Mesquite: A modular system for evolutionary analysis, version 2.74

Principal Authors:
Wayne P. Maddison, University of British Columbia
David R. Maddison, Oregon State University

Development Team:
Wayne Maddison
David Maddison
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 features.

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 features.

Getting started

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 learn Mesquite.

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.

Reporting Bugs

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 . Information on development for Mesquite is also available here, although it is out of date.