Tutorial: Investigating SARS-CoV-2 evolution and phylogeny using MNHN-Tree-Tools
The Covid-19 pandemic has caused at more than 3 million deaths by Mai this year. It had a significant impact on the daily life and the global economy. The virus has since its first recorded outbreak in China mutated into new strains. The Nextstrain project has so far been monitoring the evolution of the virus. At the same time we were developing in our lab the MNHN-Tree-Tools toolkit, primarily for the investigation of DNA repeat sequences. We have further extended MNHN-Tree-Tools to guide phylogenetics. As such the toolkit has evolved into a high performance code, allowing for a fast investigation of millions of sequences. Given the context of the pandemic it became evident that we will use our versatile tool to investigate the evolution of SARS-CoV-2 sequences. Our efforts have cumulated in this tutorial that we share with the scientific community.