partis is an HMM-based framework for B- and T-cell receptor sequence annotation, simulation, and clonal family inference. It is built on top of the ham HMM compiler, and uses the ig-sw set of Smith-Waterman annotation tools.
The following two papers describe the annotation and clonal family inference functionality of partis, respectively:
- Ralph, DK, & Matsen IV, FA (2016). Consistency of VDJ Rearrangement and Substitution Parameters Enables Accurate B Cell Receptor Sequence Annotation. PLOS Computational Biology, 12(1), e1004409.
- Ralph, DK, & Matsen IV, FA (2016). Likelihood-based Inference of B-cell Clonal Families. PLOS Computational Biology, 12(10), e1005086.
partis is free software under the GPL v3.