Muscle
Description
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.
License
Public
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of muscle and load default version of muscle as
module avail muscle/ # list available modules module load muscle # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail muscle
and choose explicit version you want to use.
Documentation
http://www.drive5.com/muscle/manual/
Web version
http://www.ebi.ac.uk/Tools/msa/muscle/