rerootTree

Reroot phylogenetic tree to have its germline sequence at a zero-length branch
to a node which is the direct ancestor of the tree's UCA. Assigns <code>uca</code>
to be the ancestral node to the tree's germline sequence, as <code>germid</code> as
the tree's germline sequence ID.

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

rerootTree function

<dl><dt>tree</dt>
<dd>An ape <code>phylo</code> object</dd>
<dt>germline</dt>
<dd>ID of the tree's predicted germline sequence</dd>
<dt>min</dt>
<dd>Maximum allowed branch length from germline to root</dd>
<dt>verbose</dt>
<dd>amount of rubbish to print</dd></dl>

Arguments

Reroot phylogenetic tree to have its germline sequence at a zero-length branch
to a node which is the direct ancestor of the tree's UCA. Assigns uca
to be the ancestral node to the tree's germline sequence, as germid as
the tree's germline sequence ID. — rerootTree

<dl>

<dt>tree</dt>
<dd>An ape <code>phylo</code> object</dd>


<dt>germline</dt>
<dd>ID of the tree's predicted germline sequence</dd>


<dt>min</dt>
<dd>Maximum allowed branch length from germline to root</dd>


<dt>verbose</dt>
<dd>amount of rubbish to print</dd>

</dl>

Reroot phylogenetic tree to have its germline sequence at a zero-length branch
to a node which is the direct ancestor of the tree's UCA. Assigns <code>uca</code>
to be the ancestral node to the tree's germline sequence, as <code>germid</code> as
the tree's germline sequence ID.

rerootTree: Reroot phylogenetic tree to have its germline sequence at a zero-length branch to a node which is the direct ancestor of the tree's UCA. Assigns `uca` to be the ancestral node to the tree's germline sequence, as `germid` as the tree's germline sequence ID.

Description

Usage

Value

Arguments