Difference between revisions of "Phylogenetics: Searching Lab"

Revision as of 03:04, 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.

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.
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;
```

@@ Line 4: / Line 4: @@
 == Part B: Searching under the parsimony criterion ==
-# '''Create the data file.''' Start PAUP*, press the Cancel button to dismiss the "Open" dialog box that appears, and choose File &gt; 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
+# '''Create the data file.''' Start PAUP*, press the Cancel button to dismiss the "Open" dialog box that appears, and choose File &gt; New from the main menu. This will open a new, empty text edit window. Click [http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/labs/angio35.nex 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.
 # '''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]]