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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.
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BMC Bioinformatics

ISSN: 1471-2105

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