Phylogenetic Trees

This week, I started learning phylogenetic analysis, which biologists use to understand evolutionary and molecular relationships. Dr. Miller gave me a book called "Phylogenetic Trees Made Easy," and I completed the first tutorial in it, which outlined the steps for creating a simple phylogenetic tree.

To make the tree, I first had to download a program called MEGA 5, which analyzes and aligns sequences from related organisms. Specifically, I looked at a sequence from the bacterium Thermotoga petrophila. I used a "search engine" called BLAST to help me find sequences that produced similar alignments to the original sequence. I chose the 6 most closely related sequences, and then used the program to produce a DNA alignment:

The final step, which was to construct a phylogenetic tree based on the alignment, was actually pretty simple. All I did was click on a button labelled "Neighbor Joining Tree," and the program created a phylogenetic tree for me! Getting the alignments was the hard part, because it's so easy to make simple mistakes, which can mess up the whole alignment. It took Dr. Miller and me several tries to get it right. 

Phylogenetic tree!