If you're looking for Mesquite Software, Inc.
or its CSIM 18 toolkit for building simulation models, go here
Current version: 0.994
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
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 email@example.com
with the following message in the body of the email:
subscribe MESQUITELIST YourFirstName YourSecondName
where you replace "YourFirstName" by your
first (given) name, and "YourSecondName" by your second
(family) name. Once you've signed up, you can send a message to
(Of course, we recognize that some messages may be more appropriately
directed directly to us. You may contact Wayne Maddison directly
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.
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.
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.
Mesquite was developed with the assistance of a Fellowship to WPM
from the David and Lucile Packard Foundation.
- July 1997 - project begun
- August 1998 - first public demonstration (Cambridge
- 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
- July 2000 - updated prototypes to developers
(ca. version 0.9.22)
- September 2000 - updated prototype to developers
- December 2000 - updated pre-release (version
- 14 March 2001 - public beta version (version
- 2 April 2001 - public beta version (version
- 24 July 2001 - version 0.98 with source code
- 21 August 2002- version 0.99 released.
- 14 September 2002- version 0.991 released.
- 27 September 2002- version 0.992 released (internal version
- 10 January 2003- version 0.993 released (internal version
- 7 February 2003- version 0.994 released (internal version
For more information about Mesquite contact Wayne Maddison and
David Maddison at firstname.lastname@example.org.
7 February 2003
© W. Maddison & D. Maddison 1999-2003