Three Dimensional Phylogenetic Relationships:

How changes in dimensional representation can influence visual relationships.


Created by George Rice, Montana State University and Gretchen A. Koch, Goucher College.


Three dimensional representation of box's in space.
Box's in 3-D created in PowerPoint by co-author Gretchen A. Koch.

In this exercise you will learn to -
  1. Use the SDSC Biology WorkBench to find a protein of interest and compare it with other related proteins.
  2. Construct a phylogenetic tree with ClustalW in Biology WorkBench that shows the relationships of the proteins in 2-D space.
  3. Transform a distance matrix created in CLUSTALW into a 3-D phylogenetic tree.
  4. Compare the 2-D and 3-D trees and think about the spatial relationships.


Exercise Overview -


  • Create an account in Biology WorkkkBench
  • Start a new session with "Protein Tools"
  • Select a data set (10 proteins that are of interest to you)
  • Create a phylogenetic tree with CLUSTALW
  • Transform your tree into a distance matrix
  • Export that matrix into MATLAB
  • Run special" whiz bang" program created by Gretchen that transforms the matrix into 3-D spatial relationships.
  • Compare the 2-D CLUSTALW tree to the 3-D graphed relationships of selected points on that tree.
  • Generally become a lot smarter and consequently better person!

Exercise Bifurcation -


  • Produce Your Own Data and perform all of the manipulations individually.
  • Use Pre-Packaged Data for an exercise overview.