Introducing Mesquite Using Mesquite How Mesquite Works What does it do? Why Mesquite? Other programs History/Acknowledgments Publishing Results Support

Mesquite A modular system for evolutionary analysis   W. Maddison & D. Maddison University of Arizona

Current version: Version 0.98 (July 2001) Mesquite web site

Mesquite is a modular system for evolutionary analysis. If you are a biologist curious about the goals of Mesquite, see the page on why Mesquite was made. If you'd like to get started working with Mesquite, see the page on using the Mesquite system. If you're a programmer wanting to learn how to program modules, see the programmer's guide to Mesquite. If you would like to know more about the design of Mesquite's modular architecture, see the developer's introduction to Mesquite's modularity in the developer's documentation. Mesquite's core libraries and at least many of its modules are distributed under the terms of the GNU Lesser General Public Licence. Mesquite's web site has source code.

Table of Contents

1. Introduction
   1. What does Mesquite do?
   2. Why was Mesquite made?
   3. Differences with other programs
   4. History and Acknowledgments
   5. Publishing results from Mesquite
   6. Reporting Bugs, seeking advice, and giving suggestions
      
      
2. Using the Mesquite system
   1. Basic concepts and vocabulary - Phylogenetic trees, characters, taxa, models, and so on.
   2. Getting help - learning about menus, tools, how to perform analyses, and so on.
   3. Tutorial
   4. Projects and Files
   5. Managing Modules
   6. Menus
   7. Scripting
      
      
3. How Mesquite works
   1. Known problems
   2. Development: A programmer's guide to Mesquite

Other packages bundled with Mesquite

Included with Mesquite in this release is the PAL library by Drummond and Strimmer and the JAMA matrix manipulation package. These are used sparingly at the moment. PAL is used for a single calculation in the Genesis package; JAMA is used in the Rhetenor package. (Both Genesis and Rhetenor are aavailable as separate downloads from the Mesquite web site.) In the future, both PAL and JAMA, and other public libraries, may be used more broadly throughout Mesquite.

THIS SOFTWARE IS PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND. WAYNE MADDISON AND DAVID MADDISON DO NOT WARRANT, GUARANTEE, OR MAKE ANY REPRESENTATIONS REGARDING THE USE OR THE RESULTS OF THE SOFTWARE OR DOCUMENTATION IN TERMS OF THEIR CORRECTNESS, RELIABILITY, CURRENTNESS, OR OTHERWISE. IN NO CASE WILL THESE PARTIES BE LIABLE FOR ANY SPECIAL, INCIDENTAL, CONSEQUENTIAL, OR OTHER DAMAGES THAT MAY RESULT FROM USE OF THIS SOFTWARE.

Mesquite is copyright ©1997-2001 W. Maddison & D. Maddison. The basic system, with core class libraries and basic modules, is free and is distributed under the terms of the GNU Lesser General Public Licence.