Multi-Species Sequence Analysis

"We be plundering the High Sequence Seas For the hidden Treasures of Conservation"

About Mussa

Mussa is a bioinformatics tool for finding and visualizing regions of conserved DNA by comparing across several species. It has been found that conserved regions are frequently enriched for regions that are functionally important. Thus Mussa is a tool to help discover previously unknown functional DNA elements.

Mussa's core algorithm is an N-way version of FamilyRelation's 2-way comparative sequence analysis software (which is a part of the Cartwheel project). Mussa analyzes the conservation between DNA sequence from N species by applying a transitivity requirement to all possible paths through all possible pairwise comparisons from the provided DNA segments to derive an N-way comparison.

For example, given sequences 1,2,3, and 4, Mussa makes 6 2-way comparisons: 1vs2, 1vs3, 1vs4, 2vs3, 2vs4, and 3vs4. It then compares all the links between these comparisons, saving those that satisfy a transitivity requirement. The saved paths are then displayed in an interactive viewer.

Mussagl in action.


  • 2013Dec20 - Mussa v1.1.1 minor efforts to update to newer versions of boost & qt. probably the same as 1.1.0
  • 2009Nov23 - Mussa v1.1.0 (build 20091123 released)
    • Updated to use Boost 1.40/1.41 and Qt 4.5.3.
  • 2009Nov17 - Mussa Updates:
    • We are in the process of updating Mussa to use Boost 1.40 and Qt 4.5.3.
    • The Mac OS X and Windows binary builds are being tested and being prepared for release. The release will be Mussa 1.1.0.
    • We will be switching the revision control system from bzr to git as well. Updated documentation for checkout of the source code will be included.
  • 2007Jan24 - Release of the first Mussa Video Tutorial.


Currently, we provide two types of binary releases for Mussagl. The first is a development build and the second is a stable release build.

Development Builds - New builds are made as new features / bug fixes are implemented. Many times these builds will be stable, but from time to time, a new feature will break something. Please report any bugs you find and hopefully we will be able to fix the bug and make a new build in a timely fashion.

Stable Releases - Stable releases are made when milestones have been reached and has been tested by our various test users.

Source - The source is available as well. Compiling from source is currently the only way to get a Linux build. Binary versions may be made available for Linux in the future, most likely Debian packages. See the bzr section of the wiki for information on downloading the latest source.

Stable Releases:

Application Version Release Date Mac OS X (Universal Binary) Windows XP (Binary) Debian Source (Linux/Mac/Win)
Mussagl 1.1.1 Dec. 20 2013 .deb (Wheezy 64bit) Source (tar.gz)
Mussagl 1.1.0 Nov. 23rd, 2009
OS X rebuilt Oct 4, 2012
Download (.dmg) Win32 Installer Source (.tar.gz)
Mussagl 1.0.0 Nov. 1st, 2006 Download (.dmg) Win32 Installer Source (.tar.gz)

Debian Install I only built it for debian wheezy amd64 architecture. (64-bit intel & amd cpus) if you'd like you can add a file /etc/apt/sources.list.d/mussa.list containing the following line to be able to install with apt-get. (There will be a key warning if you do this..)

deb ./


If you would like to contact us about Mussagl, feel free to e-mail one or both of us:

  • Diane Trout <diane (at)>
  • Brandon King <kingb (at)>


Feature Requests / Bugs

Older Mussa Versions

Development Credits

Last modified 11 years ago Last modified on 12/20/2013 04:20:17 PM

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