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Table 2 Comparison of alignment accuracy between ClustalW, MAFFT, SparseMap and mBed.

From: Sequence embedding for fast construction of guide trees for multiple sequence alignment

Method

Alignment Column Score (%)

 

BAliBase

HOMSTRAD/Pfam

Guide Trees constructed internal to method

  

ClustalW

32.66

60.12

ClustalW -quicktree -ktuple=2

32.84

59.92

MAFFT

31.97

66.51

MAFFT -retree 1

31.24

60.09

MAFFT -retree 1 -parttree

30.04

59.27

MUSCLE

35.80

NA

MUSCLE -maxiters 1

32.04

60.45

Guide Trees constructed external to method

  

MUSCLE+mBed

35.38

NA

MUSCLE -maxiters 1+ mBed

32.86

64.18

MAFFT + mBed

29.79

57.57

ClustalW + "MAFFT -retree 0 -parttree"

31.64

54.75

ClustalW + SeedMap

29.82

58.85

ClustalW + mBed

30.20

59.24

# of alignments

386

646

  1. Average Column scores (%) are given for each method. Accuracies are measured on two datasets. The HOMSTRAD-Pfam dataset comprises 646 test cases. Each test consists of a Pfam alignment containing between 3-10,000 sequences, which has been paired with a corresponding structural alignment from HOMSTRAD.
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Algorithms for Molecular Biology

ISSN: 1748-7188