Difference between revisions of "MUSCLE"
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:Alignment]] |
{|<!--Main settings - REQUIRED--> | {|<!--Main settings - REQUIRED--> | ||
|{{#vardefine:app|muscle}} | |{{#vardefine:app|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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| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#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|}} | ||
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WRITE CITATION HERE | WRITE CITATION HERE | ||
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Latest revision as of 19:55, 12 August 2022
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.
Environment Modules
Run module spider muscle to find out what environment modules are available for this application.
System Variables
- HPC_MUSCLE_DIR - installation directory