Skip to main content

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)