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.

Initial Publication Date: February 20, 2007

In this exercise you will learn to -

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

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!