= Mussa = 

Multi-Species Sequence Analysis

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

== About Mussa ==

Mussa is an N-way version of the [http://family.caltech.edu/ FamilyRelations] (which is a part of the [http://cartwheel.idyll.org/ Cartwheel] project) 2-way comparative sequence analysis software. Given DNA sequence from N species, Mussa uses all possible pairwise comparions to derive an N-wise 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 [wiki:transitivity transitivity requirement]. The saved paths are then displayed in an interactive viewer. 

[[Image(mussagl_animation.gif)]]

== Download ==

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 Build''' - New builds 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. 

[[LatestBinaryBuild]]

'''Stable Releases:'''
|| '''Application''' || '''Version''' || '''License''' || '''Linux (Binary)''' || '''Mac OS X (Binary)''' || '''Windows XP (Binary)''' || '''Source''' || '''Version Control''' ||
|| Mussagl || 1.0.0 || [http://www.opensource.org/licenses/gpl-license.php GPL v2] || N/A || Available later today || [http://woldlab.caltech.edu/~king/mussagl/1.0/mussa-v1_0_0-win32-setup.exe Win32 Installer] ||  See Version Control || [wiki:darcs darcs] ||
|| Mussagl || development builds || [http://www.opensource.org/licenses/gpl-license.php GPL v2] || See development builds above || See development builds above || See development builds above || See Version Control || [wiki:darcs darcs] ||

== Contact ==

If you would like to contact us about Mussagl, feel free to e-mail one or both of us:
 * Diane Trout <diane (at) caltech.edu>
 * Brandon King <kingb (at) caltech.edu>

== Documentation ==
 * [http://woldlab.caltech.edu/~king/mussagl_manual/ Mussagl User Guide]
 * [wiki:VideoTutorials Mussagl Video Tutorials] - Work in Progress
 * [wiki:ExampleData Example Data]
 * [/cgi-bin/mussa/roadmap Developement Roadmap]

 * [wiki:darcs Checking out Mussagl from Revision Control]
 * [/cgi-bin/mussa/timeline?daysback=90&changeset=on Recent Mussagl Changes in Revision Control]
 * [wiki:MussaglBuild Building Mussagl from Source]

 * PerformanceNotes

== Feature Requests / Bugs ==

 * [/cgi-bin/mussa/newticket Submit a new feature request/bug ticket]
 * [report:3 View existing tickets]

== Older Mussa Versions ==

 * [wiki:MussaFltk Mussa] - C++/FLTK Version 
 * [wiki:MussaProtoype Mussa Prototype (Retired)] - Python/PMW Version

== Development Credits ==

 * Mussagl: Diane Trout with assitance from Brandon King (Core algorithms retained from Mussa (C++/FLTK) )
 * C++/FLTK conversion: Tristan De Buysscher with assistance from [http://chabry.caltech.edu/~t/ Titus Brown]
 * Python/PMW prototype: [http://joiry.net/ Tristan De Buysscher] & Nora Mullaney
 * Consulting User: [http://wormbase.org/db/misc/person?name=WBPerson567;class=Person Erich Schwarz]
 * Principal Investigators: [http://woldlab.caltech.edu/ Barbara Wold], [http://www.cco.caltech.edu/%7Ewormlab/ Paul Sternberg ]

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