Matthew K. Oki Individual Journal 4

Methods & Results

1. The formal methods were followed from Activity 2 of the Exploring HIV Evolution

Activity 2, Part 1

1. Download the provided sequences of subjects 10-15 from BIOL368/F16:Week 4
   • Upload these sequences into the Biology Workbench
2. Run the multiple sequence alignment for the selected subjects and clones
   • The subjects & clones below were used:
   • The output results in the following uprooted tree:

Activity 2, Part 2

1. Three individual subjects were run through multiple sequence alignment
   • Each nucleotide difference (S) was denoted by the absence of a star as shown below:
2. Theta was then calculated
   • Theta is an estimate of the average pairwise genetic distance
   • The equation from is given below

1. Min and Max difference were calculated

Scientific Conclusion

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