IgPhyML - B cell phylogenetic inference package

IgPhyML is a program designed to build phylogenetic trees and test evolutionary hypotheses regarding B cell affinity maturation.

The biology of B cell somatic hypermutation (SHM) violates important assumptions in most standard phylogenetic substitution models; further, while most phylogenetics programs are designed to analyze single lineages, B cell repertoires typically contain thousands of lineages. IgPhyML addresses both of these issues by implementing substitution models that correct for the context-sensitive nature of SHM, and combines information from multiple lineages to give more precisely estimated repertoire-wide model parameter estimates.

IgPhyML is integrated into the Immcantation framework, meaning users can easily build and visualize B cell lineage trees and test hypotheses about mutation and selection in B cell repertoires.