Small Myco bacterium Trees!

January 24, 2014. Last Friday I didn't meet with my mentor because he was out of town. Yet, over the week I was able to successfully run the BEAST on my mentor's website (finally!!). Today we made our first attempt to generate a tree for the small mycobacterium data!

The two main outputs of BEAST are the .log and the .tree files. First we analyzed our data by using a program called Tracer. After I imported the .log file...

One of the most important columns is the effective sample size (ESS) on the left. ESS is the number of independent samples that the trace is equivalent to, and it can help identify autocorrelation in our samples that might result from poor mixing. The ideal is to have the number >200. To do that, I eventually went back to BEAUti and changed the chain length to 5,000,000 with sampling step of 2000 (that increases our sample size in trace to 2500). It is also ideal for our graph to look Normal (this one is pretty good:)).

After confirming that our data converged to a stable posterior distribution, I used TreeAnnotator to summarize the information from a sample of trees (we have 2500) produced by BEAST onto a single “target” tree. The output of TreeAnnotator is a .nex file, which was to be loaded on FigTree program for visualization.

Voila my first tree! Everything looked good except that part in the red. In our data, myco16 and 23 were genetically identical. However, the sampling time of 23 and 30 were closer together, making closer together on the tree. Therefore, we wondered how much does date vs. DNA weighed in Bayesian trees. I went back to BEAUti and excluded myco16 from the taxa so that one sequence only correspond to one sample. The order of the samples on my second tree was good except this time the "time" (in days) was way too large!

I eventually spent the rest of the time going back and forth to see what setting in BEAUti has what effects on my tree. Again, I have generated at least 10 files in this process, including some that failed in BEAST run (I had to go over ALL the steps from BEAUti to FigTree). However, at least we were finally able to get a sense of what our tree would look like:) More trees next week!