Publishing results from Mesquite

Are Mesquite's calculations well-enough tested to be reliable for published analyses? Because Mesquite is modular, the answer to the question of publication-readiness may not be 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 (simple graphical or administrative modules 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. Note however our disclaimer.

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

To help ensure that any remaining bugs are found and fixed, we urge you to pay attention to any strange, unexpected or apparently incorrect behavior of Mesquite, and to send bug reports to us at .

How to cite Mesquite?

Citing the system in general

The citation for this version of Mesquite is:

Maddison, W. P. and D.R. Maddison. 2010. Mesquite: a modular system for 
     evolutionary analysis.  Version 2.73  http://mesquiteproject.org

(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.)

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, 2008) within the Mesquite system for phylogenetic computing (Maddison and Maddison, 2010); its null distribution was determined by calculating it over 1000 trees simulated by the module Uniform of the SimSpeciation package (Za, 2008) with parameters s = 0.3 and e = 0.1." with the literature cited indicating:

Doe, J. 2008. SNIDIND: a Mesquite module for calculating the Snidely Index, 
     version 2.2.

Maddison, W. P. and D.R. Maddison. 2010. Mesquite: a modular system for 
     evolutionary analysis.  Version 2.73  http://mesquiteproject.org.

Za, T. 2008. SimSpeciation: a package of modules to simulate evolutionary 
     trees. Version 2.67.

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.
• 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 modules are reported in the citations view of each the window.

Disclaimer

THIS SOFTWARE IS PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND. WAYNE MADDISON AND DAVID MADDISON DO NOT WARRANT, GUARANTEE, OR MAKE ANY REPRESENTATIONS REGARDING THE USE OR THE RESULTS OF THE SOFTWARE OR DOCUMENTATION IN TERMS OF THEIR CORRECTNESS, RELIABILITY, CURRENTNESS, OR OTHERWISE. IN NO CASE WILL THESE PARTIES BE LIABLE FOR ANY SPECIAL, INCIDENTAL, CONSEQUENTIAL, OR OTHER DAMAGES THAT MAY RESULT FROM USE OF THIS SOFTWARE