@article {Edgar2004,
	title = {{MUSCLE: multiple sequence alignment with high accuracy and high throughput.}},
	journal = {Nucleic acids research},
	volume = {32},
	number = {5},
	year = {2004},
	pages = {1792{\textendash}7},
	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 log-expectation 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 http://www.drive5. com/muscle.},
	keywords = {Algorithms, Amino Acid Motifs, Amino Acid Sequence, Internet, Molecular Sequence Data, Protein, Protein: methods, Reproducibility of Results, Sequence Alignment, Sequence Alignment: methods, Sequence Analysis, Software, Time Factors},
	issn = {1362-4962},
	doi = {10.1093/nar/gkh340},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=390337\&tool=pmcentrez\&rendertype=abstract},
	author = {Edgar, Robert C}
}
