Clustering Results by Phylogenetic Ensemble Methods and HIV-TRACE With the Statewide Sequence Database
| Clustering Method . | HIV-TRACE 1.5% . | RAxML . | IQ-TREE . | FastTree . | FastTree aLRT . | MEGA . | Any Phylogenetic Method . |
|---|---|---|---|---|---|---|---|
| HIV-TRACE 1.5% | 22 | 22 | 22 | 22 | 22 | 22 | 22 |
| RAxML | … | 51 | 43 | 45 | 41 | 47 | 51 |
| IQ-TREE | … | … | 44 | 41 | 42 | 42 | 44 |
| FastTree | … | … | … | 46 | 39 | 43 | 46 |
| FastTree aLRT | … | … | … | … | 42 | 40 | 42 |
| MEGA | … | … | … | … | … | 47 | 47 |
| Any phylogenetic method | … | … | … | … | … | … | 52 |
| Clustering Method . | HIV-TRACE 1.5% . | RAxML . | IQ-TREE . | FastTree . | FastTree aLRT . | MEGA . | Any Phylogenetic Method . |
|---|---|---|---|---|---|---|---|
| HIV-TRACE 1.5% | 22 | 22 | 22 | 22 | 22 | 22 | 22 |
| RAxML | … | 51 | 43 | 45 | 41 | 47 | 51 |
| IQ-TREE | … | … | 44 | 41 | 42 | 42 | 44 |
| FastTree | … | … | … | 46 | 39 | 43 | 46 |
| FastTree aLRT | … | … | … | … | 42 | 40 | 42 |
| MEGA | … | … | … | … | … | 47 | 47 |
| Any phylogenetic method | … | … | … | … | … | … | 52 |
Each number shows how many index cases clustered by both the method listed in the column and the method listed in the row. As outlined further in [20], methods included phylogenetic programs FastTree (GTR + G model; 80% bootstrap support; 4.5% genetic distance), FastTree with the alternative likelihood ratio test (GTR + G model; 90% aLRT support; 3.0% genetic distance), IQ-TREE in ultrafast bootstrap mode (GTR + F + G model; 95% bootstrap support; 3.0% genetic distance), MEGA (GTR + G + I model; 80% bootstrap support; 4.5% genetic distance), and RAxML (GTRCAT model; 80% bootstrap support; 4.5% genetic distance); and the distance-only based HIV-TRACE with 1.5% distance. These parameters represent relaxed criteria to enable comparison of the yield of basing reinterview decisions on both relaxed and strict thresholds.
Clustering Results by Phylogenetic Ensemble Methods and HIV-TRACE With the Statewide Sequence Database
| Clustering Method . | HIV-TRACE 1.5% . | RAxML . | IQ-TREE . | FastTree . | FastTree aLRT . | MEGA . | Any Phylogenetic Method . |
|---|---|---|---|---|---|---|---|
| HIV-TRACE 1.5% | 22 | 22 | 22 | 22 | 22 | 22 | 22 |
| RAxML | … | 51 | 43 | 45 | 41 | 47 | 51 |
| IQ-TREE | … | … | 44 | 41 | 42 | 42 | 44 |
| FastTree | … | … | … | 46 | 39 | 43 | 46 |
| FastTree aLRT | … | … | … | … | 42 | 40 | 42 |
| MEGA | … | … | … | … | … | 47 | 47 |
| Any phylogenetic method | … | … | … | … | … | … | 52 |
| Clustering Method . | HIV-TRACE 1.5% . | RAxML . | IQ-TREE . | FastTree . | FastTree aLRT . | MEGA . | Any Phylogenetic Method . |
|---|---|---|---|---|---|---|---|
| HIV-TRACE 1.5% | 22 | 22 | 22 | 22 | 22 | 22 | 22 |
| RAxML | … | 51 | 43 | 45 | 41 | 47 | 51 |
| IQ-TREE | … | … | 44 | 41 | 42 | 42 | 44 |
| FastTree | … | … | … | 46 | 39 | 43 | 46 |
| FastTree aLRT | … | … | … | … | 42 | 40 | 42 |
| MEGA | … | … | … | … | … | 47 | 47 |
| Any phylogenetic method | … | … | … | … | … | … | 52 |
Each number shows how many index cases clustered by both the method listed in the column and the method listed in the row. As outlined further in [20], methods included phylogenetic programs FastTree (GTR + G model; 80% bootstrap support; 4.5% genetic distance), FastTree with the alternative likelihood ratio test (GTR + G model; 90% aLRT support; 3.0% genetic distance), IQ-TREE in ultrafast bootstrap mode (GTR + F + G model; 95% bootstrap support; 3.0% genetic distance), MEGA (GTR + G + I model; 80% bootstrap support; 4.5% genetic distance), and RAxML (GTRCAT model; 80% bootstrap support; 4.5% genetic distance); and the distance-only based HIV-TRACE with 1.5% distance. These parameters represent relaxed criteria to enable comparison of the yield of basing reinterview decisions on both relaxed and strict thresholds.
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