Estimate time since infection from NGS diversity

Introduction
This page implements the method to estimate the date of infection from NGS diversity data as presented in Puller et al, biorxiv, 10.1101/129387.
The estimates are based on whole genome diversity data from the eleven patients studied here with well characterized date of infection. Those data are used to estimate the rate at which intra-host diversity increases over time, which in turn is used to estimate the date of infection from diversity measurements.
Enter HXB2 coordinates and diversity

Enter diversity (average hamming distance), the cutoff used to to call minor variants, and the start and end of the region across which diversity is calculated.


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Note: "Codon position" applies only when the entire region is within one gene!

HXB2 coordinates of major landmarks

genestartend
gag7902292
p177901185
p2411861878
pol20855096
PR22532549
RT25503869
env62258795
nef87979417