Needed result: do HIV DNA sequences tend to look less evolved?

[ArtPoon]

This does not appear in the manuscript.

[brj1]

For each `good' patient in the lanl dataset I calculated the percentage of DNA samples that were below the GLM calculated from the plasma samples.

Good means that there were no processing errors and that the GLM slope converges with positive.

When I used:

1. outgroup rooting
   • 6/8 patients had more than 50% of their DNA samples below the GLM
   • overall 56.4% of the DNA samples were below the GLM
     1. root to tip regression
   • 7/11 patients had more than 50% of their DNA samples below the GLM
   • overall 57.5% of the DNA samples were below the GLM

This would suggest - though I feel not strongly - that the DNA samples are less evolved.

[ArtPoon]

Binomial regression (unsigned test) where probability parameter expresses whether HIV DNA is more or less evolved than expected.

1. Is HIV DNA less evolved generally? P < 0.5?
2. variation among patients (mixed models)
3. variation over time (since seroconversion, if available) - also mixed models