More Trees with GARLI and RAxML

Last Friday (February 21, 2014), I didn't meet with my mentor because he was out of town. Nonetheless, I continued making trees with GARLI (using the right one this time) and RAxML.

GARLI_1

The numbers on the branches are the bootstrap result. In this trial, I set a bootstrap repetition of 50. Basically, the bigger the number is, the greater support we have for that particular branch, with the greatest number of 50. Though overall the tree looks pretty decent, notice that in this tree we have only little support for myc 1,2,5,23,16, and 30.

Next, I moved on to run the samples with RAxML. The branch lengths varied significantly and I am still understanding the implication of it. The maximum bootstrap number is 100. While most of them were pretty big, the numbers for were still very small (splitto the extreme). This lack of support was due to the same sequences. myc01 is identical to myc02 where as myc16 is identical to myc23. 

Therefore, the next thing I did was to run both GARLI and RAxML again with identical sequences eliminated so that they wouldn't confuse the program.

GARLI_3 with identical samples eliminated.

RAxML_2 with identical samples eliminated.

This time the resulting trees all had branches with very high bootstrap numbers, suggesting that our trees were very strong. 

The next thing I am going to do it is to run the samples with MrBayes and compare the result topologies. I am finally meeting with my mentor this coming Friday, and hopefully we'll discuss more about the results!

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!

A Week Off

Last week I didn't meet with my mentor because I was under the weather:( We will try to catch up our work this Friday. However, it was also the Chinese New Year, so Happy Year of Horse everyone!!

Retrieved from http://eastweek.my-magazine.me/?aid=30771