Fig. 9. Misaligned catalytic residues in RdRp MSAs.

Misalignments of essential catalytic residues were identified using Palmscan. a Ten representative sequences from the Wolf2018 alignment are shown. The top seven sequences place the catalytic glycine (G) in motif B in a different column than the bottom three. Sequence logos for the relevant Palmscan PSSMs are shown above and below the alignment. b Percentages of sequences with at least one catalytic residue misalignment and the total number of residue misalignments for Wolf2018 alignment S3 and the maximum and mean values on the corresponding Muscle5 ensemble. S3 is a subset alignment used by Wolf2018 to estimate the top-level (near-root) branching order of their tree, it contains 238 sequences. The equivalent Muscle5 ensemble has 249 sequences per MSA, selecting different subsets in addition to different alignment parameters to construct replicates. Note that all Muscle5 replicates have substantially fewer errors than S3.