Mesquite: A modular system for evolutionary analysis, version 0.994

Wayne Maddison & David Maddison, University of Arizona

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). Because the analyses available in Mesquite depend on what modules are installed and loaded, a comprehensive manual cannot easily be written. For this reason, and as this manual is preliminary, many analyses available in Mesquite are not included in this manual.

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's web site is here; check it for updates.

Conventions

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).

Plans for version 1.0

This is version 0.994. It is still considered a beta-test release, although much of it is nearly ready for full release. We will consider Mesquite at version 1.0 when there are several packages of modules that have been reviewed and designated as ready for publication-quality results. This we hope will be early in 2003.

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 Wayne Maddison at develop@mesquiteproject.org. Information on development for Mesquite is also available here, although it is somewhat out of date.