University of Arizona, Department of Computer Science

CSc 120: Prettyprinting Phylogenetic Trees

The __str__() method specified for phylogenetic trees does not always make their structure easy to understand. If you want, you can use this code to print your tree in a more visually appealing manner. Download this code into the same directory as the rest of your code, import using

from prettyprint import *

and call the pretty-printing routine as pretty_print(tree) where tree is your tree. However, note that:

This is not part of the expected output for this problem, and is provided solely for your entertainment. If you use this code, make sure you turn off the pretty-printing before you submit your code.
This code is not thouroughly tested. If you choose to try and use it, we hope it works for you, but there are no guarantees.

Example: The str() representation of the phylogenetic tree obtained from the data file SARS.fasta (12 strains of the human SARS virus), with N-gram size = 6, is

((((KF514413.1, KF514423.1), (KF514415.1, KF514418.1)), ((KF514419.1, KF514422.1), KF514421.1)), (((KF514414.1, KF514416.1), KF514420.1), (KF514412.1, KF514417.1)))

The prettyprinting code mentioned above displays this tree as follows:

                    +--- KF514413.1
               +---|
              |     +--- KF514423.1
          +---|
         |    |     +--- KF514415.1
         |     +---|
     +---|          +--- KF514418.1
    |    |
    |    |          +--- KF514419.1
    |    |     +---|
    |     +---|     +--- KF514422.1
+---|         |
    |          +--- KF514421.1
    |
    |               +--- KF514414.1
    |          +---|
    |     +---|     +--- KF514416.1
    |    |    |
     +---|     +--- KF514420.1
         |
         |     +--- KF514412.1
          +---|
               +--- KF514417.1