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About libMUSCLE

libMUSCLE is a refactorization of the popular MUSCLE v3.6 alignment software into a development library. By refactoring MUSCLE into a library, the various functions implemented in MUSCLE can be called directly by C/C++ programs without forking a separate MUSCLE process. In the process of refactoring, we have fixed several bugs in the original MUSCLE v3.6 software and added a small number of new features. Perhaps most importantly, we have refactored MUSCLE to be thread-safe, so that it can be easily incorporated into shared-memory parallel programs. Note that the included Makefiles also build the standalone muscle binary and have been tested on Windows, Mac OS X, and Linux.

Source code repository

We maintain a subversion based source code repository for libMUSCLE as part of the Mauve sourceforge project. The latest source code can be obtained with the following subversion command:

svn co muscle

The source code repository can also be browsed online.


API documentation for the latest libMUSCLE is automatically generated nightly from our source code repository and available here:


The latest source code snapshot of libMUSCLE is available from:

Although nightly snapshots of libMUSCLE are not explicitly tested, they will likely work without issue because libMUSCLE is stable and no longer under active development. Tested libMUSCLE releases are generally made in conjunction with releases of the Mauve genome alignment software. Source code can be found in the versioned mauve release folders here:

Last Updated ( Sunday, 24 February 2008 )
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