IgPhyML – our program for phylogenetic analysis of antibody lineages – has been officially released. It implements a new codon substitution model that accounts for unique features of affinity maturation such as motif-sensitive hot- and cold-spot mutations, nonreversible substitution rates, and descent from a known germline sequence. It also accounts for selective effects by estimating the relative rates of nonsynonymous/synonymous mutations, which can be partitioned to estimate separate effects for FWR and CDR regions.
In the lineages we’ve tested it on, it’s shown a dramatically better fit than the standard codon model for this sort of thing (GY94), even when only adding additional mutability to symmetric WRC/GYW motifs. However, more complex motif models can be specified to include WRC/GYW, WA/TW, and/or SYC/GRS motifs, which can each be modeled as symmetric or asymmetric. It should be usable - and likely preferable to most standard phylogenetic tools - in pretty much any application of phylogenetic tree building to antibody/BCR sequences.
Let me know if you have any questions or need any help using it!
You can download IgPhyML here: https://github.com/kbhoehn/IgPhyML
and find more detail on the model in the manuscript here: