Lec5

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Working with Mesquite (created using Version 2.72; build 528). Downloading and installing Mesquite     Go to the “Download Mesquite” link in your lab’s UBLearns site. Go to the link. Select the Mesquite version for your operating system. Once the installer icon is on your desktop, install the program, following the directions. Once the program is installed you will probably be prompted to install “bug fixes” in the program. Do so. Once this is done, you will need to close all Mesquite windows and re-start the program (not your computer). When Mesquite is open, please ignore the “dos” windows that open in the background. These are not used by the user.

Create a “Mesquite” file with given taxa/species (instructions are for Lab 2: Tree Building and “Prokaryotes”, but can be modified for any tree)   Open Mesquite Select “File -> New” from the menu bar. This will cause 2 dialogue boxes to open. o First Dialogue Box: “New File”  Enter a file name which all your data will be written to. This file can be saved to any location and copied to external drives to be transferred to any computer. If your machine does not automatically add .nex to the end of your file name, manually add “.nex” at the end of the file name. The program will not work without the .nex file extension. o Second Dialogue Box: “New File Options” dialogue box  “Make Taxa Block” should be checked  The “Name” can be changed to anything desired; this will be the name for the taxa block  Enter “10” for the number of taxa (taxa/specimen will by default be named as taxon_1, taxon_2, etc.) In later labs, you will enter the number of taxa you need for that lab. Mesquite will open a tab called: Project of “YOUR FILE NAME” o This is the main tab for your project. It organizes distinct parts of your project into units called “blocks.” The first block is the Taxa block which contains information for your 10 specimens. There can also be character blocks (phenographic data, DNA sequence data, etc.), tree blocks, and more. Double clicking on one of the blocks in the project tab causes it to open the information in a new tab. The names of specific blocks can be changed by right-clicking (control-clicking for Mac users) on the block and selecting the “rename” option.



o You can double click on the “List and Manage Taxa” icon to view and modify your list of specimen/taxa. The default names should not be changed as they must correspond exactly with the names in the DNA alignment file you will be given later. o If you close your Mesquite file to come back and work on it later, open blocks will be collapsed when you reopen the file. To see the “Taxa” block (or later “Tree” blocks) click on the right arrow to expand the block. Creating and manipulating simple trees  Creating simple trees o Select “Taxa&Trees -> Make New Tree Block from -> Default trees” from the menu bar. A set of three trees representing different general types of tree structure will be created (called Symmetrical, Bush, and Ladder respectively) o A dialogue box will appear called “Trees Ready; click “Yes” to open the default trees. o It is very helpful to maximize your tree window at this point to have a full screen view of the trees. o To see the three trees, click the arrows at the top left side of the tree:



. The name of each tree is displayed below the tree next to the information symbol (e.g. ) o Trees can be drawn in many different ways to illustrate relationships between taxa. To see some different ways the relationships in your three trees can be depicted select “Drawing -> Tree Form” in the menu bar and note the options which appear. The default tree from is “Square.” Switch between different views by selecting “Diagonal”, “Curvogram”, “Circular” then “Constellation  Notice that the Constellation tree form does not have a necessary starting place (root) – it is an unrooted tree. Trees can be rooted arbitrarily, but scientists generally define a root before their analysis by...
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