Table 4

Results on uncorrelated data. Performance of various multiple sequence alignment programs on synthetic data with no dinucleotide correlations, and each base having probability 0.25. See the caption of Table 1 for explanation of the column and row labels.

q = 0.35

q = 0.45

q = 0.55

q = 0.65


No embedded WM's


Ns

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

260

0

0.01

0.00

11690

0

0.39

0.00

29154

0

0.97

0.00

dialign

0

60

0.00

1.00

80

0

0.03

0.00

1000

0

0.06

0.00

7566

0

0.25

0.00

alignm

0

0

0.00

N/A

6682

605

0.22

0.08

23338

656

0.78

0.03

28466

283

0.95

0.01

clustalw

16675

13325

0.56

0.44

26450

3550

0.88

0.12

29340

660

0.98

0.02

29828

172

0.99

0.01

mlagan

11280

18720

0.38

0.62

26874

3126

0.90

0.10

29767

233

0.99

0.01

30000

0

1.00

0.00

tcoffee

3443

26557

0.11

0.89

12475

17525

0.42

0.58

27836

2164

0.93

0.07

29810

190

0.99

0.01

6

sigma-

0

0

0.00

N/A

0

0

0.00

N/A

23583

0

0.39

0.00

58986

0

0.98

0.00

dialign

0

0

0.00

N/A

138

0

0.01

0.00

4588

0

0.08

0.00

28177

0

0.47

0.00

alignm

0

0

0.00

N/A

13090

174

0.22

0.01

53252

824

0.89

0.02

59529

139

0.99

0.00

clustalw

37040

22960

0.62

0.38

53438

6562

0.89

0.11

58432

1568

0.97

0.03

59727

273

1.00

0.00

mlagan

15987

44013

0.27

0.73

50702

9298

0.85

0.15

58621

1379

0.98

0.02

59917

83

1.00

0.00

tcoffee

13439

46561

0.22

0.78

35387

24613

0.59

0.41

58292

1708

0.97

0.03

59941

59

1.00

0.00


Siddharthan BMC Bioinformatics 2006 7:143   doi:10.1186/1471-2105-7-143

Open Data