Phylogenetics: Searching Lab

This article is part of an EEB course. Please do not edit the content of this page without the approval of the course instructor.

EEB 349: Phylogenetics

Part B: Searching under the parsimony criterion

1. Create the data file. Start PAUP*, press the Cancel button to dismiss the "Open" dialog box that appears, and choose File > New from the main menu. This will open a new, empty text edit window. Click here to see the data, use Ctrl-a to copy all of it, then paste it into the editor window in PAUP*. Save the file as angio35.nex.
2. Create a command file. Once again choose File > New from the main menu to create a second blank file, then type in the following text, saving this as run.nex:

   #nexus
   
   begin paup;
     log file=output.txt start replace;
     execute angio35.nex;
   end;