The most recent version

The MUSCLE2 development has been moved to GitHub. In order to get the recent code please refer to The offered source packages are available for any compatible operating system.

Older packages

The older packages, including sources, RPM for Scientific Linux 5 or a disk image for OS X can be downloaded from this page. The MUSCLE2 is by default installed in /opt/muscle, and you can run MUSCLE2 after running the command

source /opt/muscle/etc/muscle.profile

once per session.

Let us know

If you intend to use MUSCLE2, please send an email to muscle at jorisborgdorff dot nl or bbosak at man dot poznan dot pl