Mesquite

Introduction
Why?
How to Cite
Publication
Support
Credits

Help
FAQ
Web Site

Simplicity
Files

Menus
Windows
Charts
Scripts/Macros
Modules
How

Characters
Taxa
Trees
Glossary

New
  Features

     

Table of
    Contents

 

Character
  Evolution

Diversification

Molecular
  Data

Gene trees

Simulations &
  Randomizations

Continuous
  Characters

Use with
  Other Programs

Studies

 
     

Credits

History

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 is:

  • August 1998 - first public demonstration (Cambridge University)
  • July 1999 - limited seeding to a few developers (prototype version 0.9.2)
  • August 1999 - project web page on-line (currently at http://mesquiteproject.org/)
  • 29 September 1999 - broader release to developers (prototype version 0.9.5)
  • early 2000 - passed 100,000 lines of total code, and 200 total modules.
  • 26 June 2000 - Mesquite introduced at Evolution meetings, Bloomington, Indiana (prototype version 0.9.28)
  • 14 March 2001 - first 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)
  • 24 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 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 released (build i68; build i69 released 24 Sept and i70 released 2 Nov to fix non-substantive bugs)
  • 7 December 2007 - version 2.01 released (build j27; build j28 released 7 Dec to fix a coalescence-counting bug)
  • 9 June 2008 - version 2.5 released (build j77)
  • 24 January 2009 - version 2.6 released (build 486)
  • 27 August 2009 - version 2.7 released (build 510)
  • 7 September 2009 - version 2.71 released (build 514)
  • 11 December 2009 - version 2.72 released (build 527)
  • 24 July 2010 - version 2.73 released (build 544)
  • 3 October 2010 - version 2.74 released (build 550)
  • 30 September 2011 - version 2.75 released (build 564)

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.

Acknowledgments

Mesquite has been developed with the assistance of a Fellowship to WPM from the David and Lucile Packard Foundation, an NSERC Discovery grant to WPM, NSF support via the CIPRES project, and the patience of our families.

The following are gratefully acknowledged for direct assistance with Mesquite's programming or source code. David Swofford helped with the implementation of the likelihood calculations, and supplied code for the optimization routines. John Huelsenbeck gave us portions of the code used in calculation of change probabilities for the Ti/Tv rate matrix model. Lars Rosengreen helped us prepare the code for compilation by means other than Codewarrior.

We offer our thanks to the many users who have given suggestions and bug reports. We would like to single out Michel Laurin and Jonathan Coddington for extensive feedback. Maureen O'Leary gave advice on the use of Mesquite for large morphological data matrices.

Mesquite has benefitted from support to Wayne Maddison and David Maddison by the University of Arizona and the University of British Columbia, and the Wissenschaftskolleg zu Berlin.


Mesquite Home Page | Mesquite Manual

Copyright © 2002-2011 by Wayne P. Maddison and David R. Maddison.
 All rights reserved.