Phylogeny of early (2016–2018) influenza H3N2 HA sequences plotted by nucleotide substitutions per site on the x-axis (top) and low-dimensional embeddings of the same HA sequences concatenated with matching NA sequences by PCA (middle left), MDS (middle right), t-SNE (bottom left), and UMAP (bottom right). Tips in the tree and embeddings are colored by their TreeKnit Maximally Compatible Clades (MCCs) label which represents putative HA/NA reassortment groups. Tips from MCCs with fewer than 10 sequences are colored as ‘unassigned’. The first normalized VI values per embedding reflect the distance between HA/NA clusters and known genetic groups (MCCs). VI values in parentheses reflect the distance between HA-only clusters and known genetic groups. MCC labels appear in the tree and each embedding for larger pairs of reassortment events. MCC 9 represents two Nextstrain clades, so its labels appear twice in the tree. MCCs 14 and 11 represent a previously published reassortment event within Nextstrain clade A2 (Potter et al., 2019). Labels for MCC 14 represent the subset of its sequences from clade A2.