Mesquite: A modular system for evolutionary
analysis, version 2.72
Wayne P. Maddison,
University of British Columbia
David R. Maddison, Oregon State University
Peter Midford (2006-)
Danny Mandel (2006-7)
Jeff Oliver (2007-)
This manual introduces you to the Mesquite
system for analysis in evolutionary biology. It explains the basic
operation of the system (the links above) and some standard analyses
(the links at left). Mesquite's web site has a printable pdf version of this manual (as of version 2.0).
New features and bug fixes since version
1.0 are described on the page on new features
and history of changes. Version 2.7 is incompatible with modules
from version 1, and thus you will need to find new versions of
any third-party modules you have from version 1. Version 2.7 has a few incompatibilities with versions 2 and 2.5, and so some third-party modules may need to be replaced with newer versions.
Mesquite's analyses currently include
phylogenetic analyses (parsimony, likelihood, comparative method,
simulations and randomizations of characters and trees) and population
genetics analyses (coalescence). You can also use Mesquite as
an editor for phylogenetic data files. Mesquite is not primarily
designed to infer phylogenetic trees, but rather for diverse analyses
using already inferred trees. Mesquite's web site contains an
outline of Mesquite's
Because many analyses are possible and those available depend
on what modules are installed and loaded, a comprehensive manual
cannot easily be written. For this reason, many analyses available
in Mesquite are not included in this manual. You are encouraged
to explore, and invent new analyses. We have a special page on
how to learn about Mesquite's features.
Mesquite's web site is here;
check it for updates. We recommend you sign up to the Mesquite
discussion e-mail list to learn about updates and to discuss
To begin using Mesquite on the Mac OS, Unix/Linux or Windows,
see the installation
instructions. We encourage you to explore the example files
in the "examples" directory of the Mesquite_Folder.
See the Help page to learn how best to
The website has a list of some third-party
modules you can install. See the page on modules
for instructions on where they can be installed.
We encourage you to report bugs or misbehaviour of Mesquite.
You may find a problem that seems so obvious to you that you expect
we must have seen it. Please report it anyway, because perhaps
it occurs only in particular circumstances that we didn't test,
or it occurs with a combination of options that we haven't tested
recently. The Support page has more
details on reporting bugs.
Conventions of this manual
For compactness, we will use a special
convention to refer to menu items. For example, File>Save
File refers to the Save File menu item of the File
menu. (Tree Window)Drawing>Tree Form>Diagonal
Tree refers to the Diagonal Tree menu item of the Tree
Form submenu of the Drawing menu that is associated with the Tree
Window. By referring to a menu as "associated with"
a window, we mean that that menu is present in the menu bar at
the top of the screen when the window is frontmost (on the MacOS),
or that the menu is embedded within the window (on the Windows
OS and most other operating systems).
Information for Developers
Mesquite is modular, and can be extended by adding modules into
the folder "mesquite" in the folder "Mesquite_Folder".
Developers interested in writing modules should contact us at
on development for Mesquite is also available here,
although it is out of date.