Partis is an HMM-based framework for B- and T-cell receptor sequence annotation, simulation, clonal family, and germline inference. It is built on top of the ham HMM compiler and ig-sw set of Smith-Waterman annotation tools.

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It is described in the following papers:

• HMM framework and BCR annotation Ralph, DK, & Matsen IV, FA (2016). Consistency of [...] Enables Accurate B Cell Receptor Sequence Annotation. PLOS Computational Biology, 12(1), e1004409.
• Clonal family inference Ralph, DK, & Matsen IV, FA (2016). Likelihood-based Inference of B-cell Clonal Families. PLOS Computational Biology, 12(10), e1005086.
• Germline inference Ralph, DK, & Matsen IV, FA (accepted at PLOS Computational Biology) Per-sample immunoglobulin germline inference [...]

Partis is free software under the GPL v3.