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

Current version: 2.73

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
• Analysis of speciation and extinction rates
• 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. Mesquite is not primarily designed to infer phylogenetic trees, but rather for diverse analyses using already inferred trees.

The Mesquite manual describes in more detail why Mesquite was made.The manual is in the download, or can be browsed here, and is also available as a printable pdf (up to date as of as of version 2.0).

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.

Mesquite requires a Java virtual machine (Java 1.4 or higher). It runs reasonably well on the Mac OS 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, visit the list's webpage. Once you've signed up, you can send a message to the list.

Of course, we recognize that some messages may be more appropriately directed directly to the principal authors. You may contact us directly at . However, if your questions are about how to do something in Mesquite, or if you are having problems using the program, or have found bugs, we strongly urge you to sign up to the Mesquite list and post your question to that, so that others may learn from the response. This will also ease our burden in answering questions, as others who are on the list may know the answer and respond.

Extra packages of modules

These packages of modules are available separately:

• Opal and Opalescent: Travis Wheeler and John Kececioglu have released a version of Opal, a multiple sequence alignment program, that functions from within Mesquite using the Opalescent package by Travis Wheeler and David Maddison. Details are available on the Opalescent page.
• PDAP:PDTree: 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.
• Cartographer: David Maddison & Wayne Maddison have developed Cartographer, a package of modules for plotting species distributions ("dot maps") and for plotting phylogenies on maps.
• NINJA: Travis Wheeler has released NINJA, a fast Neighbor Joining method for phylogenetic tree inference. You can install NINJA in Mesquite using instructions here.
• Mesquite.R: Wayne Maddison and Hilmar Lapp have made Mesquite.R, which enables access to some functions in the ape and diversitree packages in the statistical language R. A companion RMesquite enables access to Mesquite from R.
• AUGIST: Jeff Oliver has developed AUGIST, which infers species trees considering the uncertainty in gene genealogies.
• CoMET: Lee, Blay, Mooers, Singh, & Oakley have developed CoMET, a package for comparing models of continuous character evolution on phylogenies.
• StratigraphicTools and StratAdd: Michel Laurin has coordinated the development of two packages of modules with tools for integrating stratigraphy with phylogeny.
• SILK: Wayne Maddison & Martín Ramírez have produced SILK (Simple Image LinKing), a package to integrate images into morphological data coding, in collaboration with the spider ATOL project.
• Tuatara: Wayne Maddison & Arne Mooers have released Tuatara, a package of modules for analyzing conservation priorities in a phylogenetic context.
• Tree Set Viz: 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. The 2004 version of Tree Set Viz is not compatible with the current Mesquite. You will have to use the forthcoming version 3 of Tree Set Viz (2010?).
• LASRDisc: Vanessa Jackson released LASRDisc, which reconstructs ancestral states of categorical characters by likelihood, providing more options than those in the built-in stochchar package of Mesquite. This package is no longer under development and does not work with version 2 of Mesquite.

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, and iText by Bruno Lowagie and Paulo Soares.

Credits & Acknowledgments

The Mesquite development team is:
  Wayne Maddison
  David Maddison
  Peter Midford (2006-)
  Danny Mandel (2006-7)
  Jeff Oliver (2007-)

Mesquite was developed with the assistance of a Fellowship to WPM from the David and Lucile Packard Foundation. Recent improvements have been assisted by funding from NSERC Canada and by funding from NSF through the CIPRES project. 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)
• 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)

For more information about Mesquite contact Wayne Maddison and David Maddison at . For questions about features, bugs, and problems you might be encountering with the program, please sign up on the Mesquite list and post your question there.

24 July 2010

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