zhang, Z., Li, J., Zhao, X.-Q., Wang, J., Wong, G. K.-S., & Yu, J. (2006). KaKs_Calculator: Calculating Ka and Ks Through Model Selection and Model Averaging. Genomics, Proteomics & Bioinformatics. https://doi.org/10.1016/s1672-0229(07)60007-2
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