Lab8_AdvancedPAUP

Lab8_AdvancedPAUP - Integrative Biology 200A PRINCIPLES OF...

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Integrative Biology 200A University of California, Berkeley PRINCIPLES OF PHYLOGENETICS Spring 2008 Lab 8 - Advanced PAUP* Today we’re going to be doing some more advanced things in PAUP* . Command line PAUP* is very powerful, but of course has the disadvantage that you have to remember all the commands. Of course, no one, not even David Swofford, (who wrote PAUP) actually knows all the commands by heart. Normal humans tend to refer quire often to the documentation, which lucky is searchable. We’re just going to use the example nexus files, but if you want to use your own data go ahead. If you are bored of PAUP and want to work on your own data, I can help you with that too. Just raise your hand and call me over. Basic Command Line PAUP* Copy the angiosperm and the primate-mtdna files from the example nexus files folder in the PAUP folder to a folder that you create on your desktop. The PAUP program can be accessed through the start menu. The PAUP folder is in C:/Program Files/IB200A/PAUP . Open PAUP* in the IB200 folder in the Start Menu. It will ask you to open a file, but cancel that step for now. As you can see there are a few pull down menus, but they don’t do a lot. The one thing that these menus do OK is deal with files. You can use these menus to open and save files, although you have to use the command line to save trees. The edit and window menus have the basic features that you would expect. Open a file File > Open > PAUP4b10 . Select the angiosperm.nex file and hit Open/Execute . Now, go back to C:/Program Files/IB200A/PAUP and open up the Cmd_ref_v2 . This is a PDF file in the PAUP folder. Open up the Bookmarks . You can use the Bookmarks to find commands. Open up the Command Reference folder in the Bookmarks window. You can also search for commands using the search tool. You will see a bunch of different folders of commands for different blocks. All nexus files are made up of a combination of these different blocks. Each block starts begin (type of block) and finishes end; . Between are a number of commands that tell the program what to do, and the commands that are allowed in each block are described in the appropriate part of the document. The
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Lab8_AdvancedPAUP - Integrative Biology 200A PRINCIPLES OF...

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