getDivergence

<code>getDivergence</code> get sum of branch lengths leading from the 
root of the tree. If the germline sequence is included in the tree,
this will equal the germline divergence. If germline removed,
this will equal the MRCA divergence

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

Susanna Marquez

Jason Vander Heiden

Steven Kleinstein

getDivergence function

<dl><dt>phy</dt>
<dd>Tree object</dd>
<dt>minlength</dt>
<dd>Branch lengths to collapse in trees</dd></dl>

Arguments

Get divergence from root of tree for each tip — getDivergence

<dl>

<dt>phy</dt>
<dd>Tree object</dd>


<dt>minlength</dt>
<dd>Branch lengths to collapse in trees</dd>

</dl>

getDivergence: Get divergence from root of tree for each tip

Description

Usage

Value

Arguments