Extended Data Fig. 3: Benchmarking with sequence-based homology searches.

a, RdRp phylogeny, as in Fig. 2a. b, Heatmap comparison of homology detection using Foldseek (as in Fig. 2), DIAMOND and InterProScan for the stated reference proteins. DIAMOND results represent a pure sequence-based recapitulation of the Foldseek search (i.e., all query and reference structures used in Foldseek were represented by their cognate protein sequences for DIAMOND analysis). Foldseek and DIAMOND data are log e-values and are colour-coded as in the key. InterProScan results provide a simple binary score: match (red) or no match (white). Vertical lines demark divisions between major clades.