Dowser is part of the Immcantation analysis framework for Adaptive Immune Receptor Repertoire sequencing (AIRR-seq). Dowser provides a set of tools for performing phylogenetic analysis on B cell receptor repertoires. It supports building and visualizing trees using multiple methods, and implements statistical tests for discrete trait analysis of B cell migration, differentiation, and isotype switching.

Dowser has 6 primary functions:

  1. Reconstruct clonal germline sequences.
  2. Build B cell lineage trees using multiple methods, such as maximum parsimony, maximum likelihood, and IgPhyML.
  3. Reconstruct intermediate sequences within lineage trees using different methods.
  4. Create publication-quality lineage tree plots.
  5. Analyze trees to detect ongoing B cell evolution over time.
  6. Understand B cell migration and differentiation.

What’s a dowser?


For help and questions please contact the Immcantation Group or use the issue tracker.


Depends: ggplot2
Imports: alakazam, ape, Biostrings, dplyr, ggtree, graphics, gridExtra, markdown, methods, phangorn, phylotate, RColorBrewer, rlang, shazam, stats, stringr, tidyselect, tidyr, utils
Suggests: knitr, rmarkdown, testthat


Kenneth Hoehn (aut, cre)
Cole Jensen (ctb)
Susanna Marquez (ctb)
Jason Vander Heiden (ctb)
Steven Kleinstein (aut, cph)


To cite the dowser package in publications, please use

Hoehn K, Pybus O, Kleinstein S (2022). “Phylogenetic analysis of migration, differentiation, and class switching in B cells.” PLoS Computational Biology. doi:10.1371/journal.pcbi.1009885,

If you use the correlationTest function for measurable evolution, please also cite

Hoehn K, Turner J, Miller F, Jiang R, Ellebedy A, Pybus O, Kleinstein S (2021). “Human B cell lineages associated with germinal centers following influenza vaccination are measurably evolving.” eLife. doi:10.7554/eLife.70873,

If you additionally use IgPhyML for building trees please also cite

Hoehn K, Van der Heiden J, Zhou J, Lunter G, Pybus O, Kleinstein S (2019). “Repertoire-wide phylogenetic models of B cell molecular evolution reveal evolutionary signatures of aging and vaccination.” PNAS. doi:10.1073/pnas.1906020116,