Lec5
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
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