Table 2 Results on technical criteria investigated in a comparative study on PRRSV sequence alignment algorithmsa
Criterion | Algorithm | ||||
|---|---|---|---|---|---|
Clustal W | MAFFT | T-Coffee | Muscle | Clustal 0mega | |
1. Handling capability of large dataset: capacity to generate results in less than 2 weeks (yes/no) | |||||
10 replicates of 238 sequences | yes | yes | yes | yes | yes |
5 replicates of 476 sequences | yes | yes | yes | yes | yes |
2 replicates of 1191 sequences | yes | yes | yes | yes | yes |
Full dataset (2383 sequences) | no | yes | no | yes | yes |
2. Rapidity: average time (minutes) necessary to align (Linux platform, 10 physical cores) | |||||
10 replicates of 238 sequences | 12.8 | 0.2 | 13.1 | 0.2 | 0.2 |
5 replicates of 476 sequences | 57.1 | 1.0 | 56.1 | 0.7 | 0.4 |
2 replicates of 1191 sequences | 1040.5 | 7.0 | 540.0 | 3.9 | 1.2 |
Full dataset (2383 sequences) | n/a | 28.5 | n/a | 17.0 | 2.9 |
3. Multiplatform availability (yes/no) | |||||
Web, Windows and Linux | yes | yes | yes | yes | yes |
4. Management of IUB ambiguity symbol characters: ability to manage symbols other than A, T, C and G | |||||
List of managed symbols | N | N, R, Y, W, S, K, M, D, V, H, B | N, R, Y, W, S, K, M, D, V, H, B | N, R, Y | N |