Examining Different Trees Using Different Programs

Last Friday (February 14, 2014), my mentor wasn't able to come because his flight was cancelled due to the snow storm. However, we did chat through Skype and accomplished some work via email. In continuing our tree making, after reading several publications, we decided to run the larger data (26 samples) at once so it might be more accurate. Wayne, one of the zoo people, sent us an updated genomic sequence of the samples this time with more identified SNPs. We also want to examine the overall topology before taking time into consideration, so that we can first get a sense of how our tree would look like. Thus, we decide to look at different tree visualization tools and software for describing the difference between any two phylogenetic trees.

The programs I will be exploring in addition to BEAST are RAxML, GARLI, and MrBayes. I ran GARLI first, and did it on my mentor's website CIPRES. The whole process took a while and was quite complicated to describe it here. Basically our goal was to find a way to get a majority rule consensus tree form GARLI output. I later found out that I chose the wrong tool to run my data (there were several GARLI choices), but I still went ahead and analyze the data. I converted the output to nexus file so it can be read on Archaeopterix, a powerful tree visualization tool that supports many file formats. My final tree look like this:

I won't know how good was this tree until I make more with other tools so that I can compare them. I will also run GARLI again, using the right tool this time!