Your learning objective is to develop an understanding of cladistics and phylogeny, to recognize the types of data which can reveal evolutionary relationships, and to gain hands on experience with tools scientists use to infer relationships between organisms using sequencing data. You will begin by investigating characteristics which might be used to develop a cladogram, select a virus of interest and obtain sequences using the National Institute of Health's "Virus Variation Resource," then analyze sequences using authentic tools.
- Virus Variation Resource (https://www.ncbi.nlm.nih.gov/genome/viruses/variation/) : Allows researchers to easily locate DNA or protein sequences of interest for a variety of viruses. Sequences can be located by host organism, data of sample collection, geographic location, or other criteria of interest.
- SeaView: Alignment tool to prepare sequences for comparison by matching like regions in multiple sequences. Results may be exported in a format useful for building phylogenic trees.
- Fig Tree: Software to develop phylogenic trees using aligned sequences. Users may apply color to highlight relationships between samples and identify patterns based on sample characteristics in the resulting trees.
You will generate a phylogenic tree including at least 20 samples. You will color code your tree according to characteristics of your choosing, to highlight relationships in your data. Finally, you will report on your findings in a one page executive summary.