Laboratory Notes for BIO 1016 & 3001

Enter data and run a cladistic analysis using Mesquite

JHW, 9 February 2015

We will be using the program Mesquite to build a matrix of taxa and characters and then use this data to create a phylogeny in tree form.

Download the programs:
  • From the menu on left, click on "Download and Installation.
  • Pick your operating system, and download the latest version and build of Mesquite
  • Save it to the drive where you want it to run.
  • Extract the files from the zip folder; this may take a while. 28.5 mb is the size on disc for Windows. You can run the program from a flash drive rather than the hard drive of the computer.

To open Mesquite and get started:
Open the Mesquite folder and double click one of the Mesquite icons to start Mesquite. (If you don't have Java installed, you will be asked to install it.)
There are three executable icons, each using different amounts of memory. We suggest you try first Mesquite [500MB]. The version Mesquite [1GB] allocates more memory; the version Mesquite [2GB] allocates even more.
When you launch Mesquite, a bunch of different windows open as the program loads its components.
Additional instructions, if you need them, are on the Mesquite Installation for Windows/Mac page.
  1. File NEW, name your file, then save.
  2. “New File Options” window will pop up:
    • Check “Make Taxa Block.”
    • Enter the number of species (or different groups of organisms) you have in your analysis (you will be able to add to this later).
    • Check “Make Character Matrix.”
    • Hit “OK.”
  3. “Name of Character Matrix” window will pop up:
    • Enter the number of characters (or traits) in your analysis (you will be able to add to this later).
    • Type of Data should be “Standard Categorical Data.”
    • Hit “OK.”
  4. Enter the data you collected into the data matrix, and save the file. Select the text tool to do this; it is a vertical line that splits in two at top and bottom. The species names are written on the vertical axis, and the traits go horizontally across the top of the matrix. The data itself should consist of 1’s and 0’s, but you may use higher numbers, as needed.
  5. Go up to the “Taxa&Trees.”
  6. “Source of distance for Cluster Analysis” window will pop up > select “Distances from Character Matrix,” hit “OK.”
  7. “Distance calculator” window will pop up > select “Uncorrected Distance (General),” hit “OK.”
  8. “Source of matrices (for Distance from Character Matrix)” window will open > select “Stored Matrices,” and hit “OK.”
  9. “Clustering method” window will pop up > select UPGMA (unweighted pair group method with arithmetic mean).
  10. MAXTREES window will pop up > enter “100” into the window.
  11. “Separate Thread?” window will pop up >select “NOT separate thread.”
  12. “Trees ready” window will pop up > select “YES.”
Trace Character History: This feature will allow you to trace the ancestral state of each trait.
  • You should be in the tree window, able to view your tree.
  • Go up to the “Analysis:Tree” tab at the top > Select “Trace character history.”
  • “Source of characters to reconstruct” window will open > Select “Stored Characters.” Hit “OK.”
  • “Ancestral State reconstruction method” will pop up > select “Parsimony Ancestral States,” hit “OK.”

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Last updated 9 feb 2015 jhw