Site-specific preferences from deep mutational scanning of influenza hemagglutinin. Thyagarajan and Bloom  performed deep mutational scanning on influenza hemagglutinin, and reported the counts of codon mutations for three biological replicates of the experiment. Here I have used dms_tools to infer the preferences. (A) Visualization of the preferences averaged across the three replicates. (B) Correlations between the preferences from each pair of replicates. Given files containing the mutation counts, the plots can be generated as logoplot.pdf, corr_1_2.pdf, corr_1_3.pdf, and corr_2_3.pdf with the following commands:.