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diff --git a/academic/muscle/README b/academic/muscle/README index 4db82130b5..2a8b2c538d 100644 --- a/academic/muscle/README +++ b/academic/muscle/README @@ -3,7 +3,29 @@ nucleotide sequences. A range of options is provided that give you the choice of optimizing accuracy, speed, or some compromise between the two. -For details and citation: -Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high -accuracy and high throughput. Nucleic Acids Res. 32(5):1792-1797. -doi:10.1093/nar/gkh340 +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 |