Triplet alignments may shift indels and cause misaligned residues. (a) At posterior probability > 0.99 the traditional sequential model supports 4 internal branches. (b) When indel information is included, the number of supported branches increases to 6. Branches colored green are supported only when indel information is incorporated. Each blue cross denotes an indel event occurring on a particular branch. Prefixes on sequence names indicate elapsed time in weeks between the initial infection and when the sequences were obtained.