Skip to main content

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).