Thanks for pointing that out, Mike. Indeed I didn’t specify what I meant by sequence distance.
Yes, distances could be Hamming for sequences of equal length, or one could use the Levenshtein distance for ones that are not. Another perspective will come from a distance that is BCR specific, such as the HLP17 model or something else that takes hotspots into account.
I agree with you about the excellent work from Murugan & co, though note in passing that partis builds analogous HMM models.