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Table 1 TC scores for different aligners and clustering schemes

From: Systematic exploration of guide-tree topology effects for small protein alignments

  Clustal-Omega MUSCLE MAFFT L-INS-i PAGAN
Default 0.757 0.722 0.718 0.754 NA
RAxML 0.743 0.731 0.718 0.740 0.532
UPGMA 0.753 0.738 0.734 0.749 0.535
NJ 0.744 0.725 0.711 0.735 0.527
Single 0.759 0.744 0.736 0.754 0.535
Complete 0.742 0.732 0.721 0.735 0.526
Mean 0.750 0.737 0.730 0.742 0.541
Ward 0.711 0.700 0.686 0.709 0.498
  1. Default guide-tree for respective aligner, ‘RAxML’ score for ML tree produced from true alignment, UPGMA/NJ trees produced by ClustalW2, single/complete/mean linkage clustering schemes, ‘Ward’ variance minimising scheme. Best scheme for each aligner in bold.