Table 1.
Performance of aligners on the BAliBASE benchmark alignments database
|
|
Ref 1 (82) |
Ref 2 (23) |
Ref 3 (12) |
Ref 4 (12) |
Ref 5 (12) |
Overall (141) |
|
||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Aligner
|
SP
|
CS
|
SP
|
CS
|
SP
|
CS
|
SP
|
CS
|
SP
|
CS
|
SP
|
CS
|
Time (mm:ss)
|
||||||
| Align-m | 76.6 | n/a | 88.4 | n/a | 68.4 | n/a | 91.1 | n/a | 91.7 | n/a | 80.4 | n/a | 19:25 | ||||||
| DIALIGN | 81.1 | 70.9 | 89.3 | 35.9 | 68.4 | 34.4 | 89.7 | 76.2 | 94.0 | 84.3 | 83.2 | 63.7 | 2:53 | ||||||
| CLUSTALW | 86.1 | 77.3 | 93.2 | 56.8 | 75.3 | 46.0 | 83.4 | 52.2 | 85.9 | 63.8 | 86.1 | 68.0 | 1:07 | ||||||
| MAFFT | 86.7 | 78.1 | 92.4 | 50.2 | 78.8 | 50.4 | 91.6 | 72.7 | 96.3 | 85.9 | 88.2 | 71.4 | 1:18 | ||||||
| T-Coffee | 86.6 | 77.4 | 93.4 | 56.1 | 78.5 | 48.7 | 91.8 | 73.0 | 95.8 | 90.3 | 88.3 | 72.2 | 21:31 | ||||||
| MUSCLE | 88.7 | 80.8 | 93.5 | 56.3 | 82.5 | 56.4 | 87.6 | 60.9 | 96.8 | 90.2 | 89.6 | 73.9 | 1:05 | ||||||
| ProbCons | 90.1 | 82.6 | 94.4 | 61.3 | 84.1 | 61.3 | 90.1 | 72.3 | 97.9 | 91.9 | 91.0 | 77.2 | 5:32 | ||||||
| ProbCons-ext
|
90.0
|
82.5
|
94.2
|
59.1
|
84.3
|
61.1
|
93.8
|
81.0
|
98.1
|
92.2
|
91.2
|
77.6
|
8:02
|
||||||
-
Columns show the average sum-of-pairs (SP) and column scores (CS) achieved by each aligner for each of the five BAliBASE references. All scores have been multiplied by 100. The number of sequences in each reference is given in parentheses. Overall numbers for the entire database are reported in addition to the total running time of each aligner for all 141 alignments. The best results in each column are shown in bold.
