Mesquite: A modular system for evolutionary analysis

Manual for version 4.0 beta2

For beginning users, we suggest the video introduction below, which introduces you to the major windows of Mesquite: the character matrix editor, the tree window, and the windows listing and managing taxa, trees, characters, and matrices. We also suggest you browse the menus here in the manual, at left, and that you take a self-guided tour through the example files (in Mesquite_Folder/examples). Look at learning Mesquite for a guide about how best to become familiar with Mesquite.

Mesquite is complex, but you can learn simple paths through it easily, just as you can with a city. We offer Youtube videos, and this manual. Because Mesquite is modular, new functions can be added by adding extra packages, which means this manual cannot be fully complete. Three extra packages that now come bundled with Mesquite have their own manuals: Zephyr (which enables Mesquite to start phylogenetic analysies for programs such as IQ-TREE, RAxML, PAUP*, and TNT, and harvest the results), Chromaseq (which enables Mesquite to process Sanger sequencing chromatograms and edit base calls), and Cartographer (which enables Mesquite to produce distribution maps with dots, stars, and other symbols).

To ask questions and find discussions about Mesquite, please go to the Mesquite Google Group. You may contact the Mesquite developers at info {at} mesquiteproject.org.

Note: This manual is not yet updated for version 4 on many pages. Some pages have a warning; others do not.

A basic introduction to Mesquite

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.

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)Form>Tree Form>Diagonal Tree refers to the Diagonal Tree menu item of the Tree Form submenu of the Form 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).