Table 3 Differences in results for analytical criteria when excluding or not recombinants for the different algorithmsa
Criterion | Algorithm | ||||
|---|---|---|---|---|---|
Clustal W | MAFFT | T-Coffee | Muscle | Clustal 0mega | |
1. Difference in similarity: average pairwise genetic similarity (%) of aligned sequences within the dataset (mean) | |||||
Replicate 1 | 0.01 | −0.05 | 0.01 | 0.01 | 0.01 |
Replicate 2 | 0.02 | 0.01 | 0.15 | 0.01 | 0.01 |
2. Difference in proportion of pairwise comparisons of sequences having ≥ 97.5% genetic similarity (%) | |||||
Replicate 1 | 0.07 | 0.07 | 0.07 | 0.07 | 0.07 |
Replicate 2 | 0.05 | 0.05 | 0.27 | 0.05 | 0.04 |
3. Difference in length of aligned dataset: number of sites per sequence in the aligned dataset | |||||
Replicate 1 | 0 | −3 | 0 | 0 | 0 |
Replicate 2 | 0 | 0 | −1 | 0 | 0 |
4. Difference in average sum of pairs (SP) score: proportion of shared homologies with reference alignment (%)b | |||||
Clustal W as reference | – | 0.01 | 0.04 | 0.01 | 0.01 |
MAFFT as reference | 0.01 | – | 0.04 | 0.01 | 0.00 |
T-Coffee as reference | 0.01 | 0.01 | – | 0.01 | 0.00 |
Muscle as reference | 0.01 | 0.01 | 0.04 | – | 0.00 |
Clustal Omega as reference | 0.01 | 0.00 | 0.04 | 0.00 | – |
Average | 0.01 | 0.01 | 0.04 | 0.01 | 0.01 |
5. Difference in 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 | – | −0.01 | 0.11 | 0.00 | 0.00 |
MAFFT as reference | −0.01 | – | 0.11 | 0.01 | 0.00 |
T-Coffee as reference | 0.11 | 0.11 | – | 0.11 | 0.11 |
Muscle as reference | 0.00 | 0.01 | 0.11 | – | 0.00 |
Clustal Omega as reference | 0.00 | 0.00 | 0.11 | 0.00 | – |
Average | 0.02 | 0.02 | 0.11 | 0.03 | 0.03 |