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MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users learn everything they need to know about MUSCLE in a few minutes—only a handful of command-line options are needed to perform common alignment tasks. 1 (By self description)

Installed version(s)

This version is installed and currently available

on environment hpc-env/8.3:

  • MUSCLE/3.8.31/GCC-8.3.0
  • MUSCLE/3.8.1551-GCC-8.3.0


To load the desired version of the module, use the command, e.g.

module load hpc-env 8.3
module load MUSCLE

Always remember: this command is case sensitive!

If you want to find out more about MUSCLE on the HPC cluster, you can use the command


to get more information about the use of MUSCLE (after loading the module).

Also, you can type in:

module spider MUSCLE

This will show you basic information e.g. a short description and the currently installed version.


The full documentation can be found here.