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Table 2 Comparing guiding tree performance on SABmark

From: Comprehensive comparison of graph based multiple protein sequence alignment strategies

 

Twilight zone (209)

Superfamily (425)

Guiding tree

FD

FM

Time(sec)

FD

FM

Time(sec)

NJ

22.63

16.69

0.56

51.26

39.71

0.50

MIN

23.75

17.29

0.53

53.88

41.27

0.49

MAX

23.02

16.83

0.54

52.42

40.31

0.50

UPGMA

23.35

16.97

0.54

53.29

40.91

0.50

WUPGMA

23.42

17.01

0.53

53.31

40.90

0.50

  1. Columns show the average developer (FD) score (equivalent to sum-of-pairs [SP] score), modeller (FM) score and run time achieved by different alignment strategies for the "Superfamily" and "Twilight Zone" sets in the SABmark database. The number of alignments in each reference is given in parentheses. The best results in each column are shown in bold. The alignment strategies differ in the algorithm used to build the guiding tree: neighbor joining (NJ), single linkage (MIN), complete linkage (MAX), UPGMA and weighted UPGMA (WUPGMA)
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BMC Bioinformatics

ISSN: 1471-2105

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