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 s...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.展开更多
This paper studies a generalized nonlinear evolution equation. Using the homotopic mapping method, it constructs a corresponding homotopic mapping transform. Selecting a suitable initial approximation and using homoto...This paper studies a generalized nonlinear evolution equation. Using the homotopic mapping method, it constructs a corresponding homotopic mapping transform. Selecting a suitable initial approximation and using homotopic mapping, it obtains an approximate solution with an arbitrary degree of accuracy for the solitary wave. From the approximate solution obtained by using the homotopic mapping method, it possesses a good accuracy.展开更多
Methods for estimating synonymous and nonsynonymous substitution rates among protein-coding sequences adopt different mutation (substitution) models with subtle yet significant differences, which lead to different est...Methods for estimating synonymous and nonsynonymous substitution rates among protein-coding sequences adopt different mutation (substitution) models with subtle yet significant differences, which lead to different estimates of evolutionary information. Little attention has been devoted to the comparison of methods for obtaining reliable estimates since the amount of sequence variations within targeted datasets is always unpredictable. To our knowledge, there is little information available in literature about evaluation of these different methods. In this study, we compared six widely used methods and provided with evaluation results using simulated sequences. The results indicate that incorporating sequence features (such as transition/transversion bias and nucleotide/codon frequency bias) into methods could yield better performance. We recommend that conclusions related to or derived from Ka and Ks analyses should not be readily drawn only according to results from one method.展开更多
基金grants from the Ministry of Science and Technology of China （No. 2001AA231061） the National Natural Science Foundation of China （No. 30270748）
文摘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.
基金supported by the National Natural Science Foundation of China(Grant Nos 40676016 and 40876010)the Knowledge Innovation Project of Chinese Academy of Sciences(Grant No KZCX2-YW-Q03-08)+1 种基金LASG State Key Laboratory Special fundE-Institutes of Shanghai Municipal Education Commission of China(Grant No E03004)
文摘This paper studies a generalized nonlinear evolution equation. Using the homotopic mapping method, it constructs a corresponding homotopic mapping transform. Selecting a suitable initial approximation and using homotopic mapping, it obtains an approximate solution with an arbitrary degree of accuracy for the solitary wave. From the approximate solution obtained by using the homotopic mapping method, it possesses a good accuracy.
基金This work was supported by the Ministry of Science and Technology of China(Grant No.2001AA231061)the National Natural Science Foundation of China(Grant No.30270748)awarded to JY.We thank Mr.Jun Li for valuable discussion.
文摘Methods for estimating synonymous and nonsynonymous substitution rates among protein-coding sequences adopt different mutation (substitution) models with subtle yet significant differences, which lead to different estimates of evolutionary information. Little attention has been devoted to the comparison of methods for obtaining reliable estimates since the amount of sequence variations within targeted datasets is always unpredictable. To our knowledge, there is little information available in literature about evaluation of these different methods. In this study, we compared six widely used methods and provided with evaluation results using simulated sequences. The results indicate that incorporating sequence features (such as transition/transversion bias and nucleotide/codon frequency bias) into methods could yield better performance. We recommend that conclusions related to or derived from Ka and Ks analyses should not be readily drawn only according to results from one method.
