Table 1. Comparison of distances calculated using various alignment algorithms when used with sequences that are trimmed or left untrimmed relative to distances calculated using sequences aligned using the NAST algorithm with the SILVA reference alignment and trimmed to common alignment coordinates.
| Region | Alignment method | Trimmed to alignment region | Slope | R2 |
|---|---|---|---|---|
| V13 | Needleman | No | 1.11 | 0.95 |
| Gotoh | No | 1.16 | 0.90 | |
| NAST-SILVA | No | 1.13 | 0.95 | |
| NAST-greengenes | Yes | 1.10 | 0.93 | |
| Infernal-RDP | Yes | 1.05 | 0.92 | |
| Needleman | Yes | 0.99 | 0.99 | |
| Gotoh | Yes | 1.01 | 0.98 | |
| V35 | Needleman | No | 1.17 | 0.95 |
| Gotoh | No | 1.18 | 0.94 | |
| NAST-SILVA | No | 1.20 | 0.96 | |
| NAST-greengenes | Yes | 1.34 | 0.95 | |
| Infernal-RDP | Yes | 1.01 | 0.97 | |
| Needleman | Yes | 0.99 | 0.99 | |
| Gotoh | Yes | 1.01 | 0.98 |
Abbreviations: Infernal, inference of RNA alignment; NAST, Nearest Alignment Space Termination; RDP, Ribosomal.Database Project.