Publishing results from Mesquite

Are Mesquite's calculations well-enough tested to be reliable for published analyses? Some, such as the parsimony calculations and simulations for parametric bootstrap, are almost ready. Others are not. Because Mesquite is modular, the answer to the question of publication-readiness is not a simple "yes" or "no". Mesquite modules are marked as either being prerelease versions (not ready for published results), or release versions. In addition, the modules are marked as substantive (possibly involved in producing results), or not (some simple graphical or administrative modules are not likely to affect results). When all of the substantive modules involved in a calculation are release versions, then we consider it as safe to publish the results as it is with any such biological software.

How do you know if any substantive modules involved in a calculation are prerelease versions? Mesquite windows currently show either (green check) or (red !) in the information bar. The indicates that at least one module involved in producing the results of the window is marked as both substantive and pre-release; a indicates that all substantive modules are release versions. Also, if you select the Modules tab of the window to see the modules involved in the window, those modules that are both substantive and pre-release are marked by the

How to cite Mesquite?

Citing the system in general

As noted above, most of Mesquite is not yet confirmed as usable nor citable for published results. However, were it to be cited now for reasons other than to report the source of published results, it would be cited as:

Maddison, W. P. and D.R. Maddison. 2003. Mesquite: a modular system for 
     evolutionary analysis.  Version 0.996.  http://mesquiteproject.org

(The version number listed above might not be up to date. Check the About Mesquite or the Project and Files window when Mesquite is running to find the version you have.)

Citing Mesquite for analyses done

When Mesquite is ready to be used and cited for published results, the following consideratons apply.

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, 2004) within the Mesquite system for phylogenetic computing (Maddison and Maddison, 2004); its null distribution was determined by calculating it over 1000 trees simulated by the module Uniform of the SimSpeciation package (Za, 2004) with parameters s = 0.3 and e = 0.1." with the literature cited indicating

Doe, J. 2004. SNIDIND: a Mesquite module for calculating the Snidely Index, 
     version 1.2.

Maddison, W. P. and D.R. Maddison. 2004. Mesquite: a modular system for 
     evolutionary analysis.  Version 1.1. http://mesquiteproject.org.

Za, T. 2004. SimSpeciation: a package of modules to simulate evolutionary 
     trees. Version 1.0.

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 tabs in the information bar of each window. The two tabs that most directly help with citations are:

• Citations tab: when touched it shows the citations for modules involved in the analysis. This is the most direct way to find citable modules for an analysis. NOTE: at present (January 2003) this view is not helpful, as the citations aren't complete and they aren't restricted to the analysis-critical modules.
• Parameters tab: 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 tab is:

• Modules tab: when touched it shows in the window 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 window (the window that appears on startup) and in the Projects window (which appears to the left of the screen following startup). The current versions of the the modules are reported in the citations are shown in the window.