PMID:15034147

Citation	Edgar, RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-7
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.
Links	PubMed PMC390337 Online version:10.1093/nar/gkh340
Keywords	Algorithms; Amino Acid Motifs; Amino Acid Sequence; Internet; Molecular Sequence Data; Reproducibility of Results; Sequence Alignment/methods; Sequence Analysis, Protein/methods; Software; Time Factors
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Annotations

Gene product	Qualifier	GO Term	Evidence Code	with/from	Aspect	Extension	Notes	Status
9BRAD:D0V0Y0		GO:0016491: oxidoreductase activity	ECO:0000255:	PMID:15034147	F		Figure 4. Phylogenetic tree comparing predicted nifH amino acid sequences among mutant phenotypes.	complete CACAO 2806
9BRAD:D0V0Y0	enables	GO:0016491: oxidoreductase activity	ECO:0000255: match to sequence model evidence used in manual assertion		F		Seeded From UniProt	Missing: with/from

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