Week 10 was a wrap up week. I was able to have my final meeting with my mentor Dr.Liu who gave me props on the research I have done this summer. We discussed future plans and what did I learn this summer. I was able to plan and structure how I wanted to write my final report for the first few days, as well as do a little more research. The last few days I spent writing my report and discussing all that I have learned throughout the summer.

Week 9 I continued to run simulations on non ultrametirc birth death trees. I was able to meet with my mentor to get a better understanding of the final project. We spoke and analyzed the sample data and connected it to the real world. I was also able to read about the robison-foulds distance for comparing two phylogenetic trees. This gave me another perspective with the research.

Week 8 I continued on with FastTree by keeping up with my readings as well as asking Julia for help. The readings helped guide me throughout the simulations as well as looking at sample data to help compare. This was a struggle for me which is why continued to read about FastTree’s and look at examples so that I could become more comfortable with this aspect of the project.

layout: post title: Week 7 — Week 7 I continued on with the simulation of the birth-death tree. I was able to follow Dr.Liu’s instructions again with using the simulated DNA sequence alignment from previous steps to run a FastTree that would estimate a maximum likelihood gene tree under the Jukes-Cantor model. I was not very familiar with any of this so I was able to look at the FastTree documemtation sent by Dr.Liu. Looking at this did help me. On the documentation it tells you what exactly a fast tree is and how it is used. There were even example simulations on FastTree’s. This was very helpful for me to continue on with my simulation.

Week 6 I was able to continue on with the tutorials, I started by using the random tree provided by Dr.Liu to run and perform a single simulation under the multi species coalescent model. Dr.liu was able to send me hints that would help guide me throughout the simulation. The hints did help but I was able to gain more hands on help by contacting the grad student Julia to see if she could run through the simulation with me. Julia has been a big help in keeping me inlvoved and making me feel comfortable enough to keep asking questions. I find that when I ask questions everything makes more sense.

Week 5 I believe i will be able to start to generate the non ultrametric birthdate tree. The grad student Julia was able to guide me through a tutorial where we both worked together. Julia was able to break down the terminology for me as well as explain what I should be doing exactly. We went through the script and she was able to tell me everything that was needed to continue the project.

Week 4, I started my hands on tutorials with my mentor and grad student mentor. As of now I am using a software called “indelible” to generate a non-ultrametric birth-date tree. This is all very new to me which led me to do even more research on what this software is and how to use it. I looked up the terminology so that I can become more familiar along the way. This week I mostly watched videos and read up on how to generate these brith death trees to become more comfortable.

Week 3, I believe i will be able to complete all of my readings as well as take notes on what I have learned. I am excited to move on in our research and see whats new for us. Gene phylogenetics and gene genealogies is new for me but I am interested in computational biology as well so this should be fun for me. I got to speak with my mentor about our next steps so that I can prepare, the next steps for us is for me to start a few tutorials to get a hands on experience with our research, then we will move on to something even more involved. Each week I feel myself growing and learning as we move on, I am already learning with my readings that I have been assigned.

Week 2, I continue to work on my readings that my mentor sent out to me. My mentor wants me to really read and undestand the research before we move on. I also got to meet with our graduate research student. We talked and got to know each other better, she made me feel more comfortable that I can also go to her for help as well, she also stated how we can both go through the readings together to gain a better understanding. This week was very interesting as I got to continue with the readings and was able to chat with the grad student. I believe it will take me a little more time to compelete the readings so that I know I have a good understanding of our project this summer.

Week 1, me my mentor discussed plans on how our research would go. We decided on a time to meet as well as decided what research path we wanted to take. We spoke over zoom and got to know each other a little better. My mentor was able to give me our graduate research mentor information so that I could stay in touch with her when I need additional help. Me and my mentor also talked about my plans for the future and how this research could help me prepare for graduate school. After we spoke and got to know each other better, my mentor gave me a schedule of what I should do over the next week or so. He sent my readings to read over to help me understand our project which will be mainly about gene genealogies and computational phylogenetics.