I used the following application softwares throughout my project to do multiple tasks:

1. Jupyter Notebook: to build my subdata sets https://github.com/ebaberga/yellow-fever/blob/gh-pages/Ipython/Yellow-fever.ipynb
2. Geneious: to do my alignments using MAFT and draw a phylogenetic tree using RAFT of the sequences I filtered out using Jupyter Notebook (The first time I did it ).
3. Command line: to make my alignments for the 3rd time, and install most of the softwares I used so far.
4. Figtree: to graphically view my phylogenetic tree and publish ready figure.
5. Beauti: a companion program in Beast that generate XML file inorder to make the file readable by Beast.
6. Beast: to infer evolutionary dynamics from sequence data.

Why is these so important to me: I have a dream of pursuing a Computer Engineering degree in the near future. Using this software will broaden my understanding of computers in general, and make me a competitive college applicant.

My final tree:

The following phylogenetic tree demonstrates the variation of hosts in East Africa, West Africa, and South America(Brazil and Venezuela):

Things I understood from my Phylogenetic tree:

• Most of the mosquito hosts are found in African counties, while most human hosts are found in Brazil.
• The virus tends to stay in a single type of host for a long time, it doesn't jump around other hosts often.
• According to my data most of the hosts are mosquitos. So mosquitos could be more compatible with the viruses function.
• The tree demonstrate that it is possible for Yellow Fever virus to jump from one species to another.

Figures and Hypothesis