Selected article for: "amino acid and codon substitution"
Author: Yasunori Watanabe; Zachary T. Berndsen; Jayna Raghwani; Gemma E. Seabright; Joel D. Allen; Jason S. McLellan; Ian A. Wilson; Thomas A. Bowden; Andrew B. Ward; Max Crispin
Title: Vulnerabilities in coronavirus glycan shields despite extensive glycosylation
  • Document date: 2020_2_21
    • ID: bnnt05fn_44
    Snippet: For the dN/dS analysis, we first estimated Bayesian molecular clock phylogenies for SARSand MERS-CoV independently using BEAST v 1.8.4 75 . For both viruses, we assumed an uncorrelated log-normal distributed molecular clock 76 , Bayesian Skyline coalescent prior 77 and a codon-structured substitution model 78 Multiple independent MCMC runs of 10-20 million steps were executed to ensure stationarity and convergence had been achieved. Empirical dis.....
    Document: For the dN/dS analysis, we first estimated Bayesian molecular clock phylogenies for SARSand MERS-CoV independently using BEAST v 1.8.4 75 . For both viruses, we assumed an uncorrelated log-normal distributed molecular clock 76 , Bayesian Skyline coalescent prior 77 and a codon-structured substitution model 78 Multiple independent MCMC runs of 10-20 million steps were executed to ensure stationarity and convergence had been achieved. Empirical distributions of time-scaled phylogenies were obtained by combining (after the removal of burnin) the posterior tree distributions from the separate runs, which were subsequently used to estimate dN/dS ratios using the renaissance counting approach 79,80 implemented in BEAST v 1.8.4. We also estimated per-site amino-acid diversity, which was calculated as the average number of amino-acid difference between two sequences at an amino-acid position in all possible pairs in the sequence alignment.

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