  B-cell repertoires are characterized by a diverse set of receptors of
distinct specificities generated through two processes of somatic
diversification: V(D)J recombination and somatic hypermutations. B cell clonal
families stem from the same V(D)J recombination event, but differ in their
hypermutations. Clonal families identification is key to understanding B-cell
repertoire function, evolution and dynamics. We present HILARy (High-precision
Inference of Lineages in Antibody Repertoires), an efficient, fast and precise
method to identify clonal families from single- or paired-chain repertoire
sequencing datasets. HILARy combines probabilistic models that capture the
receptor generation and selection statistics with adapted clustering methods to
achieve consistently high inference accuracy. It automatically leverages the
phylogenetic signal of shared mutations in difficult repertoire subsets.
Exploiting the high sensitivity of the method, we find the statistics of
evolutionary properties such as the site frequency spectrum and dN/dS ratio do
not depend on the junction length. We also identify a broad range of selection
pressures spanning two orders of magnitude.
