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MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences. A range of options is provided that give you the choice of optimizing accuracy, speed, or some compromise between the two. Default parameters are those that gave the best average benchmark accuracy in my tests. However
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MUSCLE User Guide. Multiple sequence comparison by log-expectation. by Robert C. Edgar. Version 3.5. August 2004. /muscle. email: muscle (at) drive5.com. MUSCLE is updated regularly. Send me an e-mail if you would like to be notified of new releases. Citation: Edgar, Robert C. (2004), MUSCLE: multiple sequence
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