Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level.

By Jianzhi Zhang, Rasmus Nielsen, Ziheng Yang. Molecular biology and evolution, 2005

1,759 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/198acff8b61aab30468f9be285f55fad65c6602a

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Citations in the corpus

The yak genome and adaptation to life at high altitude (2012, methodology): “To detect genes evolving under positive selection in either yak or cattle ( Supplementary Table 17 ), we used the optimized branch-site model 68 in which likelihood ratio test (LRT) P values were computed assuming that the null distribution was a 50:50 mixture of a chi-squared distribution with 1…”
INDELible: A Flexible Simulator of Biological Sequence Evolution (2009, positive): “The branchmodels (Yang 1998) and branch-sitemodels (Yang and Nielsen 2002; Yang et al. 2005; Zhang et al. 2005) are implemented in INDELible as well.”
Molecular Evolution of Human Coronavirus Genomes (2016, neutral): “Different methods allow to test a prioriwhether a branch is under selection [74,75] or tomodel different evolutionary scenarios for each branch [76].”
PAMLX: a graphical user interface for PAML. (2013, background): “2000, 2005), the branch-site models for detecting positive selection affecting a few sites on particular lineages, and the clade models for detecting functional divergence among clades (clusters of branches) (Yang and Nielsen 2002; Zhang et al. 2005; Weadick and Chang 2012).”
Gene-wide identification of episodic selection. (2015, background): “Methods that do this include the branch-site (Yang and Nielsen 2002; Zhang et al. 2005; Anisimova and Yang 2007; Yang and dos Reis 2011; Kosakovsky Pond et al. 2011; Murrell, Wertheim, et al. 2012) and covarion (Guindon et al. 2004) models of codon evolution.”
A random effects branch-site model for detecting episodic diversifying selection. (2011, methodology): “1 ), that is, those which conform to the null or the alternative model of Zhang et al. (2005), both uBS and rBS perform comparably (NC1, NC2, and SC in table 1), with similar family wise error rates (FWER) and power.”
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data (2016, neutral): “These pre-configured models include site (Yang et al. 2000; Massingham and Goldman 2005), branch (Yang and Nielsen 2002), branch-site (Zhang et al. 2005), and clade (Yang and Nielsen 2002; Bielawski and Yang 2004) models.”
Three Members of the 6-cys Protein Family of Plasmodium Play a Role in Gamete Fertility (2010, methodology): “using a comparison of site specific models of evolution [50,51].”
Mutations in smooth muscle α-actin (ACTA2) lead to thoracic aortic aneurysms and dissections (2007, background): “, and by fitting codon models that test explicitly for positive selection that is restricted to particular branches in the phylogen”