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) tools:::Rd_expr_doi("10.1371/journal.pcbi.1009885"), Hoehn et al (2021) tools:::Rd_expr_doi("10.1101/2021.01.06.425648").
Maintainer: Kenneth Hoehn kenneth.b.hoehn@dartmouth.edu
Authors:
Steven Kleinstein steven.kleinstein@yale.edu [copyright holder]
Other contributors:
Cole Jensen cole.jensen@yale.edu [contributor]
Susanna Marquez susanna.marquez@yale.edu [contributor]
Jason Vander Heiden jason.vanderheiden@gmail.com [contributor]
Useful links: