Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models.

By Ziheng Yang, Rasmus Nielsen. Molecular biology and evolution, 2000

1,701 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/d48f341a0327ed2a8c6b3c25933d7e4549f24fd1

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Citations in the corpus

Role of duplicate genes in genetic robustness against null mutations (2003, methodology): “The number of substitutions per synonymous site ( K S ) and the number of substitutions per nonsynonymous site ( K A ) between duplicate genes were estimated by the PAML packag”
RevTrans: multiple alignment of coding DNA from aligned amino acid sequences (2003, background): “In this context, proper alignment of codon boundaries is especially important for analyses that involve estimation of the ratio between non-synonymous and synonymous mutation rates (10,11).”
ParaAT: a parallel tool for constructing multiple protein-coding DNA alignments. (2012, background): “Therefore, alignments of protein-coding nucleotide sequences are more informative than their corresponding protein alignments and accordingly are more useful for a large variety of bioinformatic analyses [5–7].”
Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events (2003, neutral): “16 for α, β and γ, respectively, calculated as describe”
Phylogenetic Analysis by Maximum Likelihood (PAML) (2002, methodology): “Other small programs in the package include evolver for simulating sequence data sets, pamp for parsimony-based analysis (Yang and Kumar 1996), and yn00 for estimating synonymous and nonsynonymous substitution rates in pairwise comparisons using the method of Yang and Nielsen (2000).”
Molecular signatures of natural selection. (2005, methodology): “To overcome this problem, methods have been devised for detecting positive selection that takes variation in the dN/dS ratio into account (78, 127 ).”
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].”
The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. (2005, methodology): “…calculated the extent of nonsynonymous sequence divergence ( K A ) between each of the 551 S. cerevisiae ohnolog pairs by using the yn00 method of Yang and Nielsen (2000), and six of the 10 fastest pairs are ones newly identified in this study (Supplemental The tree is based on the data of…”
A Universal Trend of Reduced mRNA Stability near the Translation-Initiation Site in Prokaryotes and Eukaryotes (2010, background): “to detect selection pressures at the amino-acid level [1].”
The evolutionary ecology of the major histocompatibility complex (2006, background): “Tests of deviation of dN:dS from parity are becoming increasingly sophisticated (Nielsen, 1997; Yang and Nielsen, 2000; Bierne and Eyre-Walker, 2003), and can now explicitly examine which amino-acid sites show the most potent signatures of selection (Nielsen and Yang, 1998; Yang et al, 2000;…”