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Tree-thinking Session

Tree-thinking

Understanding the Role of an Evolutionary Perspective in Bioinformatics

In this set of activities you will have the chance to explore your own understanding of phylogenetic trees and their role in comparative analysis. The linked materials below will help you review the material we cover during the workshop and provide extended learning opportunties.

treeTree-thinking Paper

hillistreeHillis Tree of Life


whippoWhippo Problem Space

What! You haven’t ever seen a Whippo? What about a Whammel? Well, how do you think that whales evolved? Which mammals do you think are their closest living relatives?

http://bioquest.org/bedrock/problem_spaces/whippo/

1pdy_lobster1Evolution of Enolase

This problem space introduces basic skills in phylogenetic tree construction and protein structure exploration. We will learn to search databases for protein structures, explore them in your favorite structure viewer, and propose questions that may be answered using these tools.

http://bioquest.org/bedrock/problem_spaces/enolase/background.php

The Consurf Server

This site, enables the identification of functionally important regions on the surface of the protein or domain, of known three-dimensional protein structures.

See: Consurf Activity

http://consurf.tau.ac.il/

 

Papers on the role of evolution across biology

Baum, Smith & Donovan (2005).  Evolution:
The Tree-Thinking Challenge. 310 (5750): 979. [link to article]

Bull & Wichman (2001). Applied Evolution. Annual Review of Ecology and Systematics. 32: 183-217. [link to article]