Description
B Cell Receptor Phylogenetics Toolkit.
Description
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) <doi:10.1371/journal.pcbi.1009885>, Hoehn et al (2021) <doi:10.1101/2021.01.06.425648>.
README.md
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:
- Reconstruct clonal germline sequences.
- Build B cell lineage trees using multiple methods, such as maximum parsimony, maximum likelihood, and IgPhyML.
- Reconstruct intermediate sequences within lineage trees using different methods.
- Create publication-quality lineage tree plots.
- Analyze trees to detect ongoing B cell evolution over time.
- Understand B cell migration and differentiation.
Contact
For help and questions please contact the Immcantation Group or use the issue tracker.