Fig. 2.

The unrooted maximum likelihood topology for the SARS-CoV-2 phylogeny of 132 genomes with root probabilities of six rooting methods. Probabilities are shown for branches with probability greater than 0.05 for at least one method. Branch lengths are not to scale. Lineage assignment was performed using the pangolin software. After running the software for assignment, only lineages called for sequences where both “aLRT” and “UFbootstrap” values which quantify the branch support in phylogeny construction are $\ge$80.