More Phylo Talks!

Last Friday (November 1st, 2013), My mentor and I discussed more about the bootstrapping methods in terms of how it work. He gave me a paper, in which I will be reading this week. We also talked about the derivation of the Jukes Cantor model, which is the simplest evolutionary model used to predict the rate at which nucleotide substitutions occur during evolution. It has two main assumptions:

• Equal frequencies of the four bases
• The probability of changing from one state to a different state is always equal, i.e. A-->G is as likely to happen as G-->C

Q Matrix of Jukes Cantor Model

f(t) represents the mutation rate, which is equal for all if a nucleotide is substituted with a different nucleotide. The probability of changing from A to A is 1- f(t) since the sum of the probabilities should add to 1.

However, there are many modifications for this model later published, including Felenstein 81 (F81), Kimura 2-parameter (K2P), HKY85, TN93, GTR, etc.

While we are still waiting for the bird data for my project, Dr, Miller sent me a practice data, and he would like me to explore his website on my own first (http://www.phylo.org/). So I looked at the demo, uploaded the data, and let the data run by accepting the default setting. I found the website pretty user-friendly, yet I don't really know what those result means. Hopefully I will learn more about what I can get from these results this Friday.