18 Samples + ATCC Reference Strain

I didn't meet with my mentor last week because I was on a college visit. Nonetheless, the week before (April 11th, 2014), I had attempted to make several BEAST tress with 6 different BEAUti settings (no time included). I would totally include some visualizations since I've got some cool pictures except that my laptop decided to crash down and all the memory is lost (All the data run is probably too demanding for the computer oops). So, I will try to explain what I did in words.. please refer to my previous posts if needed!

I mainly focused on the effect of clock model and site model on the tree. Although I didn't actually look at the output tree visualization, I examine my the goodness of my output data on Tracer (see my previous posts). Out of 6, only one looked decent (approx. Normal), with the setting of Strict Clock Model and the GTR site model. So, I went on including the time of the samples in BEAUti and ran it in BEAST, yet the resulting tree didn't look so good..

However, my mentor gave me a new input file where our previous reference strain MAV104 was substituted by ATCC strain because MAV104, which was isolated from an AID patient was too distant from our M.avium samples, and that ATCC was originated in birds as well. Therefore, I ran the new data on BEAST (time included) as well as on GARLI and RAxML, where the trees were made based exclusively on the sequences. Something promising happened! The BEAST tree looks almost exactly like the RAxML tree with a little variations, which is reasonable since BEAST builds a tree based on both sequences and time. I will go ahead and analyze the GARLI tree to see if I get the resemblance.

In the meantime, I am starting to work on my final poster! Whoo the time has gone by so quick! I just got my new emergency laptop and am trying to reinstall many software. Thankfully that I ran most of my data online so I can still download them to my computer. The thing that will take a while is the actual pictures of the trees, in which I will try to rebuild them these days.

Finally, since there is no visualization in this post, I would like to share a picture from my college visit at LA! This is me standing next to my future school mascot - the Bruin! Can you guess where will I be spending my next 4 years at? Yes - UCLA!!!! I am so glad that the application process is finally over and I can't wait for my college life!!!