This is the instruction guide for using the new, repertoire-wide version of IgPhyML.

The most up-to-date description of IgPhyML can be found here:

Hoehn, KB, Vander Heiden, JA, Zhou JQ, Lunter, G, Pybus, OG, & Kleinstein SH. Repertoire-wide phylogenetic models of B cell molecular evolution reveal evolutionary signatures of aging and vaccination. Proceedings of the National Academy of Sciences, 116(45), 22664-22672. doi: https://doi.org/10.1073/pnas.1906020116

and here:

Hoehn, KB, Lunter, G, & Pybus, OG. A phylogenetic codon substitution model for antibody lineages. Genetics, 206(1), 417-427. doi: http://dx.doi.org/10.1534/genetics.116.196303