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Table 2 TC scores for chained guide-trees populated according to certain criteria

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

Aligner: Clustal Omega MUSCLE MAFFT L-INS-i PAGAN
len/a 0.731 0.711 0.697 0.723 0.453
len/d 0.700 0.693 0.671 0.684 0.447
HM/a 0.705 0.704 0.680 0.696 0.451
HM/d 0.717 0.697 0.693 0.710 0.454
HML/a 0.709 0.718 0.695 0.706 0.458
HML/d 0.706 0.692 0.678 0.695 0.453
IP/a 0.731 0.701 0.692 0.717 0.466
IP/d 0.698 0.699 0.671 0.693 0.459
IPL/a 0.717 0.701 0.691 0.707 0.449
IPL/d 0.705 0.704 0.683 0.705 0.454
hi/a 0.685 0.685 0.649 0.674 0.423
hi/d 0.745 0.731 0.724 0.742 0.483
lo/a 0.654 0.641 0.598 0.614 0.397
lo/d 0.730 0.722 0.717 0.729 0.461
def 0.757 0.722 0.718 0.754 NA
RAxML 0.743 0.731 0.718 0.740 0.532
  1. ‘len/a’ length ascending, ‘len/d’ length descending, ‘HM/a’ hydrophobic moment ascending, ‘HM/d’ HM descending, ‘HML/a’ hydrophobic moment divided by sequence length ascending, ‘HML/d’ HML descending, ‘IP/a’ isoelectric point ascending, ‘IP/d’ IP descending, ‘IPL/a’ isoelectric point divided by sequence length ascending, ‘IPL/d’ IPL descending, ‘hi/a’ highest sequence similarity ascending, ‘hi/d’ highest similarity descending, ‘lo/a’ lowest sequence similarity ascending, ‘lo/d’ lowest similarity descending. ‘def’ is the default guide tree (non for PAGAN), RAxML is the ML tree estimated from the true reference alignment. The best score for every aligner is highlighted in bold (unless RAxML).