Fig. 1.

Matrices of incongruence among the core genomic regions of the four CoV genera (A–D) based on the normalized RF method, for unrooted trees (calculated with the TreeCMP server). BioNJ phylogenetic trees were generated with the Poisson model of evolution and 500 bootstrap replicates. In addition, branch lengths <0.02 were collapsed. The orange line above each matrix displays the average Poisson distance among sequences of the same genomic region (calculated with the MegaX software). Blue bars above each matrix display the average RF value for that particular region (against all other regions).