Table 3.
Comparison of AUTO-TUNE and published thresholds from prior studies using sequences from viruses other than HIV-1. “N/A”: no distance-based clustering analyses were done. Other notation is the same as in Table 1
| Reference | Virus | Gene | N | L | E[D] | Scope | Location/Country | Timespan | Distance threshold, subs/site | |
|---|---|---|---|---|---|---|---|---|---|---|
| Published | AUTO-TUNE (score) | |||||||||
| Jia et al. (2023) | HCV | NS5B | 503 | 315 | 34.9% | Province | Yunnan, China | 2008–2018 | N/A | 1.933 (1.92) |
| 97 | 8.0% | Genotype | 1b only | ¶ 2.3 | 1.944 (2.0) | |||||
| 53 | 7.4% | Genotype | 2a only | ¶ 3.3 | 3.3 (1.3) | |||||
| 110 | 5.4% | Genotype | 3a only | ¶ 2.0 | 3.6 (1.0) | |||||
| 189 | 5.5% | Genotype | 3b only | ¶ 1.7 | 1.6 (1.0) | |||||
| Murphy et al. (2019a) | HCV | NS5B | 119 | 340–850 | 5.6% | Province | Quebec, Canada | 2001–2017 | N/A | 0.0251 (1.05) |
| Paraschiv et al. (2017) | HCV | NS5B | 117 | ∼ 300 | 24.6% | Country | Romania | 2011–2014 | N/A | 1.394 (1.11) |
| Ye et al. (2023) | HCV | NS5B | 1603/399 ● | 701 | 27.6% | Country | China | 1999–2017 | ¶ 0.010 | 0.359 (1) |
| C/E2 | 865/396 ● | 837 | 37.3% | ¶ 0.0325 | 1.572 (1.98) | |||||
| Ng et al. (2022) | Rhinovirus | VP2/VP4 | 977 | 388 | 43.2% | City | Kuala Lumpur, Malaysia | 2012–2014 | ¶ 0.005 | 0.523 (1) |