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February 15, 2008 (Vol. 28, No. 4)

MUSCLE Home Page

  • Interesting, free software
  • Not much besides the software
When you need a hand with something, a little MUSCLE isn’t bad to have. The same is true if you’re performing molecular sequence analysis and need to do multiple alignments of amino acid chains. MUSCLE (multiple sequence comparison by log-expectation) is a freely-available cross platform (Linux, Windows, Macintosh) application controlled by command line that, the author claims, is faster than CLUSTALW, Progressive POA, and the MAFFT script FFTNS1. Indeed, the accuracy is claimed equal to CLUSTALW with a speed two or three orders of magnitude greater. That’s no small potatoes! The site is not much more than a place to download the software. As the author notes, the site name sounds like one of those high-tech sites out of Silicon Valley, but, in fact, it is just a place for him to provide the software to everyone free of charge. You’ve got to admire that attitude. Check it out and let me know how you like it.
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