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History & Acknowledgments

(As of version 0.97, June 2001)

History

After MacClade version 3 was released in 1992, David Maddison worked to add various new features, including those to edit and align DNA sequences manually. He was primarily responsible for the new developments in version 4 of MacClade, as he had been for version 3. Wayne Maddison's efforts to contribute to MacClade 4 took a different turn. We had hoped to add many new tree-based analyses to MacClade, and we wanted to make it possible for other programmers to add their own calculations. Wayne therefore began to graft a modular architecture onto MacClade to allow plug-ins to extend its capabilities. After about a year of work on this, it became clear that grafting this new architecture on to an existing program was not going to work. MacClade was then returned to its original, non-modular state, and it was within this more traditional framework that David completed MacClade 4.

In order to build the desired modular architecture, Wayne had to start from scratch, and so a new project was born in July of 1997. The very first prototype, after one day of work, can be seen here (for the first few days it was called BeanTree, before it became known as Mesquite). The subsequent chronology of the project is:

• August 1998 - first public demonstration (Cambridge University)
• July 1999 - limited seeding to a few developers (prototype version 0.9d2)
• August 1999 - project web page on-line (currently at http://mesquiteproject.org/mesquite/mesquite.html
• 29 September 1999 - broader release to developers (prototype version 0.9d5)
• early 2000 - passed 100,000 lines of total code, and 200 total modules.
• 12 May 2000 - prototype version 0.9d19 posted for testers.
• 26 June 2000 - Mesquite introduced at Evolution meetings, Bloomington, Indiana (prototype version 0.9d28)
• 14 March 2001 - first public beta version (vresion 0.95 d 80)
• 2 April 2001 - public beta version (version 0.96)

From July 1997 through October 2000, the architectural design, programming and documentation for the basic Mesquite libraries and modules was done by Wayne Maddison, with occasional input from David Maddison. David entered the project in earnest in November 2000. (Other packages of modules for the Mesquite system are due to other authors: for instance, the Rhetenor package of morphometrics modules is by Eric Dyreson and Wayne Maddison.)

Acknowledgments

Mesquite was developed with the assistance of a Fellowship to WPM from the David and Lucile Packard Foundation, and the patience of our families.

For feedback, including bug reports, on various versions of Mesquite, we thank Peter Midford, Michel Laurin, Korbinian Strimmer, Alexei Drummond, Lacey Knowles, Matt Hare, Jennifer Steinbachs, and Margaret Thayer.