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Muscle: multiple sequence alignment with high accuracy and high throughput (2004)

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by Robert C. Edgar
Venue:NUCLEIC ACIDS RES
Citations:2453 - 7 self
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BibTeX

@ARTICLE{Edgar04muscle:multiple,
    author = {Robert C. Edgar},
    title = {Muscle: multiple sequence alignment with high accuracy and high throughput},
    journal = {NUCLEIC ACIDS RES},
    year = {2004},
    volume = {32},
    pages = {1792--1797}
}

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Abstract

We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the logexpectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at

Keyphrases

high accuracy    high throughput    multiple sequence alignment    source code    reference alignment    test set    multiple alignment    muscle program    average accuracy    current desktop computer    logexpectation score    progressive alignment    protein sequence    new profile function    large number    prefab test data    new benchmark    fast distance estimation    tree-dependent restricted partitioning    new computer program    tested method   

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