An HMM-based framework for B-cell receptor sequence annotation, simulation, and clonal family inference. partis is especially effective for modern large sequencing data sets because it can infer detailed parameters concerning the rearrangement process, and then perform annotation inference on each sequence in the set. It is built on top of the ham Hiden Markov Model (HMM) compiler, and also uses the ig-sw set of Smith-Waterman annotation tools.
