This project explores the genetic diversity and evolutionary relationships among HIV subtypes through a comprehensive analysis using a maximum-likelihood tree, GTR model, and gamma-distributed rate variation. It assesses the formation of monophyletic clades, genetic diversity, and temporal signals to understand the evolutionary dynamics of HIV-1.
Focusing on BEAST analysis, this project compares evolutionary rates, estimates the most recent common ancestor (MRCA) for HIV-1 sequences, and examines subtype clustering and ages. It utilizes a GTR model, relaxed molecular clock, and exponential growth coalescent to provide insights into HIV-1's evolutionary history and subtype diversification.