B Cell Receptor Phylogenetics Toolkit

Provides a set of functions for inferring, visualizing, and analyzing B cell phylogenetic trees. Provides methods to 1) reconstruct unmutated ancestral sequences, 2) build B cell phylogenetic trees using multiple methods, 3) visualize trees with metadata at the tips, 4) reconstruct intermediate sequences, 5) detect biased ancestor-descendant relationships among metadata types Workflow examples available at documentation site (see URL). Citations: Hoehn et al (2022) , Hoehn et al (2021) .

Dowser

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?

Documentation and tutorials

Full documentation, including tutorials and vignettes: Dowser ReadTheDocs site

For AI assistants/LLMs and other automated agents: llms.txt is a short curated index of Dowser's documentation, and llms-full.txt concatenates the entire documentation corpus (every vignette and function reference page) into one file.

Citation

If you use Dowser in published research, please cite:

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

Please also run citation("dowser") in R for the complete, feature-specific list — additional citations apply if you used the correlationTest measurable evolution test, built paired heavy/light chain trees, or used IgPhyML for tree building.

Contact

If you need help or have any questions, please contact the Immcantation Group.

If you have discovered a bug or have a feature request, you can open an issue using the issue tracker.

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