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Current version: 1.04

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 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 (tree similarity, Markov speciation models)

There is a brief outline of features, which includes screenshots. The Mesquite manual describes in more detail why Mesquite was made. (The manual for version 1.0 may also be downloaded as a pdf file for more convenient printing; there have been only a few changes since version 1.0.)

The manual also has a page describing new features and bug fixes since version 1.0.

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.

The manual indicates how to cite Mesquite.

Current status and system requirements

Mesquite is available for download here. It is an open source project, with source available under the LGPL.

Known bugs that could affect analytical results in the current release, if any, are listed here.

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

If you use Mesquite, we urge you to sign up to the Mesquite discussion list so that you can be notified of bugs and updates. Also, you may use the list 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(at)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 us directly at ).

Related efforts

A team of computer scientists and biologists from the University of Texas, Lehman College and University of California Davis have developed Tree Set Viz, a set of Mesquite modules for calculating consensus trees and for visualizing sets of trees according to their similarities. Available here. Make sure you have the version of Tree Set Viz that is compatible with this version of Mesquite.

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.

Lars Rosengreen has helped ensure Mesquite can be compiled with Apache Ant.

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. See the Credits page of the manual for more Acknowledgments.

Mesquite Chronology

• July 1997 - project begun
• 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)

24 September 2004

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