The protocol of classification of a massive number of viral genomes and estimation of time of most recent common ancestor (tMRCA) of SARS-CoV-2 using phylodynamic analsysis
Genome classification played a critical role in tracing the origin of pathogenic viruses, however, genome classification based on amino acid mutation did not rule out recombination and reverse mutations. In this protocol, we provide detailed methods to filter and classified the massive number of viral genomes by custom scripts, and estimate tMRCA of genome subpools.