Multiple sequence alignments and phylogenetic trees for AFI study Emma Thomson and Shirin Ashraf 30/12/2024 Multiple sequence alignments were generated using MAFFT v7.487 with local alignment and 1000 iterations. Maximum-likelihood phylogenetic analysis was carried out for viruses with at least 10 percent genome coverage using IQ-TREE multicore version 1.6.12 and with 1000 ultra-fast bootstrap replicates using relevant reference sequences. Substitution models mentioned in figure legends were best fit models as reported by IQ-TREE. Uncorrected pairwise-distances were estimated using MEGA 10.0. Sequence read data is available under Bioproject PRJNA1143542.