This project contains partial (not all) scripts used to generate results presented in my masters thesis. For context, the gp120 protein is found on the surface of HIV and is responsible for letting HIV enter and infect our own bodily cells. This pipeline was used to take in roughly ~25,000 HIV genetic sequences, process them, use MCMC / Bayesian inference to reconstruct evolutionary history (a phylogenetic tree), and model the rates of indel mutations (Hamiltonian Monte Carlo; RStan; hierarchical modelling).