Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages.

By Ziheng Yang, Rasmus Nielsen. Molecular biology and evolution, 2002

1,341 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/c0b51a90752ea11eae47042495dc8d46bb6254b8

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Citations in the corpus

RELAX: detecting relaxed selection in a phylogenetic framework. (2014, background): “2011), which were developed to overcome statistical and methodological restrictions imposed by the popular “branch-site” class of evolutionary models (Yang and Nielsen 2002).”
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).”
Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. (2005, methodology): “For identifying codons under positive selection in the foreground branches, our simulation suggests that NEB can have high false-positive rates and is unusable.”
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.”
EasyCodeML: A visual tool for analysis of selection using CodeML (2019, positive): “These models can be used to identify signals of episodic selection occurring along a specified branch after gene duplication (Yang & Nielsen, 2002; Zhang, Nielsen, & Yang, 2005).”
Molecular signatures of natural selection. (2005, methodology): “Models have also been developed that allow site-specific inferences on a particular group of lineages on a phylogeny ( 128 ).”
The UCSC Genome Browser Database: update 2009 (2008, methodology): “Orthologous genes were examined for evidence of positive selection using a series of nine likelihood ratio tests (LRTs) based on Yang and Nielsen’s ( 21 ) branch-site framework.”
Phylogenetic Analysis by Maximum Likelihood (PAML) (2002, methodology): “The lysozyme data set was also used by Yang and Nielsen (2002) to implement the so-callled “branch-site” models, which allow the ω ratio to vary both among lineages and among sites.”
Bayes empirical bayes inference of amino acid sites under positive selection. (2005, methodology): “BEB Calculations Under Branch-Site and Clade Models Yang and Nielsen (2002) implemented two branchsite models, A and B, which allow the x ratio to vary both among sites and among branches.”
PAML 4: phylogenetic analysis by maximum likelihood. (2007, background): “The branch-site models aim to detect positive selection that affects only a few sites on prespecified lineages (Yang and Nielsen 2002).”
Molecular phylogenetics: principles and practice (2012, positive): “The likelihood ratio test can be used to examine the fit of evolutionary models 59 and to test interesting biological hypotheses, such as the molecular clock 60,49 and Darwinian selection affecting protein evolution 61–63 .”
γ-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates (2009, methodology): “A major limitation of Ka/Ks methods, mentioned in literatures, is their poor ability for detecting positive selection (adaptive selection) [6,46-52].”
The Population Genetics of dN/dS (2008, background): “[3,4,27–35]) in the context of dN/dS is qualitatively different from the classic model of two alleles under recurrent mutation [25].”