If you have questions you can email the Immcantation Group.

If you’ve discovered a bug or have a feature request, you can create an issue on Bitbucket using the Issue Tracker.


To cite IgPhyML in publications please use:

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:

Hoehn, KB, Lunter, G, & Pybus, OG. A phylogenetic codon substitution model for antibody lineages. Genetics, 206(1), 417-427. doi:


IgPhyML is build using the source code of codonPhyML:

Gil, M, Zanetti, MS, Zoller, S, Anisimova, M. CodonPhyML: fast maximum likelihood phylogeny estimation under codon substitution models Mol Biol Evol. 2013 Jun;30(6):1270-80. doi: 10.1093/molbev/mst034

which is based off of PhyML:

Guindon, S, Delsuc F, Dufayard JF, Gascuel, O Estimating maximum likelihood phylogenies with PhyML Methods Mol Biol. 2009;537:113-37. doi: 10.1007/978-1-59745-251-9_6

The HLP17 and HLP19 models are based off of the GY94 model:

Nielsen R, Yang, Z Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics. 1998 Mar;148(3):929-36


This work is licensed under the GNU General Public License, verion 2 (GNU GLP v2.0).