Repository of data and code for the manuscript: Beneath the surface: Amino acid variation underlying two decades of dengue virus antigenic dynamics in Bangkok, Thailand.

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00-RawData and 02-processedData containing the data files used in the analyses. __main__.sh is the entry point to all the analyses. Scripts were called in the orders below, reflecting the flow of contents in the manuscript.

1. We first derive distances between all virus pairs present in the dataset. We then quantified amount of antigenic distance that may have arose from PRNT50 measurement uncertainties.

2. Fit effect sizes of variations present in each individual DENV protein to antigenic distances derived from 3-dimensional antigenic map

3. Examine fits to the envelope protein (E)

4. Identify candidate protein(s) that harbor signals beyond linkage with E

5. Identify sites in NS2A that contributed to the excess signals

6. Identify coevolving sites between E and NS2A

7. Quantify observable effects of point substitutions