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. 2004 Mar 19;32(5):1792–1797. doi: 10.1093/nar/gkh340

Table 4. Q scores and times on PREFAB.

Method All 0–20% 20–40% 40–70% 70–100% CPU
MUSCLE 0.645 0.473 0.813 0.937 0.980 1.7 × 104
MUSCLE-p 0.634 0.460 0.802 0.942 0.985 2.0 × 103
T-Coffee 0.615 0.464 0.795 0.935 0.976 1.0 × 106
NWNSI 0.615 0.448 0.772 0.930 0.939 1.4 × 104
FFTNS1 0.591 0.423 0.756 0.931 0.938 1.0 × 103
CLUSTALW 0.563 0.382 0.732 0.916 0.930 3.3 × 104

The average Q score for each method over all PREFAB alignments (All), and the total CPU time in seconds are given. The remaining columns show average Q scores on subsets in which the structure pairs fall within the given pairwise identity ranges. Note that T-Coffee required 10 CPU days to complete the test, compared with <5 h for MUSCLE and ∼30 min for MUSCLE-p.