Mesquite: A modular system for evolutionary
analysis, version 0.993
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.
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 0.993. 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 email@example.com. Information on development
for Mesquite is also available here,
although it is somewhat out of date.