Phylogenetic Analysis of SARS-CoV-2 Spike Gene Variants
Overview: This project performs a phylogenetic analysis of the spike gene from SARS-CoV-2 and a related virus. The goal is to investigate evolutionary relationships among different variants such as Wuhan, Alpha, Delta, and Omicron, with bat coronavirus used as outgroup.
Workflow:
Sequence Download: Spike gene sequences were retrieved from NCBI.
Sequence Alignment: FASTA sequences were aligned using AliView to identify homologous regions.
Model Selection: The best evolutionary model was determined using jModelTest.
Phylogenetic Tree Construction: The phylogenetic tree was inferred using Bayesian analysis in MrBayes.
Tree Visualization and Analysis: The resulting tree was visualized and analyzed in FigTree.
This analysis is based on a workshop I attended, which guided the workflow and tools used.