History+of+Mesquite

=History of Mesquite= Mesquite was begun in 1997, but its roots go deeper, to the initial development in 1985 of [|MacClade], which even from the start allowed interactive manipulation of trees and interpretation of character evolution. As features were added to MacClade through the years, most from Wayne Maddison in early versions (1 and 2) and from David Maddison in later versions (2, 3 and 4), MacClade developed an exploratory approach to phylogenetic calculations with a distinctive user interface. After MacClade version 3 was released in 1992, the coauthors worked to ready version 4. Almost all of the many new features in version 4, including the new facilities for molecular sequence editing, were the result of David's efforts. Wayne's efforts on MacClade 4 involved an attempt to graft a modular architecture onto MacClade to allow plug-ins so that its capabilities could be extended. This, we hoped, would allow us and other programmers to add many new tree-based analyses to MacClade. 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). Mesquite's vision, exploratory nature, and its user interface borrow extensively from ideas developed in MacClade, but the underlying architecture is quite different. Thus, Mesquite contains a mix of features borrowed directly from MacClade, features we had wanted to put into MacClade but couldn't (e.g., coordinated selection of objects, Trace Character over Trees, likelihood reconstructions), and newly conceived features.

The subsequent chronology of the Mesquite project, with links to old versions, is:
 * August 1998 - first public demonstration (Cambridge University)
 * July 1999 - limited seeding to a few developers (prototype version 0.9.2)
 * August 1999 - this web page on-line
 * 29 September 1999 - broader release to developers (prototype version 0.9.5)
 * 26 June 2000 - introduced at Evolution meetings (Bloomington, Indiana) ([|Screenshots from talk])
 * July 2000 - updated prototypes to developers (ca. version 0.9.22)
 * September 2000 - updated prototype to developers (version 0.9.38)
 * December 2000 - updated pre-release (version 0.9.60)
 * 14 March 2001 - public beta version (version 0.95.80)
 * 2 April 2001 - public beta version (version 0.96)
 * 24 July 2001 - [|version 0.98] with source code released.
 * 21 August 2002- [|version 0.99] released.
 * 14 September 2002- [|version 0.991] released.
 * 27 September 2002- [|version 0.992] released (internal version (build) d24).
 * 10 January 2003- [|version 0.993] released (build d42).
 * 7 February 2003- [|version 0.994] released (build d51).
 * 21 May 2003 - [|version 0.995] released (build e23)
 * 21 June 2003 - [|version 0.996] released (build e30)
 * 22 September 2003 - [|version 1.0 released] (build e58)
 * 14 January 2004 - [|version 1.01 released] (build e80; build e81 released 17 January to fix cosmetic bug)
 * 6 May 2004 - [|version 1.02 released] (build g6; build g7 released 12 May to fix non-substantive bug)
 * 1 July 2004 - [|version 1.03 released] (build g19)
 * 1 September 2004 - [|version 1.04 released] (build g21)
 * 29 September 2004 - [|version 1.05 released] (build g24)
 * 30 August 2005 - [|version 1.06 released] (build g97)
 * 18 May 2006 - [|version 1.1 released] (build h60; build h61 released 23 May to fix a few non-substantive bugs)
 * 21 June 2006 - [|version 1.11 released] (build h64) [20th anniversary of first [|MacClade] release!]
 * 23 September 2006 - [|version 1.12 released] (build h66)
 * 21 September 2007 - [|version 2.0] (build i68; build i69 released 24 Sept. to fix a non-substantive bug; build i70 released 30 Oct. for Mac OS X only, to work around a bug in Java 1.4 on OS X 10.3)
 * 7 December 2007 - [|version 2.01] (build j27; build j28 released 7 Dec. to fix a coalescence-counting bug)
 * 9 June 2008 - [|version 2.5] (build j77)
 * 24 January 2009 - [|version 2.6] (build 486)
 * 27 August 2009 - [|version 2.7] (build 510)
 * 7 September 2009 - [|version 2.71] (build 514)
 * 11 December 2009 - [|version 2.72] (build 527; build 528 released 20 Dec. to fix a few non-substantive bugs)
 * 24 July 2010 - [|version 2.73] (build 544)
 * 3 October 2010 - [|version 2.74] (build 550)
 * 30 September 2011 - [|version 2.75] (build 564)
 * for versions 3.0 and following, see page on release dates.

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. In 2006 Peter Midford joined the development team full-time thanks to the support of the CIPRES project. He has written code for new likelihood methods for understanding character evolution and diversification (e.g., Pagel's 1994 correlation test and Maddison, Midford and Otto's BiSSE method) and has helped with the core architecture. Danny Mandel also joined the team, and was instrumental in arranging Mesquite's transition to a new development system (Eclipse) and in improving the logistics of the release of new versions. In 2007 Jeff Oliver started his contributions to the tree manipulation and display code, the manual, and other aspects. In 2013 Daisie Huang joined the development team, with initial major contributions being her efforts on moving the code to GitHub.