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(updated July 2001)
This page gives you an overview of using Mesquite, and links to more detailed information. Because Mesquite is untraditional and potentially confusing, we have a special Help page describing how to learn how to use Mesquite.
Mesquite uses Java 1.1, and as such can run on various platforms. It runs as an independent application accessing local files (a special version can also run an applet embedded within a web page). Currently (July 2001) this means it can run as an independent application under the MacOS 8 or 9 using MRJ 2.2 (MRJ 2.1 not recommended), Mac OS X, Windows using JRE 1.1.8 or JDK 1.1.8, JRE/JDK 1.2, or JRE/JKD 1.3, and under various versions of Linux and UNIX. Some window managers under Linux/UNIX and some virtual machines cause problems for Mesquite. You may get best results using a virtual machine from Sun (java.sun.com) if several are available. We have found Mesquite to work fairly well under Red Hat Linux 7 using Gnome or KDE and the Sun JDK (1.2.2 or 1.3). In practice, a computer slower than a PowerPC 604e 250MHz, or a Pentium II 300 MHz, may be painfully slow running Mesquite. Depending on the nature of the virtual machine, Mesquite may use a lot of memory.
Currently, you can start up Mesquite on a MacOS computer by double clicking the Mesquite alias icon or a data file belonging to Mesquite. You can also drop the data file's icon on the Mesquite alias icon. On a Windows computer, start up the executable in the Mesquite folder, or drop a file onto the executable's icon. On a Unix system, you can ask the Java virtual machine to execute application whose main class is mesquite.Mesquite (within the Mesquite Folder). Once started up, go to the File menu and choose Open File.
Mesquite is a thoroughly modular system, and this has consequences on how it behaves. Users may find its behavior to be somewhat unlike that of programs they are used to. It is useful for users to be aware of Mesquite's modularity, because it will help them understand how to use it more effectively.
A discussion of Mesquite's modular system is given in the page on How Mesquite Works (there is also a programmer's introduction to Mesquite's modular architecture in the developer's documentation). At times you will perform calculations that involve many cooperating modules; Mesquite can help you understand which modules are being used, as described in the page on managing modules.
Mesquite makes use of comparative data, phylogenetic trees, assumptions and so on that are usually read from text files. Mesquite can open and read local files on the user's computer, and it can also read files at specified URLs on the web. To open up a file you can use the Open File or Open URL menu items.
Often, the information used in an analysis (data, trees, etc.) will all reside in one file on disk or a web server. However, it is possible for Mesquite to accumulate information from several files. For this reason, Mesquite makes a distinction between a collection of information called a project (which may come from several files) and the physical files on disks or web servers. For more information about this distinction, see the page on Projects and Files.
Mesquite's purpose is to perform calculations for comparative and evolutionary biology. How you give commands to perform a calculation depends upon the particular module in control of the calculation, and so the user must refer to the documentation for the modules for specific information on commands.
However, in general a user will give commands by selecting menu items or touching on buttons on the screen. Mesquite's menus change as different analyses are performed, since different calculations require different controls. A menu item to control a particular calculation may show up under various menus, depending on the context. While this may seem confusing, the rules are simple and we hope users will have no trouble finding what they need. The menus are discussed more on the page about Mesquite's menus. You can learn about the menu items that appear for a window by selecting Menu & Control Explanations from the Window menu of Mesquite.
Mesquite has some consistent types of buttons that the user will see repeatedly. For instance, the two triangular blue buttons to scroll to the next tree or next character in a tree window may appear in various contexts. Such controls are described in the page on Mesquite's windows. You can learn about the buttons in a window by selecting Menu & Control Explanations from the Window menu of Mesquite
Mesquite can also be controlled by a scripting language, described in the next section.
Many modules are scriptable. That is, by sending them text commands like "setCharacter 7" you can get the module to do something, like (in this case) set the character traced to the seventh character. Each module defines its own commands, but the general syntax of the scripting language is described on the page concerning scripting. Scripting commands currently available can be found via the Scripting Commands menu item in the Help menu of Mesquite, and on the module Information pages linked from the Modules Installed page available in the Help menu of Mesquite.
Mesquite has a built-in logging system for commands given. It is not complete. The log window is available in the Windows menu under Mesquite log. The log is also saved to a text file called "Mesquite Log".