analysisContains all most of the scripts for final analysis and plots (using the numbering_table data) including the network graphs and the paneled plots.data_tableContains the numbering_table file which contains all of the important data for the final plots.distance_plotsContains the structures and information to do all of the structural plots.epitope_dataContains all of the epitope data from the FluDB, the alignments, the counts, and the scripts for that analysis.frequency_shiftNot relevant to the manuscript. Contains a currently broken, brief, and slightly different implementation of the work in the Shih and Li paper.PapersContains all of the papers that seemed compositionally relevant to this project. It is missing some that I found toward the end.sequence_dataContains all of the initial sequence and structure data. The sequences are separated into folders by year where year 1 is the 1991-1992 flu season. Combined contains the actual analysis used in the manuscript. Structure contains the actual scripts used to produce the data for the distance plots.
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