Protein and amino-acid similarity comparison between HRV-A, HRV-B and HEV. A) Schematic representation of HEV and HRV genome organization showing boundaries of encoded proteins. B) Protein similarity comparison. For each protein, the following is shown: – top row: a simplified tree representation of the relationships between HRV-A (A), HRV-B (B) and HEV (E), according to the corresponding ML tree (see additional file 1). Three cases are possible: HRV-B closer to HRV-A; HRV-B closer to HEV; and undecided (none of the above clearly more likely than the other). – bottom row: an all-versus-all sequence identity matrix (darker colorus indicate higher identity percentage). The similarity values are given in additional file 2. C) Close-up of the identity matrix for VP1. D) Bootscanning. The whole polyprotein alignment was divided into windows of 200 aa starting every 50 aa, and a 100-bootstrap ML tree was computed on each window. The black curve indicates the degree of support (as a percentage of bootstrap replicates) for either the "HRV-B closer to HRV-A" (upper half) or "HRV-B closer to HEV" (lower half) topology at each position along the whole genome (see Methods for details). The background colour reflects the log likelihood of the tree at each position which is a measure of overall confidence in the tree. Darker colour indicates higher confidence.