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Table 1 Average SP and TC scores on OXBench

From: PnpProbs: a better multiple sequence alignment tool by better handling of guide trees

  ALL (0–100 %) 0 %–20 % 20 %–50 % 50 %–100 % Time
  SP TC SP TC SP TC SP TC mm:ss
PNPProbs 90.41 82.23 48.98 24.88 83.47 68.79 98.05 95.18 2:58
GLProbs 90.38 82.14 47.29 22.95 83.48 68.65 98.05 95.18 3:15
MSAProbs 90.07 81.75 44.83 22.08 82.77 67.74 98.01 95.08 4:04
Probalign 89.97 81.68 43.58 20.51 82.53 67.46 98.05 95.18 2:10
CONTRAlign 89.34 79.87 44.76 17.83 81.56 64.75 97.55 94.10 10:19
ProbCons 89.68 80.86 44.15 20.30 82.06 66.33 97.84 94.61 1:48
MUSCLE 89.50 80.67 45.64 21.90 81.75 66.15 97.63 94.28 0:19
MAFFT 88.00 77.96 37.82 13.27 78.99 60.86 97.41 93.68 0:19
T-Coffee 89.52 80.50 43.99 19.11 81.82 65.85 97.75 94.38 15:05
Clustal Ω 88.91 79.99 39.09 16.38 80.71 64.49 97.76 94.58 0:12
ClustalW 89.43 80.16 42.94 18.23 81.67 65.01 97.76 94.40 0:22
PicXAA 89.64 80.74 45.11 22.04 81.86 65.91 97.84 94.55 4:26
DIALIGN 83.97 72.41 26.03 8.07 72.67 52.57 95.21 89.54 3:17
Align-m 86.95 76.06 28.36 12.74 76.35 57.54 96.95 92.60 21:14
  1. The table shows the average SP and average TC score (multiplied by 100). The best and second best results in each column are marked in bold and with *, respectively. The last column shows the running time using a single CPU thread. Note that we use default parameters for all tools