MUSCLE: multiple sequence alignment with high accuracy and high throughput

We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences

R. C. Edgar


Scholarcy highlights

  • Multiple alignments of protein sequences are important in many applications, including phylogenetic tree estimation, structure prediction and critical residue identi®cation
  • Quality scores and CPU times are summarized in Tables 1±7; rankings and statistical signi®cance on PREFAB and BAliBASE for all pairs of methods are given in Table 8
  • On all test sets and quality measures, MUSCLE achieves the highest ranking, and MUSCLE-p is statistically indistinguishable from T-Coffee and NWNSI
  • The Q score on PREFAB is best able to distinguish between methods, giving statistically signi®cant rankings to MUSCLE > MUSCLE-p, MUSCLE > T-Coffee, MUSCLE > NWNSI and MUSCLE-p > NWNSI
  • We have described a new multiple sequence alignment algorithm, MUSCLE, and presented evidence that it creates alignments with average accuracy comparable with or superior to the best current methods
  • MUSCLE is comparable in speed with CLUSTALW, completing a test set averaging 49 sequences of length 240 in about half the time
  • Average accuracy statistically indistinguishable from T-Coffee and the most accurate MAFFT script, is the fastest algorithm known to the author for large numbers of sequences, able to align 5000 sequences of average length 350 in 7 min on a current desktop computer

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