Fig. 1: Maximum likelihood phylogenetic trees showing sequences of representative members of the family Coronaviridae (circular tree) and all representative members of the Sarbecovirus subgenera (rectangular tree).
From: Beyond COVID-19: the promise of next-generation coronavirus vaccines
Full-length genomes were obtained from GenBank (https://www.ncbi.nlm.nih.gov/genbank/), and alignments were built with MAFFT (FFT-NS-1 algorithm181. Maximum likelihood phylogenetic tree was constructed using IG-TREE2182 with the best model for distance estimates identified with the ModelFinder function183 as the one with the lowest Bayesian information criterion (BIC). Branch support was assessed using both ultrafast bootstrap approximation (ufBoot, 1000 replicates)184 and SH-like approximate likelihood ratio test (SH-aLRT). The tree was visualized in FigTree (http://tree.bio.ed.ac.uk/software/figtree/), and midpoint rooted for purposes of clarity. Only bootstrap values greater than 70% are shown. Bars indicate nucleotide substitutions per site.
