This contains the Snakefile and scripts which will produce the figures and perform the analyses described in "Evolution, geographic spreading, and demographic distribution of Enterovirus D68" (link will be added when online).

This repository should be located in the same folder as a clone of the repository which performs the Enterovirus D68 Nextstrain analysis (get it here) and both the VP1 and full-genome analyses should be run. This is because this repository will look for the enterovirus_d68 folder and use the results therein to produce further analyses and figures.