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Muscle: multiple sequence alignment with high accuracy and high throughput (2004)
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| Venue: | NUCLEIC ACIDS RES |
| Citations: | 2501 - 7 self |
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
