Molecular Phylogenetics with PAUP*

Import the TPI alignment you prepared previously.

• If you never finished your TPI alignment, there is a copy in the Class Data Files folder on the server Flora.

1. To import:
   1. Use FTP to transfer the MSF file from your GCG account to your desktop computer
   2. Launch PAUP*
   3. Use the menu command File -> Import File -> GCG MSF to import the MSF file
   4. Open the editor window and inspect how the MSF file format has been modified to make it a valid NEXUS file.

Execute the file and perform a parsimony search

1. Select File -> Execute <filename>
• To perform analyses with a NEXUS file, PAUP* must first load the data matrix and assumptions into memory in a format it can work with.
• Note the keyboard shortcut: command-R
• If there are any error messages during execution, you have probably modified the file since it was imported as and MSF file. Fix any syntax errors and reexecute the file.
2. Start a parsimony search
   1. Parsimony is the default optimality criterion, so you should see it "checked" on the Analysis menu.
   2. Inspect the settings in the parsimony options dialog box
      1. Select Analysis -> Parsimony Options
      2. Dialog boxes are used to control the behavior of the search
      3. Notice that this dialog box has five sub-screens, which may be stepped through by clicking on the tiny arrow on the upper left side of the dialog box, or selected directly by clicking in the text-box to the right of the double arrows.
      4. Contemplate the settings in this dialog box, but do not change any of the settings.
         • Notice the Defaults button in the lower left corner of the dialog box. If you lose control of what settings you have made, this feature can be used to return the settings to the 'factory' settings.
         • Remember! It is most unwise to change any settings you don't understand.
   3. Perform an exhaustive search
      1. Select the Exhauustive Search dialog box (Analysis -> Exhaustive Search).
      2. Enjoy the options, then press the Search button.
      3. Note how long the search takes to finish
      4. Inspect the tree-length histogram
   4. Inspect the tree found with the exhaustive search
      1. Note the length of the tree.
      2. Select Trees -> Show Trees
   5. Exclude characters that are ambiguously aligned, or for which there are only minimal data available
   6. Select Data -> Include-Exclude Characters
   7. Highlight the characters you wish to exclude, and click on >> Exclude >> to move them to the excluded column.
   8. If you want to re-include some characters, select them in the excluded column and click on the << Include << button.
   9. Close the Include-Exclude dialog box
   10. Select Data -> Show Character Status to review the character status

Compare the Performance of Different Search Techniques

1. Exhaustive
2. Branch and Bound
3. Heuristic
4. Heuristic search with random addtion sequences

Edit the PAUP file to automate tasks

1. Open the editor window for your NEXUS file
2. Create an Assumptions Block, and use this to define a character set
3. Re-execute the file; this will make your character set available in the appropriate dialog boxes
4. Use the Include-Exclude Characters dialog box to select this character set
   1. The pop-up menu at the bottom of the character list to select the character set

BEGIN ASSUMPTIONS;
CHARSET unreliablechars = 1-20 23-28 500-.;
TAXSET mygroup = taxon1 taxon2 taxon3;
ENDBLOCK;

• Make the exclusion of characters automatic by creating a paup block
• If you have defined the charset unreliablechars in the assumptions block as above, and creat a paup block with an exclusion statement as below, then whenever you execute the file, the character set will automatically be excluded.
  

BEGIN PAUP;
EXCLUDE unreliablechars;
ENDBLOCK;