Are Mesquite's calculations well-enough tested to be reliable for published analyses? Because Mesquite is modular and still under development, the answer to that question 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 or in the information bar. The red ! indicates that at least one module involved in producing the results of the window is marked as both substantive and pre-release; a green check 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 red !
At this writing (version 0.98, July 2001) this system isn't too helpful yet, since many non-substantive modules are still marked as substantive (which is the default). Also, there are many substantive modules that are marked pre-release that are actually in good enough condition to be marked as release versions. We simply haven't got around to checking them out and marking them as release versions. It is a high priority to fix this. Over the next few months we hope to review the modules and mark whether or not they are ready for published results.
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. 2001. Mesquite: a modular system for evolutionary analysis. version 0.98. 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.)
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, 2001) within the Mesquite system for phylogenetic computing (Maddison and Maddison, 2001); its null distribution was determined by calculating it over 1000 trees simulated by the module Uniform of the SimSpeciation package (Za, 2001) with parameters s = 0.3 and e = 0.1." with the literature cited indicating
Doe, J. 2001. SNIDIND: a Mesquite module for calculating the Snidely Index, version 1.2. Maddison, W. P. and D.R. Maddison. 2002. Mesquite: a modular system for evolutionary analysis. Version 1.1. http://mesquiteproject.org. Za, T. 2001. SimSpeciation: a package of modules to simulate evolutionary trees. Version 1.0.
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:
Another relevant tab is:
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.