Author: Rahaman, Jordon; Siltberg-Liberles, Jessica
Title: Avoiding Regions Symptomatic of Conformational and Functional Flexibility to Identify Antiviral Targets in Current and Future Coronaviruses Document date: 2016_11_9
ID: pygykil7_10
Snippet: For every protein family, the amino acid substitution rate per site in its multiple sequence alignment was calculated using empirical Bayesian estimation as implemented in Rate4Site (Mayrose et al. 2004) . Substitution rates were calculated using 16 gamma categories, the JTT substitution matrix (Jones et al. 1992) , and the reconstructed phylogenies. The rates were normalized per protein family with an average across all sites equal to zero and S.....
Document: For every protein family, the amino acid substitution rate per site in its multiple sequence alignment was calculated using empirical Bayesian estimation as implemented in Rate4Site (Mayrose et al. 2004) . Substitution rates were calculated using 16 gamma categories, the JTT substitution matrix (Jones et al. 1992) , and the reconstructed phylogenies. The rates were normalized per protein family with an average across all sites equal to zero and SD equal to 1. This means that sites with a rate <0 are evolving slower than average, whereas sites with a rate >0 are evolving faster than average.
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