E Treefit


Aim:    To determine the fits of characters on alternative trees.



1. Read the input file 'data.nex' using the unix command 'more'.  Note that
there is a data block and a trees block.  The trees block contains fifteen
trees.  We shall use examine the fits of characters to these trees.

2. Read the data file into paup's memory.  Use the showmatrix command to ensure
that the dataset has been successfully read by the program.

3. Which characters are parsimony uninformative?

4. Determine the parsimony scores for each tree.  You can find the options by
typing the command followed by a question mark.

    paup> pscores ?;
    
*Note that this command has two discrete parts.  Immediately following the
command, you must supply a tree or number of trees, so that paup can return the
figures that are relevant for these trees.  If you want to modify the default
output for the options within the 'pscores' command, you must first use a slash
(/).  In this case, you might issue a command like:

    paup> pscores 1 /total=no;
    
    or
    
    paup> pscores 5 /total=yes;
    
    try these options now.  You can find out the parsimony scores for all trees
using the command:
    
    paup> pscores all;
    

5. Exclude the parsimony-uninformative scores and determine the scores again. 
Why are there differences?

6. Which tree is the most parsimonious?

7. Using the 'pscores' command, find out the character statistics for every
'single' character for tree number 1.

8. Reconstruct the evolution of character 8 on tree number 11.  Draw the answer
in your lab book.  *Note that the reconstruct command also has an unusual
syntax.





Quit the program.






