Dowser
R package for B cell receptor phylogenetic analysis. Implements statistical tests for discrete trait analysis of B cell migration, differentiation, and isotype switching, as well as more recent tests developed to detect ongoing evolution in B cell lineages.
IgPhyML
https://igphyml.readthedocs.io
Phylogenetic analysis program designed for analyzing B cell receptor sequence data. Implements phylogenetic models capable of accounting for features of affinity maturation such as context dependent hotspot mutations and nonreversible sequence evolution.