If you're looking for Mesquite Software, Inc.
or its CSIM 18 toolkit for building simulation models, go here
Current version: 1.06
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
Markov speciation models)
There is a brief outline of features,
which includes screenshots. The
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.
Supplementary material may be available
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:
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 us directly at ).
These packages of modules are available
- 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. Make sure you have the version
of Tree Set Viz that is compatible with this version of
- 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.
Vanessa Jackson has released LASRDisc,
which reconstructs ancestral states of categorical characters
by likelihood, providing more options than those in the
built-in stochchar package of Mesquite.
David Maddison & Wayne Maddison have developed Cartographer,
a package of modules for plotting species distributions
("dot maps") and for plotting phylogenies on maps.
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.
Mesquite was developed with the assistance of a Fellowship
to WPM from the David and Lucile Packard Foundation. See the
page of the manual for more Acknowledgments.
- 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 released.
- 21 August 2002- version
- 14 September 2002- version
- 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
- 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
- 29 September 2004 - version
1.05 released (build g24)
- 30 August 2005 - version 1.06
released (build g97)
For more information about Mesquite contact Wayne Maddison and
David Maddison at .
30 August 2005
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© Wayne P. Maddison & David R. Maddison 1999-2005