Difference between revisions of "MUSCLE"
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Revision as of 16:32, 10 August 2012
Description
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, benchmark accuracy is a rather dubious measure; see: Edgar, R.C. (2010) Quality measures for protein alignment benchmarks, Nucleic Acids Res., 2010, 1–9.
Execution Environment and Modules
To use muscle with the environment modules system at HPC the following commands are available:
Get module information for muscle:
$module spider muscle
Load the default application module:
$module load muscle
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_MUSCLE_DIR - directory where muscle is located.