Version 3.2
This version is obsolete. Current version here.

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

Manual as a PDF file
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.