MUSCLE can be downloaded from http://www.drive5.com/muscle/download3.6.html. Currently, there are two versions, 3.6 and 3.7.

Instructions for installing MUSCLE 3.6:
First download the

$ wget http://www.drive5.com/muscle/downloads3.6/muscle3.6_linux_ia32.tar.gz
$ tar xzvf muscle3.6_linux_ia32.tar.gz
$ cd muscle
$ cp muscle /usr/local/bin

Instructions for installing MUSCLE 3.7:

$ wget http://www.drive5.com/muscle/downloads3.7/muscle3.7_src.tar.gz
$ tar xzvf muscle3.7_src.tar.gz
$ cd muscle
$ make
$ cp muscle /usr/local/bin

Instructions for installing MUSCLE 3.8:
Download muscle from http://www.drive5.com/muscle/downloads.htm
Copy to /usr/local/bin or /usr/bin
That's it!

Installing Muscle on Ubuntu

$ sudo apt-get install muscle