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Table 1 Comparing guiding tree performance on BAliBASE

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

  RV11 (38) RV12 (44) RV20 (41) RV30 (30) RV40 (49) RV50 (16) Overall (218)  
Guiding tree SP TC SP TC SP TC SP TC SP TC SP TC SP TC Time(sec)
NJ 0.554 0.275 0.877 0.664 0.881 0.280 0.798 0.366 0.864 0.413 0.855 0.450 0.805 0.408 23.71
MIN 0.587 0.286 0.908 0.772 0.902 0.357 0.832 0.457 0.884 0.483 0.871 0.540 0.831 0.483 24.00
MAX 0.575 0.284 0.901 0.744 0.888 0.313 0.822 0.393 0.850 0.385 0.839 0.389 0.813 0.418 23.30
UPGMA 0.585 0.302 0.905 0.761 0.891 0.329 0.828 0.431 0.863 0.422 0.859 0.469 0.822 0.452 23.32
WUPGMA 0.583 0.294 0.905 0.761 0.896 0.329 0.829 0.432 0.860 0.423 0.850 0.453 0.821 0.448 23.52
  1. Columns show the average sum-of-pairs (SP) and true-column (TC) scores achieved by different alignment strategies for each of the six BAliBASE references. The number of alignments in each reference is given in parentheses. Overall values for the entire database are reported in addition to the mean execution time of each strategy. The best results in each column are shown in bold. The 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)