Difference between revisions of "MUSCLE"
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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: [http://nar.oxfordjournals.org/cgi/content/short/gkp1196v1?rss=1 Edgar, R.C. (2010) Quality measures for protein alignment benchmarks, Nucleic Acids Res., 2010, 1–9]. | 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: [http://nar.oxfordjournals.org/cgi/content/short/gkp1196v1?rss=1 Edgar, R.C. (2010) Quality measures for protein alignment benchmarks, Nucleic Acids Res., 2010, 1–9]. | ||
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==Required Modules== | ==Required Modules== | ||
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===Serial=== | ===Serial=== | ||
*{{#var:app}} | *{{#var:app}} | ||
| + | ==System Variables== | ||
| + | * HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory | ||
{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | ||
Revision as of 19:20, 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.
Required Modules
Serial
- muscle
System Variables
- HPC_{{#uppercase:muscle}}_DIR - installation directory