Running MUSCLE via the Web
Here is the MUSCLE Web server. This service is provided by Kimmen Sjolander's group at Berkeley.

Running MUSCLE locally
You can run MUSCLE locally as a command-line program. It has been compiled for Windows, Mac and Linux, and should be readily portable to other platforms. The source code is freely available. It is very simple to install, all you have to do is copy the binary file. Any standard PC that is used to run bioinformatics software should be able to run MUSCLE. I am happy to help port to other platforms.

Downloads
You can download MUSCLE here. 

Citing MUSCLE
Please cite:

Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.

Complete description of the algorithm
The NAR paper above gives only a brief overview of the algorithm and implementation details. For a full discussion of the method and many of the non-default options that it offers, please see:

Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5(1): 113.

News and updates
MUSCLE is updated frequently, typically a new version is posted every two or three months. E-mail me if you would like to be notified of new versions. See here for latest news.