mirror of
https://github.com/Ponce/slackbuilds
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63daf9f79a
Signed-off-by: Heinz Wiesinger <pprkut@slackbuilds.org> |
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muscle.1 | ||
muscle.info | ||
muscle.SlackBuild | ||
README | ||
References | ||
slack-desc |
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. Fast, accurate and easy to use MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users learn everything they need to know about MUSCLE in a few minutes—only a handful of command-line options are needed to perform common alignment tasks. NOTE about the "-stable" option no longer being supported: The "-stable" option had a bug, which sometimes resulted in incorrect alignments to be produced. The author has created a python script to be used as a workaround. The SlackBuild includes it and its usage is: python muscle-stable.py input.fasta aligned.fasta > stable.fasta Papers There are two papers. The first (NAR) introduced the algorithm, and is the primary citation if you use the program. The second (in BMC Bio- informatics) gives more technical details, including descriptions of non-default options. Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32(5):1792-1797 Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity BMC Bioinformatics, (5) 113