In defense of statistical methods for detecting positive selection
- 8 September 2009
- journal article
- letter
- Published by Proceedings of the National Academy of Sciences in Proceedings of the National Academy of Sciences
- Vol. 106 (36) , E95
- https://doi.org/10.1073/pnas.0904550106
Abstract
In a highly publicized article, Nozawa et al. (1) claimed that the branch-site model (BSM) (2, 3) was unreliable because it produced excessive false positives in their simulation experiment. BSM uses a likelihood ratio test to detect positive selection that affects particular branches and codons in protein-coding genes, indicated by accelerated nonsynonymous substitution rates. The authors' conclusion, … 1To whom correspondence should be addressed. E-mail: z.yang{at}ucl.ac.ukKeywords
This publication has 5 references indexed in Scilit:
- Reliabilities of identifying positive selection by the branch-site and the site-prediction methodsProceedings of the National Academy of Sciences, 2009
- PAML 4: Phylogenetic Analysis by Maximum LikelihoodMolecular Biology and Evolution, 2007
- Evaluation of an Improved Branch-Site Likelihood Method for Detecting Positive Selection at the Molecular LevelMolecular Biology and Evolution, 2005
- Bayes Empirical Bayes Inference of Amino Acid Sites Under Positive SelectionMolecular Biology and Evolution, 2005
- Accuracy and Power of Statistical Methods for Detecting Adaptive Evolution in Protein Coding Sequences and for Identifying Positively Selected SitesGenetics, 2004