Table 4.
An application of AUTO-TUNE to subtype stratified HIV-1 pol sequences from the LANL database. Fraction clustered is the proportion of all sequences that are connected to at least one other sequence. Subtypes are sorted by the inferred threshold, lowest first. Other notation is the same as in Table 1
| Subtype | N | E[D] | AUTO-TUNE | Fraction Clustered, % | Mean Degree | ρ | |
|---|---|---|---|---|---|---|---|
| Threshold, % | Score | ||||||
| CRF55 | 2237 | 2.6 | 0.187 | 1.20 | 29.6 | 1.41 | 2.41 |
| CRF07 | 11682 | 3.3 | 0.26 | 1.00 | 26.9 | 3.42 | 1.87 |
| CRF63 | 1649 | 3.6 | 0.505 | 1.01 | 22.1 | 4.85 | 1.8 |
| 01B | 2237 | 7.8 | 0.518 | 1.08 | 22.2 | 0.97 | 5.05 |
| A6 | 11991 | 4.6 | 0.558 | 1.09 | 18.6 | 5.55 | 1.6 |
| CRF08 | 2538 | 3.9 | 0.82 | 1.95 | 25.6 | 1.95 | 2.12 |
| CRF01 | 25689 | 5.1 | 0.875 | 1.73 | 47.0 | 1.94 | 5.54 |
| B | 106261 | 6.4 | 1.084 | 2.00 | 46.4 | 4.77 | 1.95 |
| D | 3561 | 6.6 | 1.133 | 1.12 | 20.8 | 3.65 | 0.79 |
| C | 30714 | 6.7 | 1.438 | 2.00 | 19.3 | 1.26 | 2.22 |
| A1 | 7154 | 7.0 | 1.89 | 2.00 | 17.0 | 5 | 1.7 |
| CRF02 | 7821 | 6.3 | 1.97 | 1.01 | 34.3 | 10.44 | 1.53 |
| BF1 | 4825 | 8.1 | 2.046 | 1.03 | 25.1 | 2.27 | 1.95 |
| G | 2162 | 7.3 | 2.407 | 1.03 | 49.0 | 9.1 | 1.66 |
| F1 | 3986 | 7.6 | 2.941 | 1.34 | 50.4 | 15.03 | 1.40 |
| A1D | 1284 | 8.9 | 3.23 | 1.70 | 27.5 | 1 | 4.3 |
| BC | 2724 | 8.0 | 3.54 | 1.00 | 81.4 | 71.2 | 1.32 |
|
| |||||||
| Wertheim et al. (2014) | 84527 | . | 1.0 | N/A | 15.6 | 3.84 | 1.74 |