Version 3.0
This version is obsolete. Current version here.


Download and use of MUSCLE implies acceptance of the License Agreement.

Version 3.0 posted January 2004

Install files for Linux (.tar.gz format)
Install files for Windows NT/2000/XP (ZIP format)
Source code (.tar.gz format)

Some browsers open the PDF file and the Web page manuals instead of starting a download. If this happens to you, try right-clicking on the link and choosing an option named "Save Target As..." or similar.

The Linux install and source code downloads are named *.tar.gz. Some browsers decompress (gunzip) such files but fail to remove the .gz extension on the file name. If you have trouble with gunzip, try renaming the file to *.tar.