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ICHEC Software

Information about software packages installed on the ICHEC systems.


Versions Installed

Stokes: 3.8.31


MUSCLE (MUltiple Sequence Comparison by Log-Expectation) 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 give the best average accuracy in the authors' tests. Using versions current at the time of writing, the author's tests show MUSCLE can achieve both better average accuracy and better speed than CLUSTALW or T-Coffee, depending on the chosen options.


MUSCLE is offered freely to anyone who wants to use it.



Additional Notes

To use MUSCLE load the relevant environment module:

module load muscle

Further information can be obtained from http://www.drive5.com/muscle/index.htm.

How to cite MUSCLE:

Edgar R.C. (2004)
MUSCLE: multiple sequence alignment with high accuracy and high throughput.
Nucleic Acids Research 32(5): 1792-1797.

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