Hoehn KB, Lunter G, Pybus OG (2017) A phylogenetic codon substitution model for antibody lineages. Genetics 206:417-27

Author: Kenneth Hoehn

Source code & manual:  https://github.com/kbhoehn/IgPhyML


IgPhyML is a program for the phylogenetic analysis of B cell receptor (immunoglobulin) sequences, using a maximum likelihood framework. The program implements a new codon substitution model (HLP17) that represents important aspects of the molecular evolution of immunoglobulin sequences during affinity maturation, such as context-dependent mutation hotspots, non-reversible codon change, and descent from a known germline sequence. The HLP17 model also estimates nonsynonymous/synonymous rate ratios and transition/transversion bias.

When applied to long-lived antibody lineages the HLP17 model provides a much  better model fit compared to standard models such as GY94. It can also perform parameter estimation and phylogenetic topology heuristic searches.

IgPhyML was modified from the source code for codonPhyML, which itself was derived from PhyML.