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Dowser
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Dowser is part of the [Immcantation](https://immcantation.readthedocs.io) 
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?](https://en.wikipedia.org/wiki/Dowsing)


Documentation and tutorials
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Full documentation, including tutorials and vignettes: [Dowser ReadTheDocs site](https://dowser.readthedocs.io)

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

Citation
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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
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If you need help or have any questions, please contact the [Immcantation Group](mailto:immcantation@googlegroups.com).

If you have discovered a bug or have a feature request, you can open an issue using the [issue tracker](https://github.com/immcantation/dowser/issues).

To receive alerts about Immcantation releases, news, events, and tutorials, join the [Immcantation News](https://groups.google.com/g/immcantation-news) Google Group. [Membership settings](https://groups.google.com/g/immcantation-news/membership) can be adjusted to change the frequency of email updates.

