KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies
Chinese Academy of Sciences · Beijing Institute of Genomics · +3 more institutions
Abstract
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 gamma-NG, gamma-LWL, gamma-MLWL, gamma-LPB, gamma-MLPB, gamma-YN and gamma-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…
Citation impact
- FWCI
- 3.13
- Percentile
- 100%
- References
- 14
Authors
5- DWDapeng Wang
Chinese Academy of Sciences, Beijing Institute of Genomics, University of Chinese Academy of Sciences
- YZYubin Zhang
Chinese Academy of Sciences, Beijing Institute of Genomics, Institute of Computing Technology, University of Chinese Academy of Sciences
- ZZZhang Zhang
King Abdullah University of Science and Technology
- JZJiang Zhu
Chinese Academy of Sciences, Beijing Institute of Genomics, University of Chinese Academy of Sciences
- JYJun YuCorresponding
Chinese Academy of Sciences, Beijing Institute of Genomics, Institute of Computing Technology
Topics & keywords
- Calculator
- Series (stratigraphy)
- Window (computing)
- Sliding window protocol
- Computer science
- R package
- Computer graphics (images)
- Programming language