Difference between revisions of "Phylogenetics: Parsimony Lab"

Revision as of 14:39, 28 January 2007

Part A: Using PAUP* to check your answers for homework #2

1. Create a NEXUS data file containing the data for the one DNA site you examined for homework assignment #2. To do this, start PAUP*, cancel the opening dialog box (because you have not created a file to open yet), then select File > New from the main menu to create an empty file. Referring to the description of a nexus data block from the previous lab, build a NEXUS file containing 4 taxa and 1 character corresponding to the data in homework assignment #2. Be sure to save the file, giving it a name like homework2.nex.
2. Execute your new data file to make sure there were no mistakes. Even though you are not yet finished setting up the file, it is always a good idea to periodically check to make sure PAUP* can interpret the contents. If you wait too long before doing this check, then you end up making multiple mistakes and it gets increasingly hard to figure out how to fix all of them! If it is still open, you can execute it in PAUP* using the key combination <Ctrl-r>. If it is not open, use File > Open... to open it again. If your file executes successfully, you should see a line such as the following:

   Processing of file "homework2.nex" completed.

3. Add a stepmatrix definition to specify that transitions should cost 1 step while transvesions should cost 2 steps. Add an assumptions block to your data file (note: do not add another "#nexus" to your file, this should appear only as the first thing in a NEXUS file). Your assumptions block should look like this:

   begin assumptions;
    usertype my_ctype stepmatrix=4
        A C G T
    [A] . 2 1 2
    [C] 2 . 2 1
    [G] 1 2 . 2
    [T] 2 1 2 .
    ;
   end;

   Feel free to replace "my_ctype" with a name of your choosing (but avoid using spaces or punctuation; note that I used an underscore character instead of a space). Save your file (using <Ctrl-s> is easiest), then re-execute using <Ctrl-r> to ensure that you haven't made any mistakes.
4. Apply the newly-defined stepmatrix to character 1.First use the PAUP* cstatus command to examine the current status of your single character:

   cstatus full

   The full keyword produces a list showing information about each character individually. What is the current type of character? Which variant of parsimony would you be using were you to perform an analysis at this point (Wagner, Fitch, Transversion, or Generalized)? Use the PAUP* ctype command to apply your new usertype to character 1 as follows:

   ctype my_ctype: 1;

   PAUP* will not respond with any confirmation, but check to make sure that your stepmatrix has been applied to character 1 using the cstatus command again. Note that this time PAUP* says

   All characters are of user-defined type "my ctype"

   You may be wondering where the underscore character went: when producing output, PAUP* converts underscore characters to spaces in taxon, tree, character, and usertype names.