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_9
Snippet: Multiple sequence alignments were constructed for the selected BLAST hits using MAFFT (Katoh et al. 2002) . Phylogenetic trees were constructed using MrBayes 3.2.2 with a four category gamma distribution and the mixed model for amino acid substitution (Huelsenbeck and Ronquist 2001; Ronquist and Huelsenbeck 2003) . Each tree ran for five million generations, with a sample frequency of 100. The final tree was constructed from the last 75% of sampl.....
Document: Multiple sequence alignments were constructed for the selected BLAST hits using MAFFT (Katoh et al. 2002) . Phylogenetic trees were constructed using MrBayes 3.2.2 with a four category gamma distribution and the mixed model for amino acid substitution (Huelsenbeck and Ronquist 2001; Ronquist and Huelsenbeck 2003) . Each tree ran for five million generations, with a sample frequency of 100. The final tree was constructed from the last 75% of samples, discarding the first 25% of samples as the default burnin, and using the half-compatible parameter, to avoid weakly supported nodes (i.e., with a posterior probability <0.5). All trees were midpoint rooted.
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