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figures		figures
README.md		README.md
antigen-analysis.nb		antigen-analysis.nb
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out.timeseries		out.timeseries
out.tips		out.tips
out.trees		out.trees

README.md

Timeseries

Prevalence

Incidence

Diversity

TMRCA

Virus samples

Map

Distance from origin

Cluster turnover

Incidence by cluster

Tree

Tree with clusters

Tree with geography

Time vs AG1

AG1 vs AG2