create_MRCA_prior_germline

Takes an airr clone object and returns BEAST2 XML for MRCA prior of the germline sequence

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>.

Kenneth Hoehn

dowser

B Cell Receptor Phylogenetics Toolkit

Cole Jensen

Jessie Fielding

Hunter Melton

Susanna Marquez

Jason Vander Heiden

Steven Kleinstein

create_MRCA_prior_germline function

<dl><dt>clone</dt>
<dd>an <code>airrClone</code> object</dd>
<dt>id</dt>
<dd>unique identifer for this analysis</dd>
<dt>germline_range</dt>
<dd>Possible date range of germline tip</dd></dl>

Arguments

Takes an airr clone object and returns BEAST2 XML for MRCA prior of the germline sequence — create_MRCA_prior_germline

<dl>

<dt>clone</dt>
<dd>an <code>airrClone</code> object</dd>


<dt>id</dt>
<dd>unique identifer for this analysis</dd>


<dt>germline_range</dt>
<dd>Possible date range of germline tip</dd>

</dl>

create_MRCA_prior_germline: Takes an airr clone object and returns BEAST2 XML for MRCA prior of the germline sequence

Description

Usage

Value

Arguments