KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies
By Dapeng Wang, Yubin Zhang, Zhang Zhang, Jiang Zhu, Jun Yu. Genomics, Proteomics & Bioinformatics, 2010
1,659 citations recorded by the source corpus.
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/.
Subfields: Analytical Chemistry, Biomedical Engineering, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/727448871e676908060345d8529f06b8c3d28045
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Citations in the corpus
- Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome. (2017, neutral): “0 (Wang et al., 2010) https://sourceforge.net/projects/ kakscalculator2/ BLASTZ (Schwartz et al., 2003) genomewiki.ucsc.edu/index.php/Blastz DAGchainer (Haas et al., 2004) http://dagchainer.sourceforge.net/ SynMap at CoGe website (Lyons et al., 2008)…”
- 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.”