Mesquite: A modular system for evolutionary analysis

Version: 3.70

Mesquite is modular, extendible software for evolutionary biology, designed to help biologists organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Because it is modular, the analyses available depend on the modules installed.

Mesquite also has many features for managing and processing data, including processing of chromatograms, sequence alignment, editing of morphometric data, and others.

More examples of Mesquite's features can be found in What Mesquite Does. There is also an outline of Mesquite's features. Additional packages can be installed to extend Mesquite's capabilities to interacting with RAxML and other tree-inference programs, processing chromatograms and making base calls, tree set visualization, and so on.

This manual introduces you to the Mesquite system for analysis in evolutionary biology. Its organization follows the manual of Mesquite 2.75, but we are planning to restructure it to serve as a better introduction to Mesquite's use. Some aspects of this documentation may be out of date, for example referring to menus that have moved or been renamed. If you find an obsolete reference, please contact us at info {at} mesquiteproject.org.

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.

Once you have installed Mesquite, we recommend that you read the Learning Mesquite page to learn how best to become familiar Mesquite. And, although reading this documentation will help, not all features are described here. 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 any written manual. It is thus important to learn how to discover Mesquite's capabilities from the program itself, and documented on the Learning Mesquite page. You are encouraged to explore, and invent new analyses.

Should you wish to install additional features that are beyond the core Mesquite installation, please see the page on Installing Additional Packages.

Mesquite is complex, but it is approachable

Because its modularity, and the zeal of the development team, Mesquite has many, many options. This give it a lot of power, as it enables complex, custom-built analyses, but it also means that it can be rather complex if you only want to do something simple. The interface is also a bit unusual, and needs to be learned. However, by reading the documentation, watching the Youtube videos, and following through the example files, you will find that it can be quite approachable.

If you encounter problems

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 Bugs and Troubleshooting 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)Display>Tree Form>Diagonal Tree refers to the Diagonal Tree menu item of the Tree Form submenu of the Display 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).