Supplementary Data Tables Table S1: Virus characteristics including abbreviation, family, order, tax id, sequence length threshold (for nearly complete genomes), vaccination status, mode of transmission, circulation (human or human/zoonotic), available treatment, and disease progression (acute or chronic). Table S2: Sequence IDs of outgroup constituents. Table S3: GISAID acknowledgements for the SARS-CoV-2 sequences used in this study. Table S4: Summary of manual sequence curation indicating lab- or vaccine-related keywords used to prune sequences. Table S5: Sequence IDs for EVA and H3N2 e10, e100, d10, and d100 subtrees. Table S6: Sequence IDs for ML and GL lineages. Table S7: Sequence IDs for the H3N2 ���new��� and ���old��� subtrees. Table S8: Mutation rates (in units of nucleotide substitutions per site per year) and estimated dates for the last common ancestor of all tree/subtrees. Negative dates represent years prior to 0 CE. Table S9: Mean dN/dS values. Table S10: Yearly viral cases and generation time estimations (with references). Table S11: Metadata including the sequence ID, host, date of isolation, location of isolation, and subtype. Table S12: Overview of key parameters including number of GLs N, Ne, and MRCA for each virus species as well as the mean over all species. Directories Alignments ORFeome alignments (excluding stop codons) with the exception of SARS-CoV-2. Correlated Subtrees Subtrees representing all correlated-clades (genealogical lineages; GL) in Newick format. Diversity TMRCA and Skyline Plots .png files. e/d/n/o Subtrees EVA and H3N2 subtrees, evenly and diversely sampled as well as ���early��� and ���late��� subtrees for H3N2. Genealogical Trees Including global topologies (.main), subtrees, and grafted trees (.grafted). Maximally Diverse Subtrees: Genealogical trees sampled to contain the same number of leaves as each respective tree in the Simulated Trees directory. ORF References The first and last nucleotide of each ORF in the reference sequence. Redundancy Tables List of all redundant isolates and the corresponding representative in the ORFeome-unique alignment. Reference Sequences Genbank page for all reference sequences. Rooted Trees Global topologies for each virus. Simulated Trees: Neutral models, based on Yule-Harding, for each virus. Ultrametric Trees For each global topology. Ultrametric Trees For each global topology.