If you're looking for Mesquite Software, Inc. or its CSIM 18 toolkit for building simulation models, go here

Current version: 0.993

Mesquite is software for evolutionary biology, designed to help biologists analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Because it is modular, the analyses available depend on the modules installed. Analyses being developed include:

• Reconstruction of ancestral states (parsimony, likelihood)
• Tests of process of character evolution, including correlation
• Simulation of character evolution (categorical, DNA, continuous)
• Parametric bootstrapping (integration with programs such as PAUP* and NONA)
• Morphometrics (PCA, CVA, geometric morphometrics)
• Coalescence (simulations, other calculations)
• Tree comparisons and simulations (consensus, Markov speciation models)

The Mesquite manual describes in more detail why Mesquite was made.

Mesquite is modular: when it starts up it surveys to find the installed modules, which then become available to be combined to perform analyses. Some modules handle graphics (charts, editors) and user interface, others do the analytical calculations. The analyses may come from different fields such as phylogenetics, population genetics, morphometrics. By combining different graphical and analytical modules, a large number of alternative analyses can be composed by the user, including novel analyses that bring together questions from different disciplines. Thus, not only theoreticians, but also empirical biologists can invent new analyses as their science demands.

If you're interested, you can check out screenshots, and the older screenshots available from the talk introducing Mesquite at the 2000 Evolution meetings. There is also a tutorial introducing the basics of using Mesquite.

Current status and system requirements

Mesquite has been released as version 0.99, available for download here. Of concern to biologists is whether its results are reliable enough to be used in publications. While we believe that most modules are publication-ready, we have only just begun reviewing the modules to confirm this. We do not expect to confirm the publication readiness of all aspects of Mesquite simultaneously, but rather it will mature on a per-module or per-package basis. Because of its modular nature, we expect that Mesquite will continue to be a mix of both well-tested and experimental modules. Calculations using experimental modules are clearly labeled as such.

Mesquite requires a Java virtual machine (Java 1.1 or higher). It runs reasonably well on the Mac OS (8, 9, and X), on Windows, and on Linux. On the Macintosh operating system, the Java virtual machine is built in; in other operating systems you may have to install it (see the download page for instructions).

Mesquite discussion list

A discussion list (LISTSERV) is available for the community of Mesquite users. Please feel free to use it to request advice about using Mesquite, to report bugs, and to give suggestions. To sign up for the discussion list, send an email (from the email address you wish to use for the list) to listserv@listserv.arizona.edu with the following message in the body of the email:

(Of course, we recognize that some messages may be more appropriately directed directly to us. You may contact Wayne Maddison directly at wmaddisn@u.arizona.edu).

Related efforts

Jeff Klingner, Nina Amenta, and others have developed a set of Mesquite modules for calculating consensus trees and for visualizing sets of trees according to their similarities. Available here.

Peter Midford, Ted Garland and Wayne Maddison have released a Mesquite version of PDAP:PDTree, which analyzes continuous-valued data in a phylogenetic context using Independent Contrasts. Available here.

Some parts of Mesquite use PAL by Drummond and Strimmer, JAMA by The MathWorks and NIST, and JSci by Mark Hale, Jaco van Kooten and others. The Mesquite class libraries use BrowserLauncher by Eric Albert, and corejava.Format by Cay S. Horstmann & Gary Cornell.

Acknowledgments

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

Mesquite Chronology

• July 1997 - project begun
• August 1998 - first public demonstration (Cambridge University)
• July 1999 - limited seeding to a few developers (prototype version 0.9d2)
• August 1999 - this web page on-line
• 29 September 1999 - broader release to developers (prototype version 0.9d5)
• 26 June 2000 - introduced at Evolution meetings (Bloomington, Indiana) (Screenshots from talk)
• July 2000 - updated prototypes to developers (ca. version 0.9d22)
• September 2000 - updated prototype to developers (version 0.9d38)
• December 2000 - updated pre-release (version 0.9d60)
• 14 March 2001 - public beta version (version 0.95d80)
• 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.
• 10 January 2003- version 0.993 released.

10 January 2003