MUSCLE: Difference between revisions

From UFRC
Jump to navigation Jump to search
m Text replacement - "#uppercase" to "uc"
No edit summary
 
(2 intermediate revisions by the same user not shown)
Line 1: Line 1:
__NOTOC__
__NOTOC__
__NOEDITSECTION__
__NOEDITSECTION__
[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]]
[[Category:Software]][[Category:Biology]][[Category:Alignment]]
{|<!--Main settings - REQUIRED-->
{|<!--Main settings - REQUIRED-->
|{{#vardefine:app|muscle}}
|{{#vardefine:app|muscle}}
Line 20: Line 20:
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].
<!--Modules-->
<!--Modules-->
==Required Modules==
==Environment Modules==
[[Modules|modules documentation]]
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
===Serial===
*{{#var:app}}
==System Variables==
==System Variables==
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
Line 42: Line 40:
WRITE CITATION HERE
WRITE CITATION HERE
|}}
|}}
=Validation=
* Validated 4/5/2018

Latest revision as of 19:55, 12 August 2022

Description

muscle website  

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