partis is an HMM-based framework for B-cell receptor sequence annotation, simulation, and clonal family inference. It is built on top of the ham HMM compiler, and also uses the ighutil 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. In press, PLOS Computational Biology.
partis is free software under the GPL v3.