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31 lines
1.4 KiB
Text
31 lines
1.4 KiB
Text
MUSCLE is a program for creating multiple alignments of amino acid or
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nucleotide sequences. A range of options is provided that give you the
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choice of optimizing accuracy, speed, or some compromise between the
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two.
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Fast, accurate and easy to use
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MUSCLE is one of the best-performing multiple alignment programs
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according to published benchmark tests, with accuracy and speed that
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are consistently better than CLUSTALW. MUSCLE can align hundreds of
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sequences in seconds. Most users learn everything they need to know
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about MUSCLE in a few minutes—only a handful of command-line options
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are needed to perform common alignment tasks.
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NOTE about the "-stable" option no longer being supported:
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The "-stable" option had a bug, which sometimes resulted in incorrect
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alignments to be produced. The author has created a python script to
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be used as a workaround. The SlackBuild includes it and its usage is:
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python muscle-stable.py input.fasta aligned.fasta > stable.fasta
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Papers
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There are two papers. The first (NAR) introduced the algorithm, and is
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the primary citation if you use the program. The second (in BMC Bio-
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informatics) gives more technical details, including descriptions of
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non-default options.
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Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high
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accuracy and high throughput. Nucleic Acids Res. 32(5):1792-1797
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Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with
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reduced time and space complexity BMC Bioinformatics, (5) 113
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