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Table 3 Results on synthetic plasmodium-like data. Performance of various multiple sequence alignment programs on synthetic data generated with dinucleotide correlations that mimic the Plasmodium falciparum genome. See the caption of Table 1 for explanation of the column and row labels.

From: Sigma: multiple alignment of weakly-conserved non-coding DNA sequence

   q = 0.35 q = 0.45 q = 0.55 q = 0.65
No embedded WM's
N s Prog N + N - Sen Er N + N - Sen Er N + N - Sen Er N + N - Sen Er
3 sigma+ 0 0 0.00 N/A 0 0 0.00 N/A 1036 0 0.03 0.00 24617 0 0.82 0.00
  sigma- 66 1070 0.00 0.94 9175 372 0.31 0.04 27959 0 0.93 0.00 29547 0 0.98 0.00
  dialign 292 1471 0.01 0.83 800 1582 0.03 0.66 4185 929 0.14 0.18 14957 104 0.50 0.01
  alignm 753 1563 0.03 0.67 5889 2085 0.20 0.26 20462 1846 0.68 0.08 27433 728 0.91 0.03
  clustalw 12057 17943 0.40 0.60 23528 6472 0.78 0.22 27965 2035 0.93 0.07 29814 186 0.99 0.01
  mlagan 7974 22026 0.27 0.73 21709 8291 0.72 0.28 29145 855 0.97 0.03 30000 0 1.00 0.00
  tcoffee 6865 23135 0.23 0.77 15398 14602 0.51 0.49 25261 4739 0.84 0.16 29043 957 0.97 0.03
6 sigma+ 0 0 0.00 N/A 48 0 0.00 0.00 8033 0 0.13 0.00 54293 0 0.90 0.00
  sigma- 1684 8161 0.03 0.83 26675 4113 0.44 0.13 57619 86 0.96 0.00 59411 0 0.99 0.00
  dialign 294 7229 0.00 0.96 3423 5362 0.06 0.61 15806 2521 0.26 0.14 46203 75 0.77 0.00
  alignm 0 50 0.00 1.00 3678 237 0.06 0.06 42406 972 0.71 0.02 57938 610 0.97 0.01
  clustalw 26172 33828 0.44 0.56 46240 13760 0.77 0.23 55270 4730 0.92 0.08 59234 766 0.99 0.01
  mlagan 13737 46263 0.23 0.77 40430 19570 0.67 0.33 57668 2332 0.96 0.04 59931 69 1.00 0.00
  tcoffee 19149 40851 0.32 0.68 40764 19236 0.68 0.32 56346 3654 0.94 0.06 59532 468 0.99 0.01