The DOI matches its Crossref record; 12 of the 12 references it cites were found in a registry or an index.
KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies
Open accessAbstract
We present an integrated stand-alone software package named KaKs_Calculator 2.0 as an updated version. It incorporates 17 methods for the calculation of nonsynonymous and synonymous substitution rates; among them, we added our modified versions of several widely used methods as the gamma series including γ-NG, γ-LWL, γ-MLWL, γ-LPB, γ-MLPB, γ-YN and γ-MYN, which have been demonstrated to perform better under certain conditions than their original forms and are not implemented in the previous version. The package is readily used for the identification of positively selected sites based on a sliding window across the sequences of interests in 5’ to 3’ direction of protein-coding sequences, and have improved the overall performance on sequence analysis for evolution studies. A toolbox, including C++ and Java source code and executable files on both Windows and Linux platforms together with a user instruction, is downloadable from the website for academic purpose at https://sourceforge.net/projects/kakscalculator2/.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0
Tamura, K., Dudley, J., Nei, M., & Kumar, S. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm092 · Cited by 28,730
DnaSP v5: a software for comprehensive analysis of DNA polymorphism data
Librado, P., & Rozas, J. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp187 · Cited by 16,017
PAML 4: Phylogenetic Analysis by Maximum Likelihood
Yang, Z. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm088 · Cited by 13,879
HyPhy: hypothesis testing using phylogenies
Pond, S. L. K., Frost, S. D. W., & Muse, S. V. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti079 · Cited by 2,866
The Bioperl Toolkit: Perl Modules for the Life Sciences
Stajich, J. E., Block, D., Boulez, K., Brenner, S. E., Chervitz, S. A., Dagdigian, C., Fuellen, G., Gilbert, J. G. R., Korf, I., Lapp, H., et al. (2002) · Genome Research · doi:10.1101/gr.361602 · Cited by 1,654
KaKs_Calculator: Calculating Ka and Ks Through Model Selection and Model Averaging
Zhang, Z., Li, J., Zhao, X.-Q., Wang, J., Wong, G. K.-S., & Yu, J. (2006) · Genomics, Proteomics & Bioinformatics · doi:10.1016/s1672-0229(07)60007-2 · Cited by 1,231
Self-citationTas1r3, encoding a new candidate taste receptor, is allelic to the sweet responsiveness locus Sac
Max, M., Shanker, Y. G., Huang, L., Rong, M., Liu, Z., Campagne, F., Weinstein, H., Damak, S., & Margolskee, R. F. (2001) · Nature Genetics · doi:10.1038/ng0501-58 · Cited by 526
γ-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates
Wang, D., Wan, H., Zhang, S., & Yu, J. M. (2009) · Biology Direct · doi:10.1186/1745-6150-4-20 · Cited by 153
Self-citationCorrelation Between Ka/Ks and Ks is Related to Substitution Model and Evolutionary Lineage
Li, J., Zhang, Z., Vang, S., Yu, J. M., Wong, G. K., & Wang, J. (2009) · Journal of Molecular Evolution · doi:10.1007/s00239-009-9222-9 · Cited by 123
Self-citationHow Do Variable Substitution Rates Influence Ka and Ks Calculations?
Wang, D., Zhang, S., He, F., Zhu, J., Hu, S., & Yu, J. M. (2009) · Genomics Proteomics & Bioinformatics · doi:10.1016/s1672-0229(08)60040-6 · Cited by 82
Self-citation
Cited by
Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome
Bowman, J. L., Kohchi, T., Yamato, K. T., Jenkins, J., Shu, S., Ishizaki, K., Yamaoka, S., Nishihama, R., Nakamura, Y., Berger, F., et al. (2017) · Cell · doi:10.1016/j.cell.2017.09.030 · Cited by 1,205
Chen, Z. J., Sreedasyam, A., Ando, A., Song, Q., De Santiago, L. M., Hulse-Kemp, A. M., Ding, M., Ye, W., Kirkbride, R. C., Jenkins, J., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0614-5 · Cited by 462
Xie, T., Chen, C., Li, C., Liu, J., Liu, C., & He, Y. (2018) · BMC Genomics · doi:10.1186/s12864-018-4880-x · Cited by 398
Genome evolution and diversity of wild and cultivated potatoes
Tang, D., Jia, Y., Zhang, J., Li, H., Cheng, L., Wang, P., Bao, Z., Liu, Z., Feng, S., Zhu, X., et al. (2022) · Nature · doi:10.1038/s41586-022-04822-x · Cited by 367
The opium poppy genome and morphinan production
Guo, L., Winzer, T., Yang, X., Li, Y., Ning, Z., He, Z., Teodor, R., Lu, Y., Bowser, T. A., Graham, I. A., et al. (2018) · Science · doi:10.1126/science.aat4096 · Cited by 341
Metadata
- Authors
- Wang, D., Zhang, Y., Zhang, Z., Zhu, J., & Yu, J.
- Venue
- Genomics, Proteomics & Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-03-01
- Volume
- 8
- Issue
- 1
- Pages
- 77-80
- ISSN
- 1672-0229 (ISSN-L)
- 2210-3244
- OpenAlex
- W1982372752
- Cited by
- 2,084
- References
- 12
- FWCI
- 2.72
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies. https://app.cochat.ai/papers/10.1016/s1672-0229(10)60008-3
- The paper
- Wang, D., Zhang, Y., Zhang, Z., Zhu, J., & Yu, J. (2010). KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies. Genomics, Proteomics & Bioinformatics. https://doi.org/10.1016/s1672-0229(10)60008-3
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
