Difference between revisions of "Phylogenetics: Searching Lab"

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== Part B: Searching under the parsimony criterion ==
 
== Part B: Searching under the parsimony criterion ==
  
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# '''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. Copy the data from [http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/labs/angio35.nex here] into the (blank) editor window that appears, and save it as angio35.nex
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# '''Create a command file.''' Once again choose File &gt; New from the main menu to create a second blank file, then type in the following text, saving this as run.nex:<pre>#nexus&#10;&#10;begin paup;&#10;  log file=output.txt start replace;&#10;  execute angio35.nex;&#10;end;</pre>
  
 
[[Parsimony Lab|Go back to part a: Using PAUP* to check your answers for homework #2]]
 
[[Parsimony Lab|Go back to part a: Using PAUP* to check your answers for homework #2]]

Revision as of 02:56, 29 January 2007

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

Adiantum.png 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. Copy the data from here into the (blank) editor window that appears, and save it 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;

Go back to part a: Using PAUP* to check your answers for homework #2