TY - JOUR
T1 - KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies
AU - Wang, Dapeng
AU - Zhang, Yubin
AU - Zhang, Zhang
AU - Zhu, Jiang
AU - Yu, Jun
N1 - KAUST Repository Item: Exported on 2020-10-01
PY - 2010/5/6
Y1 - 2010/5/6
N2 - 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/.
AB - 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/.
UR - http://hdl.handle.net/10754/552548
UR - http://linkinghub.elsevier.com/retrieve/pii/S1672022910600083
UR - http://www.scopus.com/inward/record.url?scp=77951682635&partnerID=8YFLogxK
U2 - 10.1016/S1672-0229(10)60008-3
DO - 10.1016/S1672-0229(10)60008-3
M3 - Article
C2 - 20451164
SN - 1672-0229
VL - 8
SP - 77
EP - 80
JO - Genomics, Proteomics & Bioinformatics
JF - Genomics, Proteomics & Bioinformatics
IS - 1
ER -