How+to+Cite+Mesquite

=How to cite Mesquite=

Citing the software system in general
The citation for this version of the Mesquite sofware is: code Maddison, W. P. and D.R. Maddison. 2018. Mesquite: a modular system for evolutionary analysis. Version 3.40 http://mesquiteproject.org code (The version number listed above might not be up to date. Check the Mesquite Startup window or the Project and Files window when Mesquite is running to find the version you have.)

If you are using an additional Mesquite package (e.g., PDAP, Zephyr, TreeSetViz,Hypha, Chromaseq) you may need to cite that as well; check the documentation of that package for citation information.

Citing the documentation
The citation for this documentation is: code The Mesquite Project Team. 2018. Documentation for Mesquite: a modular system for evolutionary analysis. https://mesquiteproject.wikispaces.com code

You should probably include the access date and the specific page to which you are referring in the citation.

Note that there are a few pages in this documentation that have separate authorship and citation requirements; please check to see if the page you are citing is so marked.

Citing Mesquite for analyses done
Mesquite's unusual modular nature may give great flexibility in calculations, but it can make it difficult to compose a citation for the calculation of published analyses. Here is a hypothetical example. If the analysis were mostly done by a module written by J. Doe and another by T. Za, one possible citation would be as follows: "The Snidely Index was calculated using the module SNIDIND (Doe, 2012) within the Mesquite system for phylogenetic computing (Maddison and Maddison, 2018); its null distribution was determined by calculating it over 1000 trees simulated by the module Uniform of the SimSpeciation package (Za, 2014) with parameters s = 0.3 and e = 0.1." with the literature cited indicating: code Doe, J. 2012. SNIDIND: a Mesquite module for calculating the Snidely Index, version 3.5.

Maddison, W. P. and D.R. Maddison. 2018. Mesquite: a modular system for evolutionary analysis. Version 3.40 http://mesquiteproject.org.

Za, T. 2014. SimSpeciation: a package of modules to simulate evolutionary trees. Version 3.14159. code

How to figure out what modules to cite
A single Mesquite analysis may be the result of the cooperation of many modules, some of which are worth citing (like a module that calculates a key value), some of which are not (like a module that draws the shape of the tree). While we could expect the user to keep track of the calculations requested and what modules to cite, Mesquite has some built-in features to help, via view modes of each window. The two views that most directly help with citations are:
 * **Citations view**: Available through Window>View Mode>Citations, this shows the citations for modules involved in the analysis. This is the most direct way to find citable modules for an analysis.
 * **Parameters view**: Available through Window>View Mode>Parameters, this shows the parameters of the modules. These may include settings such as rates, weights, population sizes, the tree being used, and so on. They can be very important to help you keep track of the assumptions and input behind your results.

Another relevant view is:
 * **Modules view**: Available through Window>View Mode>Modules, this shows the employee tree of modules involved in producing the window. This includes modules involved in calculations shown. It is useful to help you understand what modules are in use, but it includes all of the modules involved, not just the ones worth citing.

Which version is being used?
The current version of the Mesquite system being used is shown the in Mesquite log window (the window that appears on startup) and in the Projects window (which appears to the left of the screen following startup). You can also see it by choosing the About Mesquite menu item. The current versions of the modules are reported in the citations view of each the window.