Table 1 Results on analytical criteria investigated in a comparative study on PRRSV sequence alignment algorithmsa
Criterion | Algorithm | ||||
|---|---|---|---|---|---|
Clustal W | MAFFT | T-Coffee | Muscle | Clustal 0mega | |
1. Similarity: average pairwise genetic similarity (%) of aligned sequences within the dataset (mean ± standard deviation) | |||||
Replicate 1 (1191 sequences) | 88.77 ± 4.19 | 88.84 ± 4.17 | 88.71 ± 4.23 | 88.78 ± 4.19 | 88.78 ± 4.19 |
Replicate 2 (1191 sequences) | 88.68 ± 4.11 | 88.69 ± 4.11 | 88.28 ± 4.31 | 88.69 ± 4.11 | 88.69 ± 4.11 |
2. Proportion of pairwise comparisons of sequences having ≥ 97.5% genetic similarity (%) | |||||
Replicate 1 (1191 sequences) | 5.17 | 5.17 | 5.19 | 5.17 | 5.17 |
Replicate 2 (1191 sequences) | 4.91 | 4.91 | 4.66 | 4.91 | 4.91 |
3. Length of aligned dataset: number of sites per sequence in the aligned dataset | |||||
Replicate 1 (1191 sequences) | 603 | 606 | 607 | 603 | 603 |
Replicate 2 (1191 sequences) | 603 | 603 | 609 | 603 | 603 |
4. Average sum of pairs (SP) score: proportion of shared homologies with reference alignment (%)b | |||||
Clustal W as reference | – | 99.93 | 99.74 | 99.91 | 99.94 |
MAFFT as reference | 99.93 | – | 99.78 | 99.97 | 99.97 |
T-Coffee as reference | 99.92 | 99.96 | – | 99.94 | 99.97 |
Muscle as reference | 99.91 | 99.97 | 99.76 | – | 99.95 |
Clustal Omega as reference | 99.94 | 99.97 | 99.78 | 99.95 | – |
Average | 99.92 | 99.95 | 99.76 | 99.94 | 99.95 |
5. Congruent cells ≥ 97.5% similarity: proportion of cells between two pairwise similarity matrices having the same binary value (0: < 97.5%; 1: ≥97.5%) for genetic similarityb | |||||
Clustal W as reference | – | 100.00 | 99.86 | 99.99 | 99.99 |
MAFFT as reference | 100.00 | – | 99.86 | 99.99 | 99.99 |
T-Coffee as reference | 99.86 | 99.86 | – | 99.86 | 99.86 |
Muscle as reference | 99.99 | 99.99 | 99.86 | – | 99.99 |
Clustal Omega as reference | 99.99 | 99.99 | 99.86 | 99.99 | – |
Average | 99.96 | 99.96 | 99.86 | 99.95 | 99.95 |