Author: Xiaojun Li; Elena E. Giorgi; Manukumar Honnayakanahalli Marichann; Brian Foley; Chuan Xiao; Xiang-peng Kong; Yue Chen; Bette Korber; Feng Gao
Title: Emergence of SARS-CoV-2 through Recombination and Strong Purifying Selection Document date: 2020_3_22
ID: 7v5aln90_25
Snippet: Cumulative plots of the average behavior of each codon for all pairwise comparisons in the input data, for insertions and deletions (indels), synonymous (syn), and nonsynonymous (nonsyn) mutations and values of the ratios of the rate of synonymous nucleotide substitutions per synonymous site and nonsynonymous substitutions per nonsynonymous site (dN/dS, or w) were obtained using the LANL database tool SNAP (42) . In order to avoid counting instan.....
Document: Cumulative plots of the average behavior of each codon for all pairwise comparisons in the input data, for insertions and deletions (indels), synonymous (syn), and nonsynonymous (nonsyn) mutations and values of the ratios of the rate of synonymous nucleotide substitutions per synonymous site and nonsynonymous substitutions per nonsynonymous site (dN/dS, or w) were obtained using the LANL database tool SNAP (42) . In order to avoid counting instances where synonymous mutations were saturated, averages of all pairwise dN/dS ratios were calculated excluding pairs that yielded dS values greater than 1. Sequences were analyzed for episodic selection pressure using the mixed effects model of evolution (MEME) (43) from the datamonkey server (www.datamonkey.org).
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