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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.