Sunday, February 23, 2014

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!
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4 comments:

  1. LindsayMarch 1, 2014 at 1:27 PM

    I was glad to read your comment below and see the result of your efforts. I'm impressed that you continue to work even when your mentor is not available. I look forward to hearing more after you meet with him.

    ReplyDelete
  2. UnknownMarch 3, 2014 at 5:41 PM

    Peggy, I am impressed with your independence and phylogenetic skills! You seem to be making good progress toward your goal of microbe identification.

    Please remember to add a section indicating how your work connects with the larger scope of your project. This will help you focus, and it should allow the rest of us to follow your very technical project.

    ReplyDelete
  3. UnknownMarch 9, 2014 at 4:52 PM

    Peggy, remember to blog every week, even if you miss a visit.

    ReplyDelete
  4. UnknownMarch 20, 2014 at 4:45 AM

    Peggy, you seem to have a two week gap. Please update your blog ASAP, and remember to write posts for missed dates in the future. Also, try to do some online work on days that are canceled.

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