Table 9 Open in new tab Summary of the...

Table 9

Summary of the benchmarking results of several MSA program on BAliBASE 3.0 [123]

Program	R1-1	R1-2	R2	R3	R4	R5	Avg Score	Tot time(s)
MSAProbs [122]	0.441	0.865	0.464	0.607	0.622	0.608	0.607	12382.00
Probalign [84]	0.453	0.862	0.439	0.566	0.603	0.549	0.589	10095.20
MAFFT [14]	0.439	0.831	0.450	0.581	0.605	0.591	0.588	1475.40
Probcons [17]	0.417	0.855	0.406	0.544	0.532	0.573	0.558	13086.30
Clustal Omega [123]	0.358	0.789	0.450	0.575	0.579	0.533	0.554	539.91
T-Coffee [71]	0.410	0.848	0.402	0.491	0.545	0.587	0.551	81041.50
Kalign [72]	0.365	0.790	0.360	0.476	0.504	0.435	0.501	21.88
MUSCLE [15]	0.318	0.804	0.350	0.409	0.450	0.460	0.475	789.57
FSA [136]	0.270	0.818	0.187	0.259	0.474	0.398	0.419	53648.10
DiAlign [12]	0.265	0.696	0.292	0.312	0.441	0.425	0.415	3977.44
PRANK [137]	0.223	0.680	0.257	0.321	0.360	0.356	0.376	128355.00
ClustalW [11]	0.227	0.712	0.220	0.272	0.396	0.308	0.374	766.47

Program	R1-1	R1-2	R2	R3	R4	R5	Avg Score	Tot time(s)
MSAProbs [122]	0.441	0.865	0.464	0.607	0.622	0.608	0.607	12382.00
Probalign [84]	0.453	0.862	0.439	0.566	0.603	0.549	0.589	10095.20
MAFFT [14]	0.439	0.831	0.450	0.581	0.605	0.591	0.588	1475.40
Probcons [17]	0.417	0.855	0.406	0.544	0.532	0.573	0.558	13086.30
Clustal Omega [123]	0.358	0.789	0.450	0.575	0.579	0.533	0.554	539.91
T-Coffee [71]	0.410	0.848	0.402	0.491	0.545	0.587	0.551	81041.50
Kalign [72]	0.365	0.790	0.360	0.476	0.504	0.435	0.501	21.88
MUSCLE [15]	0.318	0.804	0.350	0.409	0.450	0.460	0.475	789.57
FSA [136]	0.270	0.818	0.187	0.259	0.474	0.398	0.419	53648.10
DiAlign [12]	0.265	0.696	0.292	0.312	0.441	0.425	0.415	3977.44
PRANK [137]	0.223	0.680	0.257	0.321	0.360	0.356	0.376	128355.00
ClustalW [11]	0.227	0.712	0.220	0.272	0.396	0.308	0.374	766.47

Several benchmarking results on BAliBASE 3.0 are summarized. This table presents total column (TC) scores for six references, average TC scores on all references, and total running times. The best results in each column are put in bold.

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